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Gholi Zadeh Kharrat F, Gagne C, Lesage A, Gariépy G, Pelletier JF, Brousseau-Paradis C, Rochette L, Pelletier E, Lévesque P, Mohammed M, Wang J. Explainable artificial intelligence models for predicting risk of suicide using health administrative data in Quebec. PLoS One 2024; 19:e0301117. [PMID: 38568987 PMCID: PMC10990247 DOI: 10.1371/journal.pone.0301117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Suicide is a complex, multidimensional event, and a significant challenge for prevention globally. Artificial intelligence (AI) and machine learning (ML) have emerged to harness large-scale datasets to enhance risk detection. In order to trust and act upon the predictions made with ML, more intuitive user interfaces must be validated. Thus, Interpretable AI is one of the crucial directions which could allow policy and decision makers to make reasonable and data-driven decisions that can ultimately lead to better mental health services planning and suicide prevention. This research aimed to develop sex-specific ML models for predicting the population risk of suicide and to interpret the models. Data were from the Quebec Integrated Chronic Disease Surveillance System (QICDSS), covering up to 98% of the population in the province of Quebec and containing data for over 20,000 suicides between 2002 and 2019. We employed a case-control study design. Individuals were considered cases if they were aged 15+ and had died from suicide between January 1st, 2002, and December 31st, 2019 (n = 18339). Controls were a random sample of 1% of the Quebec population aged 15+ of each year, who were alive on December 31st of each year, from 2002 to 2019 (n = 1,307,370). We included 103 features, including individual, programmatic, systemic, and community factors, measured up to five years prior to the suicide events. We trained and then validated the sex-specific predictive risk model using supervised ML algorithms, including Logistic Regression (LR), Random Forest (RF), Extreme Gradient Boosting (XGBoost) and Multilayer perceptron (MLP). We computed operating characteristics, including sensitivity, specificity, and Positive Predictive Value (PPV). We then generated receiver operating characteristic (ROC) curves to predict suicides and calibration measures. For interpretability, Shapley Additive Explanations (SHAP) was used with the global explanation to determine how much the input features contribute to the models' output and the largest absolute coefficients. The best sensitivity was 0.38 with logistic regression for males and 0.47 with MLP for females; the XGBoost Classifier with 0.25 for males and 0.19 for females had the best precision (PPV). This study demonstrated the useful potential of explainable AI models as tools for decision-making and population-level suicide prevention actions. The ML models included individual, programmatic, systemic, and community levels variables available routinely to decision makers and planners in a public managed care system. Caution shall be exercised in the interpretation of variables associated in a predictive model since they are not causal, and other designs are required to establish the value of individual treatments. The next steps are to produce an intuitive user interface for decision makers, planners and other stakeholders like clinicians or representatives of families and people with live experience of suicidal behaviors or death by suicide. For example, how variations in the quality of local area primary care programs for depression or substance use disorders or increased in regional mental health and addiction budgets would lower suicide rates.
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Affiliation(s)
- Fatemeh Gholi Zadeh Kharrat
- Institut Intelligence et Données (IID), Université Laval, Québec, Québec, Canada
- Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada
| | - Christian Gagne
- Institut Intelligence et Données (IID), Université Laval, Québec, Québec, Canada
| | - Alain Lesage
- Department of Psychiatry and Addiction, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, Québec, Canada
| | - Geneviève Gariépy
- Centre for Surveillance and Applied Research, Health Promotion and Chronic Disease Prevention Branch, Public Health Agency of Canada, Ottawa, Canada
- Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, Canada
- Montreal Mental Health University Institute Research Center, Montreal, Canada
| | - Jean-François Pelletier
- Department of Psychiatry and Addiction, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, Québec, Canada
| | - Camille Brousseau-Paradis
- Department of Psychiatry and Addiction, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, Québec, Canada
| | - Louis Rochette
- Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada
| | - Eric Pelletier
- Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada
| | - Pascale Lévesque
- Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada
| | - Mada Mohammed
- Department of Community Health and Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - JianLi Wang
- Department of Community Health and Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Canada
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Lemane T, Lezzoche N, Lecubin J, Pelletier E, Lescot M, Chikhi R, Peterlongo P. Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA. Nat Comput Sci 2024; 4:104-109. [PMID: 38413777 DOI: 10.1038/s43588-024-00596-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.
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Affiliation(s)
- Téo Lemane
- Univ. Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, France.
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France.
| | - Nolan Lezzoche
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
| | | | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France
| | - Magali Lescot
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, CNRS, Paris, France
| | - Rayan Chikhi
- Institut Pasteur, Université Paris Cité, G5 Sequence Bioinformatics, Paris, France
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3
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Meng L, Delmont TO, Gaïa M, Pelletier E, Fernàndez-Guerra A, Chaffron S, Neches RY, Wu J, Kaneko H, Endo H, Ogata H. Genomic adaptation of giant viruses in polar oceans. Nat Commun 2023; 14:6233. [PMID: 37828003 PMCID: PMC10570341 DOI: 10.1038/s41467-023-41910-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/24/2023] [Indexed: 10/14/2023] Open
Abstract
Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus-host network at the polar-nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
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Affiliation(s)
- Lingjie Meng
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
| | - Morgan Gaïa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, F-75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Russell Y Neches
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Junyi Wu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hiroto Kaneko
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan.
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4
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Wutkowska M, Vader A, Logares R, Pelletier E, Gabrielsen TM. Linking extreme seasonality and gene expression in Arctic marine protists. Sci Rep 2023; 13:14627. [PMID: 37669980 PMCID: PMC10480425 DOI: 10.1038/s41598-023-41204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Tove M Gabrielsen
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
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5
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Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, Madan A, Qin S, Sun H, Du H, Pepin K, Artiguenave F, Robert C, Cruaud C, Brüls T, Jaillon O, Friedlander L, Samson G, Brottier P, Cure S, Ségurens B, Anière F, Samain S, Crespeau H, Abbasi N, Aiach N, Boscus D, Dickhoff R, Dors M, Dubois I, Friedman C, Gouyvenoux M, James R, Madan A, Mairey-Estrada B, Mangenot S, Martins N, Ménard M, Oztas S, Ratcliffe A, Shaffer T, Trask B, Vacherie B, Bellemere C, Belser C, Besnard-Gonnet M, Bartol-Mavel D, Boutard M, Briez-Silla S, Combette S, Dufossé-Laurent V, Ferron C, Lechaplais C, Louesse C, Muselet D, Magdelenat G, Pateau E, Petit E, Sirvain-Trukniewicz P, Trybou A, Vega-Czarny N, Bataille E, Bluet E, Bordelais I, Dubois M, Dumont C, Guérin T, Haffray S, Hammadi R, Muanga J, Pellouin V, Robert D, Wunderle E, Gauguet G, Roy A, Sainte-Marthe L, Verdier J, Verdier-Discala C, Hillier L, Fulton L, McPherson J, Matsuda F, Wilson R, Scarpelli C, Gyapay G, Wincker P, Saurin W, Quétier F, Waterston R, Hood L, Weissenbach J. Publisher Correction: The DNA sequence and analysis of human chromosome 14. Nature 2023; 620:E17. [PMID: 37491470 DOI: 10.1038/s41586-023-06403-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Affiliation(s)
- Roland Heilig
- Genoscope-Centre National de Séquençage, 91000, Evry, France.
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France.
| | - Ralph Eckenberg
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | - Jean-Louis Petit
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | - Núria Fonknechten
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | - Corinne Da Silva
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | | | - Michaël Levy
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Valérie Barbe
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | - Eric Pelletier
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | - Virginie Vico
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Lee Rowen
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Anup Madan
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Shizhen Qin
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Hui Sun
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | - Hui Du
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | - Kymberlie Pepin
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | | | | | - Corinne Cruaud
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Thomas Brüls
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Olivier Jaillon
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | | | - Gaelle Samson
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | | | - Susan Cure
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Franck Anière
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Sylvie Samain
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Hervé Crespeau
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Nissa Abbasi
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Nathalie Aiach
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Didier Boscus
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Rachel Dickhoff
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Monica Dors
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Ivan Dubois
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | - Rose James
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Anuradha Madan
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | | | - Sophie Mangenot
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Manuela Ménard
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Sophie Oztas
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Amber Ratcliffe
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Tristan Shaffer
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Barbara Trask
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Benoit Vacherie
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Caroline Belser
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | - Magali Boutard
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | | | - Carolyne Ferron
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | | | | | - Emilie Pateau
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | - Arnaud Trybou
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Elodie Bataille
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Elodie Bluet
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Maria Dubois
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Corinne Dumont
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Thomas Guérin
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Rachid Hammadi
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | | | | | - Edith Wunderle
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Gilbert Gauguet
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Alice Roy
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - Jean Verdier
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | | | - LaDeana Hillier
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | - Lucinda Fulton
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | - John McPherson
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | | | - Richard Wilson
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | | | - Gábor Gyapay
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Patrick Wincker
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - William Saurin
- Genoscope-Centre National de Séquençage, 91000, Evry, France
| | - Francis Quétier
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
| | - Robert Waterston
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, 98103, USA
| | - Jean Weissenbach
- Genoscope-Centre National de Séquençage, 91000, Evry, France
- UMR-8030, CNRS et Université d'Evry, 91000, Evry, France
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Gaïa M, Meng L, Pelletier E, Forterre P, Vanni C, Fernandez-Guerra A, Jaillon O, Wincker P, Ogata H, Krupovic M, Delmont TO. Mirusviruses link herpesviruses to giant viruses. Nature 2023; 616:783-789. [PMID: 37076623 PMCID: PMC10132985 DOI: 10.1038/s41586-023-05962-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/16/2023] [Indexed: 04/21/2023]
Abstract
DNA viruses have a major influence on the ecology and evolution of cellular organisms1-4, but their overall diversity and evolutionary trajectories remain elusive5. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria6, with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.
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Affiliation(s)
- Morgan Gaïa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Lingjie Meng
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, Gif sur Yvette, France
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Chiara Vanni
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.
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7
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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8
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Wang J, Gholi Zadeh Kharrat F, Pelletier JF, Rochette L, Pelletier E, Lévesque P, Massamba V, Brousseau-Paradis C, Mohammed M, Gariépy G, Gagné C, Lesage A. A case-control study on predicting population risk of suicide using health administrative data: a research protocol. BMJ Open 2023; 13:e066423. [PMID: 36849211 PMCID: PMC9972456 DOI: 10.1136/bmjopen-2022-066423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
INTRODUCTION Suicide has a complex aetiology and is a result of the interaction among the risk and protective factors at the individual, healthcare system and population levels. Therefore, policy and decision makers and mental health service planners can play an important role in suicide prevention. Although a number of suicide risk predictive tools have been developed, these tools were designed to be used by clinicians for assessing individual risk of suicide. There have been no risk predictive models to be used by policy and decision makers for predicting population risk of suicide at the national, provincial and regional levels. This paper aimed to describe the rationale and methodology for developing risk predictive models for population risk of suicide. METHODS AND ANALYSIS A case-control study design will be used to develop sex-specific risk predictive models for population risk of suicide, using statistical regression and machine learning techniques. Routinely collected health administrative data in Quebec, Canada, and community-level social deprivation and marginalisation data will be used. The developed models will be transformed into the models that can be readily used by policy and decision makers. Two rounds of qualitative interviews with end-users and other stakeholders were proposed to understand their views about the developed models and potential systematic, social and ethical issues for implementation; the first round of qualitative interviews has been completed. We included 9440 suicide cases (7234 males and 2206 females) and 661 780 controls for model development. Three hundred and forty-seven variables at individual, healthcare system and community levels have been identified and will be included in least absolute shrinkage and selection operator regression for feature selection. ETHICS AND DISSEMINATION This study is approved by the Health Research Ethnics Committee of Dalhousie University, Canada. This study takes an integrated knowledge translation approach, involving knowledge users from the beginning of the process.
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Affiliation(s)
- JianLi Wang
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | - Louis Rochette
- Institut national de sante publique du Quebec (INSPQ), Quebec City, Quebec, Canada
| | - Eric Pelletier
- Institut national de sante publique du Quebec (INSPQ), Quebec City, Quebec, Canada
| | - Pascale Lévesque
- Institut national de sante publique du Quebec (INSPQ), Quebec City, Quebec, Canada
| | - Victoria Massamba
- Institut national de sante publique du Quebec (INSPQ), Quebec City, Quebec, Canada
| | | | - Mada Mohammed
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Geneviève Gariépy
- Public Health Agency of Canada, Ottawa, Ontario, Canada
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Québec, Canada
| | - Christian Gagné
- Department of Electrical Engineering and Computer Engineering, Laval University, Quebec, Quebec, Canada
| | - Alain Lesage
- Institut universitaire en sante mentale de Montreal, Montreal, Québec, Canada
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9
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Da Silva O, Ayata SD, Ser-Giacomi E, Leconte J, Pelletier E, Fauvelot C, Madoui MA, Guidi L, Lombard F, Bittner L. Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea. Environ Microbiol 2022; 24:6086-6099. [PMID: 36053818 PMCID: PMC10087736 DOI: 10.1111/1462-2920.16171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/09/2022] [Indexed: 01/12/2023]
Abstract
For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.
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Affiliation(s)
- Ophélie Da Silva
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France
| | - Enrico Ser-Giacomi
- Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France.,Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Cécile Fauvelot
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Nouméa, New Caledonia
| | - Mohammed-Amin Madoui
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Lionel Guidi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Fabien Lombard
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Institut Universitaire de France (IUF), Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Institut Universitaire de France (IUF), Paris, France
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10
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Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife 2022; 11:78129. [PMID: 35920817 PMCID: PMC9348854 DOI: 10.7554/elife.78129] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton. Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These ‘marine plankton’ are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth’s oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.
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Affiliation(s)
- Daniel J Richter
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Romain Watteaux
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,CEA, DAM, DIF, F-91297, Arpajon Cedex, France
| | - Thomas Vannier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM, Marseille, France
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Gabriel Reygondeau
- Changing Ocean Research Unit, Institute for the Oceans and Fisheries, University of British Columbia. Aquatic Ecosystems Research Lab, Vancouver, Canada.,Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Nicolas Maillet
- Institut pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Gaëtan Benoit
- Univ Rennes, CNRS, Inria, IRISA-UMR 6074, Rennes, France
| | - Ophélie Da Silva
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Samir Suweis
- Dipartimento di Fisica e Astronomia 'G. Galilei' & CNISM, INFN, Università di Padova, Padova, Italy
| | - Romain Narci
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cédric Berney
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Damien Eveillard
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Nantes Université, Ecole Centrale Nantes, CNRS, LS2N, Nantes, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Lionel Guidi
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Eric Mahieu
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, United States
| | - Céline Dimier
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Directors' Research European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Picheral
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Sarah Searson
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, United States.,Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, United States
| | | | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Yonsei Frontier Lab, Yonsei University, Seoul, Republic of Korea.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg, Zurich, Switzerland
| | - Fabien Lombard
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, United States
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, United States.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, United States.,Center of Microbiome Science, The Ohio State University, Columbus, United States.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, United States
| | - Eric Karsenti
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Directors' Research European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Ian Probert
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | | | | | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
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11
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Vernette C, Lecubin J, Sánchez P, Sunagawa S, Delmont TO, Acinas SG, Pelletier E, Hingamp P, Lescot M. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Res 2022; 50:W516-W526. [PMID: 35687095 PMCID: PMC9252727 DOI: 10.1093/nar/gkac420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
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Affiliation(s)
- Caroline Vernette
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France
| | | | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Tom O Delmont
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91057 Evry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Eric Pelletier
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91057 Evry, France
| | - Pascal Hingamp
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Magali Lescot
- Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France
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12
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Dominguez-Huerta G, Zayed AA, Wainaina JM, Guo J, Tian F, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S, Sullivan MB. Diversity and ecological footprint of Global Ocean RNA viruses. Science 2022; 376:1202-1208. [PMID: 35679415 DOI: 10.1126/science.abn6358] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.
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Affiliation(s)
- Guillermo Dominguez-Huerta
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Jiarong Guo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA.,The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | | | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, F-06230 Villefranche-sur-mer, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,Directors' Research European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Alexander Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA.,The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
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13
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Delmont TO, Gaia M, Hinsinger DD, Frémont P, Vanni C, Fernandez-Guerra A, Eren AM, Kourlaiev A, d'Agata L, Clayssen Q, Villar E, Labadie K, Cruaud C, Poulain J, Da Silva C, Wessner M, Noel B, Aury JM, de Vargas C, Bowler C, Karsenti E, Pelletier E, Wincker P, Jaillon O, Acinas SG, Bork P, Karsenti E, Bowler C, Sardet C, Stemmann L, de Vargas C, Wincker P, Lescot M, Babin M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Jaillon O, Kandels S, Iudicone D, Ogata H, Pesant S, Sullivan MB, Not F, Lee KB, Boss E, Cochrane G, Follows M, Poulton N, Raes J, Sieracki M, Speich S. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genom 2022; 2:100123. [PMID: 36778897 PMCID: PMC9903769 DOI: 10.1016/j.xgen.2022.100123] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 12/10/2021] [Accepted: 04/04/2022] [Indexed: 12/20/2022]
Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
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Affiliation(s)
- Tom O. Delmont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Corresponding author
| | - Morgan Gaia
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Damien D. Hinsinger
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Chiara Vanni
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at Oldenburg, Germany
| | - Artem Kourlaiev
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Leo d'Agata
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Quentin Clayssen
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Emilie Villar
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Cruaud
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Tara Oceans CoordinatorsSunagawaShinichi12AcinasSilvia G.13BorkPeer141516KarsentiEric171819BowlerChris1718SardetChristian1720StemmannLars1720de VargasColomban1721WinckerPatrick1722LescotMagali1723BabinMarcel1724GorskyGabriel1720GrimsleyNigel172526GuidiLionel1720HingampPascal1723JaillonOlivier1722KandelsStefanie1417IudiconeDaniele27OgataHiroyuki28PesantStéphane2930SullivanMatthew B.313233NotFabrice21LeeKarp-Boss34BossEmmanuel34CochraneGuy35FollowsMichael36PoultonNicole37RaesJeroen383940SierackiMike37SpeichSabrina4142Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, EtH Zürich, Zürich, SwitzerlandDepartment of Marine Biology and Oceanography, Institute of Marine Sciences–CsiC, Barcelona, SpainStructural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, GermanyMax Delbrück Center for Molecular Medicine, Berlin, GermanyDepartment of Bioinformatics, Biocenter, University of Würzburg, Würzburg, GermanyResearch Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOsee, Paris, FranceInstitut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, FranceDirectors’ Research, European Molecular Biology Laboratory, Heidelberg, GermanySorbonne Université, CNRS, Laboratoire D’Océanographie de Villefranche, Villefranche- sur- Mer, FranceSorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, FranceGénomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l’Énergie Atomique, CNrs, Université Evry, Université Paris- Saclay, Evry, FranceAix Marseille Universit/e, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, FranceDépartement de Biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)–CNRS (France), Université Laval, Quebec, QC, CanadaCNRS UMR 7232, Biologie Intégrative des Organismes Marins, Banyuls- sur- Mer, FranceSorbonne Universités Paris 06, OOB UPMC, Banyuls- sur- Mer, FranceStazione Zoologica Anton Dohrn, Naples, ItalyInstitute for Chemical Research, Kyoto University, Kyoto, JapanPaNGaea, University of Bremen, Bremen, GermanyMaruM, Center for Marine Environmental Sciences, University of Bremen, Bremen, GermanyDepartment of Microbiology, The Ohio State University, Columbus, OH, USADepartment of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USACenter for RNA Biology, The Ohio State University, Columbus, OH, USASchool of Marine Sciences, University of Maine, Orono, ME, USAEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UKDepartment of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USABigelow Laboratory for Ocean Sciences, East Boothbay, ME, USADepartment of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, BelgiumCenter for the Biology of Disease, VIB KU Leuven, Leuven, BelgiumDepartment of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, BelgiumDepartment of Geosciences, Laboratoire de Météorologie Dynamique, École Normale Supérieure, Paris, FranceOcean Physics Laboratory, University of Western Brittany, Brest, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France,Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
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14
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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15
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Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E. Correction to: Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME J 2022; 16:1203. [PMID: 35058585 PMCID: PMC8940913 DOI: 10.1038/s41396-021-01173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.
| | - Juan José Pierella Karlusich
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Iva Veseli
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Fuessel
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University Stockholm, Stockholm, 10691, Sweden
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
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16
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Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour 2022; 23:16-40. [PMID: 35108459 PMCID: PMC10078663 DOI: 10.1111/1755-0998.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Eric Pelletier
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Fabien Lombard
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), 06230, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Sébastien Colin
- European Molecular Biology Laboratory, Heidelberg, Germany.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France
| | - Nicolas Henry
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Patrick Wincker
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Colomban de Vargas
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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17
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Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME J 2021; 16:927-936. [PMID: 34697433 DOI: 10.1038/s41396-021-01135-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022]
Abstract
Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.
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Affiliation(s)
- Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. .,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.
| | - Juan José Pierella Karlusich
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Iva Veseli
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Fuessel
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University Stockholm, Stockholm, 106 91, Sweden
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
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18
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Godard-Sebillotte C, Strumpf E, Sourial N, Rochette L, Pelletier E, Vedel I. Avoidable Hospitalizations in Persons with Dementia: a Population-Wide Descriptive Study (2000-2015). Can Geriatr J 2021; 24:209-221. [PMID: 34484504 PMCID: PMC8390329 DOI: 10.5770/cgj.24.486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background Whether avoidable hospitalizations in community-dwelling persons with dementia have decreased during primary care reforms is unknown. Methods We described the prevalence and trends in avoidable hospitalizations in population-based repeated yearly cohorts of 192,144 community-dwelling persons with incident dementia (Quebec, 2000-2015) in the context of a province-wide primary care reform, using the provincial health administrative database. Results Trends in both types of Ambulatory Care Sensitive Condition (ACSC) hospitalization (general and older population) and 30-day readmission rates remained constant with average rates per 100 person-years: 20.5 (19.9-21.1), 31.7 (31.0-32.4), 20.6 (20.1-21.2), respectively. Rates of delayed hospital discharge (i.e., alternate level of care (ALC) hospitalizations) decreased from 23.8 (21.1-26.9) to 17.9 (16.1-20.1) (relative change -24.6%). Conclusions These figures shed light on the importance of the phenomenon, its lack of improvement for most outcomes over the years, and the need to develop evidence-based policies to prevent avoidable hospitalizations in this vulnerable population.
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Affiliation(s)
| | - Erin Strumpf
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, QC.,Department of Economics, McGill University, Montreal, QC
| | - Nadia Sourial
- Department of Family Medicine, McGill University, Montreal, QC
| | - Louis Rochette
- Department of Economics, McGill University, Montreal, QC.,Institut national de santé publique du Québec (INSPQ), Quebec City, QC
| | - Eric Pelletier
- Department of Economics, McGill University, Montreal, QC.,Institut national de santé publique du Québec (INSPQ), Quebec City, QC
| | - Isabelle Vedel
- Department of Family Medicine, McGill University, Montreal, QC
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19
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Vodopivez C, Curtosi A, Pelletier E, Saint-Louis R, Spairani LU, Hernández EA, Zakrajsek A, Genez A, Mac Cormack WP. Low levels of PAHs and organotin compounds in surface sediment samples from a broad marine area of 25 de Mayo (King George) Island, South Shetland Islands. Sci Total Environ 2021; 785:147206. [PMID: 33957587 DOI: 10.1016/j.scitotenv.2021.147206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
The Northern region of the Antarctic Peninsula constitutes the area with the highest human presence in West Antarctica. The human presence, with all the activities associated such as logistic, scientific and tourism operations, represents a potential risk of chemical pollution with both, organic and inorganic contaminants. Under these conditions knowledge about the presence and levels of the main persistent organic pollutants (POPs) is essential to evaluate the environmental status of this ecologically relevant and sensitive area. In this work, which complements our previous study regarding trace elements, we performed the first regional-scale monitoring of 24 PAHs (16 of them included in EPA list of primary pollutant), and organotin compounds (OTCs:TBT, DBT and MBT) in surface sediment from 68 sites comprising six different areas in Maxwell Bay, southeast coast of 25 de Mayo (King George) Island. POPs were quantified in surface sediment samples (20-30 m depth) obtained during two summer Antarctic expeditions by gas chromatography-mass spectrometry (GC-MS). The two most anthropized areas (South Fildes and Potter Cove) showed moderated evidence of pollution for PAHs and OTC. In some sampling sites the concentration of total PAHs was higher than 100 ng/g dw, while TBT was detected in only five samples, two of them located in Potter Cove (ranged between 14 and 18 ng/g dw), and three, located in South Fildes area (ranged between 118 and 416 ng/g dw). Although POPs contamination was evidenced in some samples close to scientific stations, a pollution pattern was not clearly identified.
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Affiliation(s)
- C Vodopivez
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - A Curtosi
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - E Pelletier
- Institut des Sciences de la Mer de Rimouski (ISMER), Université du Québec à Rimouski, 310 Allée des Ursulines, Rimouski G5L 3A1, Canada
| | - R Saint-Louis
- Département de biologie, chimie et géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski G5L 3A1, Canada
| | - L U Spairani
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - E A Hernández
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto NANOBIOTEC UBA-CONICET, Junín 956 6to piso, CABA, Argentina
| | - A Zakrajsek
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - A Genez
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - W P Mac Cormack
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto NANOBIOTEC UBA-CONICET, Junín 956 6to piso, CABA, Argentina..
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20
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Latorre F, Deutschmann IM, Labarre A, Obiol A, Krabberød AK, Pelletier E, Sieracki ME, Cruaud C, Jaillon O, Massana R, Logares R. Niche adaptation promoted the evolutionary diversification of tiny ocean predators. Proc Natl Acad Sci U S A 2021; 118:e2020955118. [PMID: 34155140 PMCID: PMC8237690 DOI: 10.1073/pnas.2020955118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs.
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Affiliation(s)
- Francisco Latorre
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain;
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Aurélie Labarre
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Aleix Obiol
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo N-0316, Norway
| | - Eric Pelletier
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology & Evolution, FR2022/Tara Oceans Global Ocean System Ecology & Evolution, 75016 Paris, France
| | - Michael E Sieracki
- Ocean Science Division, National Science Foundation, Alexandria, VA 22314
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, 91000 Evry, France
| | - Olivier Jaillon
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology & Evolution, FR2022/Tara Oceans Global Ocean System Ecology & Evolution, 75016 Paris, France
| | - Ramon Massana
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain;
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21
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Bernasconi SM, Daëron M, Bergmann KD, Bonifacie M, Meckler AN, Affek HP, Anderson N, Bajnai D, Barkan E, Beverly E, Blamart D, Burgener L, Calmels D, Chaduteau C, Clog M, Davidheiser‐Kroll B, Davies A, Dux F, Eiler J, Elliott B, Fetrow AC, Fiebig J, Goldberg S, Hermoso M, Huntington KW, Hyland E, Ingalls M, Jaggi M, John CM, Jost AB, Katz S, Kelson J, Kluge T, Kocken IJ, Laskar A, Leutert TJ, Liang D, Lucarelli J, Mackey TJ, Mangenot X, Meinicke N, Modestou SE, Müller IA, Murray S, Neary A, Packard N, Passey BH, Pelletier E, Petersen S, Piasecki A, Schauer A, Snell KE, Swart PK, Tripati A, Upadhyay D, Vennemann T, Winkelstern I, Yarian D, Yoshida N, Zhang N, Ziegler M. InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards. Geochem Geophys Geosyst 2021; 22:e2020GC009588. [PMID: 34220359 PMCID: PMC8244079 DOI: 10.1029/2020gc009588] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Increased use and improved methodology of carbonate clumped isotope thermometry has greatly enhanced our ability to interrogate a suite of Earth-system processes. However, interlaboratory discrepancies in quantifying carbonate clumped isotope (Δ47) measurements persist, and their specific sources remain unclear. To address interlaboratory differences, we first provide consensus values from the clumped isotope community for four carbonate standards relative to heated and equilibrated gases with 1,819 individual analyses from 10 laboratories. Then we analyzed the four carbonate standards along with three additional standards, spanning a broad range of δ47 and Δ47 values, for a total of 5,329 analyses on 25 individual mass spectrometers from 22 different laboratories. Treating three of the materials as known standards and the other four as unknowns, we find that the use of carbonate reference materials is a robust method for standardization that yields interlaboratory discrepancies entirely consistent with intralaboratory analytical uncertainties. Carbonate reference materials, along with measurement and data processing practices described herein, provide the carbonate clumped isotope community with a robust approach to achieve interlaboratory agreement as we continue to use and improve this powerful geochemical tool. We propose that carbonate clumped isotope data normalized to the carbonate reference materials described in this publication should be reported as Δ47 (I-CDES) values for Intercarb-Carbon Dioxide Equilibrium Scale.
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Affiliation(s)
| | - M. Daëron
- Laboratoire des Sciences du Climat et de l’EnvironnementLSCE/IPSLCEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - K. D. Bergmann
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Bonifacie
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
| | - A. N. Meckler
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - H. P. Affek
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - N. Anderson
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - D. Bajnai
- Institute of GeosciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - E. Barkan
- Institute of Earth SciencesHebrew University of JerusalemJerusalemIsrael
| | - E. Beverly
- Now at Department of Earth and Atmospheric SciencesUniversity of HoustonHoustonTXUSA
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - D. Blamart
- Laboratoire des Sciences du Climat et de l’EnvironnementLSCE/IPSLCEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - L. Burgener
- Department of Marine, Earth and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | - D. Calmels
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Now at Geosciences Paris Sud (GEOPS)Université Paris‐SaclayCNRSOrsayFrance
| | - C. Chaduteau
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
| | - M. Clog
- Scottish Universities Environmental Research Centre (SUERC)ScotlandUK
| | | | - A. Davies
- Now at Stockholm UniversityStockholmSweden
- Imperial CollegeLondonUK
| | - F. Dux
- Now at School of Earth and Life SciencesUniversity of WollongongWollongongAustralia
- School of GeographyUniversity of MelbourneMelbourneAustralia
| | - J. Eiler
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - B. Elliott
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | | | - J. Fiebig
- Institute of GeosciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - S. Goldberg
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - M. Hermoso
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Univ. Littoral Côte d’OpaleUniv. LilleCNRSLaboratoire d’Océanologie et de Géosciences (UMR 8187 LOG)WimereuxFrance
| | | | - E. Hyland
- Department of Marine, Earth and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | - M. Ingalls
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
- Now at Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - M. Jaggi
- Geological InstituteETH ZürichZürichSwitzerland
| | | | - A. B. Jost
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - S. Katz
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - J. Kelson
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - T. Kluge
- Imperial CollegeLondonUK
- Now at Karlsruher Institut für Technologie KITKarlsruheGermany
| | - I. J. Kocken
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| | - A. Laskar
- Institute of Earth SciencesAcademia SinicaTaipeiTaiwan
| | - T. J. Leutert
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
- Now at Max Planck Institute for ChemistryMainzGermany
| | - D. Liang
- Institute of Earth SciencesAcademia SinicaTaipeiTaiwan
| | - J. Lucarelli
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - T. J. Mackey
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Now at Department of Earth and Planetary SciencesUniversity of New MexicoAlbuquerqueNMUSA
| | - X. Mangenot
- Université de ParisInstitut de Physique du Globe de ParisCNRSParisFrance
- Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - N. Meinicke
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - S. E. Modestou
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
| | - I. A. Müller
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
| | | | - A. Neary
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - N. Packard
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - B. H. Passey
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - E. Pelletier
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - S. Petersen
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - A. Piasecki
- Bjerknes Centre for Climate Research and Department of Earth ScienceUniversity of BergenBergenNorway
- Now at Department of Earth SciencesDartmouth CollegeHanoverNHUSA
| | | | | | - P. K. Swart
- Department of Marine GeosciencesRostiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFLUSA
| | - A. Tripati
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - D. Upadhyay
- Department of Earth, Planetary, and Space SciencesUniversity of California Los AngelesLos AngelesCAUSA
| | - T. Vennemann
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - I. Winkelstern
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
- Now at Geology DepartmentGrand Valley State UniversityAllendaleMIUSA
| | - D. Yarian
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMIUSA
| | - N. Yoshida
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
- National Institute of Information and Communications TechnologyTokyoJapan
| | - N. Zhang
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - M. Ziegler
- Department of Earth SciencesUniversity of UtrechtUtrechtThe Netherlands
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22
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Godard-Sebillotte C, Strumpf E, Sourial N, Rochette L, Pelletier E, Vedel I. Primary care continuity and potentially avoidable hospitalization in persons with dementia. J Am Geriatr Soc 2021; 69:1208-1220. [PMID: 33635538 DOI: 10.1111/jgs.17049] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND/OBJECTIVE To measure the association between high primary care continuity and potentially avoidable hospitalization in community-dwelling persons with dementia. Our hypothesis was that high primary care continuity is associated with fewer potentially avoidable hospitalizations. DESIGN Population-based retrospective cohort (2012-2016), with inverse probability of treatment weighting using the propensity score. SETTING Quebec (Canada) health administrative database, recording most primary, secondary and tertiary care services provided via the public universal health insurance system. PARTICIPANTS Population-based sample of 22,060 community-dwelling 65 + persons with dementia on March 31st, 2015, with at least two primary care visits in the preceding year (mean age 81 years, 60% female). Participants were followed for 1 year, or until death or long-term care admission. EXPOSURE High primary care continuity on March 31st, 2015, i.e., having had every primary care visit with the same primary care physician, during the preceding year. MAIN OUTCOME MEASURES Primary: Potentially avoidable hospitalization in the follow-up period as defined by ambulatory care sensitive conditions (ACSC) hospitalization (general and older population definitions), 30-day hospital readmission; Secondary: Hospitalization and emergency department visit. RESULTS Among the 22,060 persons, compared with the persons with low primary care continuity, the 14,515 (65.8%) persons with high primary care continuity had a lower risk of ACSC hospitalization (general population definition) (relative risk reduction 0.82, 95% CI 0.72-0.94), ACSC hospitalization (older population definition) (0.87, 0.79-0.95), 30-day hospital readmission (0.81, 0.72-0.92), hospitalization (0.90, 0.86-0.94), and emergency department visit (0.92, 0.90-0.95). The number needed to treat to prevent one event were, respectively, 118 (69-356), 87 (52-252), 97 (60-247), 23 (17-34), and 29 (21-47). CONCLUSION Increasing continuity with a primary care physician might be an avenue to reduce potentially avoidable hospitalizations in community-dwelling persons with dementia on a population-wide level.
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Affiliation(s)
| | - Erin Strumpf
- Department of Epidemiology, Biostatics, and Occupational Health, McGill University, Montreal, Quebec, Canada.,Department of Economics, McGill University, Montreal, Quebec, Canada
| | - Nadia Sourial
- Department of Family Medicine, McGill University, Montreal, Quebec, Canada
| | - Louis Rochette
- Institut national de santé publique du Québec (INSPQ), Montreal, Quebec, Canada
| | - Eric Pelletier
- Institut national de santé publique du Québec (INSPQ), Montreal, Quebec, Canada
| | - Isabelle Vedel
- Department of Family Medicine, McGill University, Montreal, Quebec, Canada
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23
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Smargiassi A, Sidi EAL, Robert LE, Plante C, Haddad M, Gamache P, Burnett R, Goudreau S, Liu L, Fournier M, Pelletier E, Yankoty I. Exposure to ambient air pollutants and the onset of dementia in Québec, Canada. Environ Res 2020; 190:109870. [PMID: 32739624 DOI: 10.1016/j.envres.2020.109870] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/20/2020] [Accepted: 06/20/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Effects of air pollutants are related to oxidative stress which is also linked to the pathogenesis of dementia including Alzheimer's and related diseases. OBJECTIVE We assessed associations between exposure to air pollutants and the onset of dementia; the association with the distance between residence and major roads was also assessed for the island of Montreal. METHODS We created an open cohort of adults aged 65 years and older starting in 2000 and ending in 2012 in the province of Québec, Canada using linked medico-administrative databases. New cases of dementia were defined based on a validated algorithm. Annual residential levels of nitrogen dioxide (NO2) and fine particles (PM2.5) at residential levels were estimated for each year of follow up using estimates based on satellite images and ground air monitoring data. Hazard ratios (HRs) were assessed with Extended (time dependent exposure) Cox models with age as the time axis and stratified for sex, for the annual exposure level at each residential address. Models were adjusted for the calendar year, area-wide social and material deprivation indexes and for NO2 or PM2.5; they were also indirectly adjusted for smoking. RESULTS 1,807,133 persons (13,242,270 person-years) were followed and 199,826 developed dementia. From models (adjusted for calendar year, social and material deprivation indexes), HRs for an interquartile range (IQR) increase in time-varying exposure to NO2 (IQR 13.26 ppb), PM2.5 (IQR 3.90 μg/m³), and distance to major roads (IQR 150 m, in Montreal only), were 1.005 (CI 95% 0.994-1.017), 1.016 (CI 95% 1.003-1.028) and 0.969 (CI 95% 0.958-0.980), respectively. CONCLUSIONS Results suggest that the onset of dementia may be related to residential exposure to PM2.5, NO2, and distance to major roads.
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Affiliation(s)
- Audrey Smargiassi
- School of Public Health, Centre of Public Health Research, University of Montreal and CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montreal, Canada; Institut national de la santé publique du Québec, Québec, Canada.
| | | | | | - Céline Plante
- Direction régionale de santé publique de Montréal, Québec, Canada
| | - Mona Haddad
- School of Public Health, Centre of Public Health Research, University of Montreal and CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montreal, Canada
| | - Philippe Gamache
- Institut national de la santé publique du Québec, Québec, Canada
| | - Rick Burnett
- Environmental Health Science and Research Bureau, Health, Canada
| | - Sophie Goudreau
- Direction régionale de santé publique de Montréal, Québec, Canada
| | - Ling Liu
- Environmental Health Science and Research Bureau, Health, Canada
| | - Michel Fournier
- Direction régionale de santé publique de Montréal, Québec, Canada
| | - Eric Pelletier
- Institut national de la santé publique du Québec, Québec, Canada
| | - Ines Yankoty
- School of Public Health, Centre of Public Health Research, University of Montreal and CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montreal, Canada
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24
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2020; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. Video Abstract
A catalog of 47 million genes was generated from 370 globally distributed metagenomes Meta-omics data integration disentangled the mechanisms of changes in transcript pools Transcript pool changes of metabolic marker genes show distinct mechanistic patterns Community turnover as a response to ocean warming may be strongest in polar regions
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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25
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, Berardinis V, Zaparucha A, Champion JA, Bommarius AS, Vergne‐Vaxelaire C. Metagenomic Mining for Amine Dehydrogenase Discovery. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000094] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Adam A. Caparco
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Jean Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Aurélie Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Bettina R. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Véronique Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Julie A. Champion
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Carine Vergne‐Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
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27
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Sordino P, D'Aniello S, Pelletier E, Wincker P, Nittoli V, Stemmann L, Mazzocchi MG, Lombard F, Iudicone D, Caputi L. Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability. Mol Ecol 2019; 29:292-307. [PMID: 31793138 DOI: 10.1111/mec.15321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/07/2023]
Abstract
The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.
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Affiliation(s)
| | | | - Eric Pelletier
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Patrick Wincker
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | | | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | | | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
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28
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Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, Bachelerie P, Rosnet T, Pelletier E, Sunagawa S, Hingamp P. The Ocean Gene Atlas: exploring the biogeography of plankton genes online. Nucleic Acids Res 2019; 46:W289-W295. [PMID: 29788376 PMCID: PMC6030836 DOI: 10.1093/nar/gky376] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
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Affiliation(s)
- Emilie Villar
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, France.,Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Thomas Vannier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Caroline Vernette
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Magali Lescot
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Aurélien Alexandre
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Paul Bachelerie
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Thomas Rosnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Pascal Hingamp
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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29
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Busseni G, Vieira FRJ, Amato A, Pelletier E, Pierella Karlusich JJ, Ferrante MI, Wincker P, Rogato A, Bowler C, Sanges R, Maiorano L, Chiurazzi M, d'Alcalà MR, Caputi L, Iudicone D. Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes. Mol Biol Evol 2019; 36:2522-2535. [PMID: 31259367 PMCID: PMC6805229 DOI: 10.1093/molbev/msz157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/05/2019] [Accepted: 06/22/2019] [Indexed: 01/27/2023] Open
Abstract
Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.
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Affiliation(s)
- Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CEA, INRA, CNRS. BIG, 17 rue des Martyrs Grenoble cedex 9, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,FR2022/Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
| | - Juan J Pierella Karlusich
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,FR2022/Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
| | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, Italy
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, Trieste, Italy
| | - Luigi Maiorano
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza", Viale dell'Università 32, Roma, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, Italy
| | | | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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30
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Vodopivez C, Curtosi A, Pelletier E, Spairani LU, Hernández EA, Mac Cormack WP. Element concentrations of environmental concern in surface sediment samples from a broad marine area of 25 de Mayo (King George) Island, South Shetland Islands. Sci Total Environ 2019; 646:757-769. [PMID: 30064102 DOI: 10.1016/j.scitotenv.2018.07.174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Western Antarctica (WA) constitutes the area with the highest human presence in the white continent and also the region where the effects of global warming are more evident worldwide. Such human presence represents a potential risk of pollution with both, organic and inorganic contaminants. Global warming also could modify dynamics and transport of the pollutants, increasing summer water runoff, ice melting and iceberg scouring. Under this fast-changing scenario, knowledge about the concentration of contaminants is essential to evaluate the environmental status of this ecologically relevant area. In this work, we performed the first regional-scale monitoring of 9 trace elements (Cr, Co, Ni, Cu, Zn, As, Pb, Cd and Hg), as well as Fe and Mn, in surface sediment from 64 sites comprising six different areas in Maxwell Bay, 25 de Mayo (King George) Island. Target elements were quantified in surface sediment samples (20-30 m depth) obtained during two summer Antarctic expeditions: 2010/11 and 2011/12 by inductively coupled plasma linked to a quadrupole mass spectrometer (ICP-MS). Based on the average values observed for the reference areas, baseline values were defined for the studied region. A regional enrichment in Cu (compared with the global mean upper crust) was observed and related to the widespread mineralization of volcanic rocks. The most anthropized area (South Fildes) mainly showed sediment class 3 (moderately polluted) for Pb, Cd and Hg with a number samples revealing some highly contaminated hot spots. Although elemental contamination in some samples close to scientific stations or sites where logistic operations were evidenced, a pollution pattern was not clearly identified. The present work represents the first regional-scale attempt to define the baseline values and the anthropic impacts in this region of the WA and also provides the first data about Hg concentration in surface sediment of the study area.
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Affiliation(s)
- C Vodopivez
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - A Curtosi
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina
| | - E Pelletier
- Institut des Sciences de la Mer de Rimouski (ISMER), Université du Québec à Rimouski, 310 Allée des Ursulines, Rimouski G5L 3A1, Canada.
| | - L U Spairani
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina.
| | - E A Hernández
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto NANOBIOTEC UBA-CONICET, Junín 956 6to piso, CABA, Argentina.
| | - W P Mac Cormack
- Instituto Antártico Argentino, 25 de Mayo 1143, San Martín B1650HMK, Provincia de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto NANOBIOTEC UBA-CONICET, Junín 956 6to piso, CABA, Argentina.
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Perron L, Chang SL, Daigle JM, Vandal N, Theberge I, Diorio C, Lemieux J, Pelletier E, Brisson J. Breast cancer subtype and screening sensitivity in the Quebec Mammography Screening Program. J Med Screen 2018; 26:154-161. [PMID: 30572782 DOI: 10.1177/0969141318816736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective In mammography screening, interval cancers present a problem. The metric ‘screening sensitivity’ monitors both how well a programme detects cancers and avoids interval cancers. To our knowledge, the effect of breast cancer surrogate molecular subtypes on screening sensitivity has never been evaluated. We aimed to measure the 2-year screening sensitivity according to breast cancer subtypes. Methods We studied 734 women with an invasive breast cancer diagnosed between 2003 and 2007 after participating in one regional division of Quebec’s Mammography Screening Program. They represented 83% of all participating women with an invasive BC diagnosis in that region for that period. Tumours were categorized into ‘luminal A-like’, ‘luminal B-like’, ‘triple-negative’ and ‘HER2-positive’ subtypes. We used logistic regression and marginal standardization to estimate screening sensitivity, sensitivity ratios (SR) and sensitivity differences. We also assessed the mediating effect of grade. Results Adjusted 2-year screening sensitivity was 75.4% in luminal A-like, 66.1% in luminal B-like, 52.9% in triple-negative and 45.3% in HER2-positive, translating into sensitivity ratios of 0.88 (95% confidence interval [CI] = 0.78–0.98) for luminal B-like, 0.70 (CI = 0.56–0.88) for triple-negative and 0.60 (CI = 0.39–0.93) for HER2-positive, when compared with luminal A-like. Grade entirely mediated the subtype-sensitivity association for triple negative and mediated it partly for HER2-positive. Screening round (prevalent vs. incident) did not modify results. Conclusion There was substantial variation in screening sensitivity according to breast cancer subtypes. Aggressive phenotypes showed the lowest sensitivity, an effect that was mediated by grade. Tailoring screening according to women’s subtype risk factors might eventually lead to more efficient programs.
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Affiliation(s)
- Linda Perron
- 1 Institut national de sante publique du Quebec, Quebec, Canada
| | - Sue-Ling Chang
- 2 Centre de recherche du CHU de Québec-Université Laval, Quebec, Canada
| | | | - Nathalie Vandal
- 1 Institut national de sante publique du Quebec, Quebec, Canada
| | | | - Caroline Diorio
- 2 Centre de recherche du CHU de Québec-Université Laval, Quebec, Canada
| | - Julie Lemieux
- 2 Centre de recherche du CHU de Québec-Université Laval, Quebec, Canada
| | - Eric Pelletier
- 1 Institut national de sante publique du Quebec, Quebec, Canada
| | - Jacques Brisson
- 2 Centre de recherche du CHU de Québec-Université Laval, Quebec, Canada
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Sutter B, Pelletier E, Blaskowitz M, Ravera C, Stolze C, Reim C, Langlois E, Breuer D. Sampling and Analysis of Bitumen Fumes: Comparison of German and French Methods to Determine a Conversion Formula. Ann Work Expo Health 2018; 62:721-732. [PMID: 29985976 DOI: 10.1093/annweh/wxy029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 04/13/2018] [Indexed: 11/13/2022] Open
Abstract
Bitumen is classed as possibly carcinogenic to humans according to the International Agency for Research on Cancer. Data on individual exposure to bitumen fumes is therefore required to highlight the exposing situations and develop methods to prevent them. The Institute for Occupational Safety and Health of the German Social Accident Insurance (IFA) and the French National Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS) have both developed methods to measure individual exposure. The objective of this study was to determine a conversion factor to allow interconversion of data acquired by the two methods. To develop this conversion factor, comparative laboratory and workplace tests were performed according to both the IFA method (No. 6305) and the INRS method (MetroPol M-2). The amounts of organic material collected on the filters and XAD-2 beds were compared. The results revealed differences between the sampling and analytical methods that could be linked to sampler design, extraction solvent, and the detection method used. The total quantification returned by the two methods-the sum of the masses quantified on filter and XAD-2 bed for each sampler-were correlated in both controlled and real-life tests. A conversion equation was therefore determined, based on field tests: CIFA = 1.76 CINRS ± 0.39 (R2 = 0.99) that is applicable to total quantification data. This formula can be applied to data acquired by the two institutes to increase the number of data points available on exposure to bitumen fumes in various conditions, and thus increase the statistical power of studies into occupational prevention.
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Affiliation(s)
- Benjamin Sutter
- French National Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Vandoeuvre les Nancy Cedex, France
| | - Eric Pelletier
- French National Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Vandoeuvre les Nancy Cedex, France
| | - Morten Blaskowitz
- Institute for Occupational Safety and Health of the German Social Accident Insurance (IFA), Sankt Augustin, Germany
| | - Christel Ravera
- French National Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Vandoeuvre les Nancy Cedex, France
| | - Christopher Stolze
- BG BAU - Berufsgenossenschaft der Bauwirtschaft, Gebersdorfer Straße, Nürnberg, Germany
| | - Christian Reim
- BG BAU - Berufsgenossenschaft der Bauwirtschaft, Landsberger Straße, München, Germany
| | - Eddy Langlois
- French National Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Vandoeuvre les Nancy Cedex, France
| | - Dietmar Breuer
- Institute for Occupational Safety and Health of the German Social Accident Insurance (IFA), Sankt Augustin, Germany
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33
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Lemasson M, Haesebaert J, Rochette L, Pelletier E, Lesage A, Patry S. Electroconvulsive Therapy Practice in the Province of Quebec: Linked Health Administrative Data Study from 1996 to 2013. Can J Psychiatry 2018; 63:465-473. [PMID: 29069982 PMCID: PMC6099779 DOI: 10.1177/0706743717738492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE As part of a quality improvement process, we propose a model of routinely monitoring electroconvulsive therapy (ECT) in Canadian provinces using linked health administrative databases to generate provincial periodic reports, influence policy, and standardise ECT practices. METHODS ECT practice in Quebec was studied from 1996 to 2013, using longitudinal data from the Quebec Integrated Chronic Disease Surveillance System of the Institut National de Santé Publique du Québec, which links 5 health administrative databases. The population included all persons, aged 18 y and over, eligible for the health insurance registry, who received an ECT treatment at least once during the year. RESULTS Among recorded cases, 75% were identified by physician claims and hospitalisation files, 19% exclusively by physician claims, and 6% by hospitalisation files. From 1996 to 2013, 8,149 persons in Quebec received ECT with an annual prevalence rate of 13 per 100,000. A decline was observed, which was more pronounced in women and in older persons. On average, each patient received 9.7 treatments of ECT annually. The proportion of acute ECT decreased whereas maintenance treatment proportions increased. A wide variation in the use of ECT was observed among regions and psychiatrists. CONCLUSION This study demonstrates the profitable use of administrative data to monitor ECT use in Quebec, and provides a reliable method that could be replicated in other Canadian provinces. Although Quebec has one of the lowest utilisation rates reported in industrialized countries, regional disparities highlighted the need for a deeper examination of the quality and monitoring of ECT care and services.
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Affiliation(s)
- Morgane Lemasson
- 1 Centre d'Excellence en Électroconvulsivothérapie du Québec, Institut universitaire en santé mentale de Montréal, Montreal, Quebec.,2 Department of Psychiatry, University of Montreal, Montreal. Quebec.,3 Centre de recherche de l'Institut universitaire en santé mentale de Montréal, Montreal, Quebec.,4 Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Quebec, Quebec
| | - Julie Haesebaert
- 4 Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Quebec, Quebec
| | - Louis Rochette
- 4 Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Quebec, Quebec
| | - Eric Pelletier
- 4 Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Quebec, Quebec
| | - Alain Lesage
- 1 Centre d'Excellence en Électroconvulsivothérapie du Québec, Institut universitaire en santé mentale de Montréal, Montreal, Quebec.,2 Department of Psychiatry, University of Montreal, Montreal. Quebec.,3 Centre de recherche de l'Institut universitaire en santé mentale de Montréal, Montreal, Quebec.,4 Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Quebec, Quebec
| | - Simon Patry
- 1 Centre d'Excellence en Électroconvulsivothérapie du Québec, Institut universitaire en santé mentale de Montréal, Montreal, Quebec.,2 Department of Psychiatry, University of Montreal, Montreal. Quebec
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Meng A, Marchet C, Corre E, Peterlongo P, Alberti A, Da Silva C, Wincker P, Pelletier E, Probert I, Decelle J, Le Crom S, Not F, Bittner L. A de novo approach to disentangle partner identity and function in holobiont systems. Microbiome 2018; 6:105. [PMID: 29885666 PMCID: PMC5994019 DOI: 10.1186/s40168-018-0481-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/13/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept. RESULTS We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited. CONCLUSIONS In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.
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Affiliation(s)
- Arnaud Meng
- Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005 Paris, France
| | - Camille Marchet
- Univ Rennes, CNRS, Inria, IRISA - UMR 6074, F-35000 Rennes, France
| | - Erwan Corre
- Sorbonne Universités, CNRS - FR2424, ABiMS, Station biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | | | - Adriana Alberti
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Da Silva
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Patrick Wincker
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
- UMR8030, CNRS, Evry, France
| | - Eric Pelletier
- Institut de biologie François Jacob, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
- UMR8030, CNRS, Evry, France
| | - Ian Probert
- Sorbonne Université, CNRS - FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France
| | - Johan Decelle
- Helmholtz Centre for Environmental Research – UFZ, Department of Isotope Biogeochemistry, Permoserstraße 15, 04318 Leipzig, Germany
| | - Stéphane Le Crom
- Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005 Paris, France
| | - Fabrice Not
- Sorbonne Université, CNRS - UMR7144 - Ecology of Marine Plankton Group, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lucie Bittner
- Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005 Paris, France
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Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. The metagenomic data life-cycle: standards and best practices. Gigascience 2018. [PMID: 28637310 PMCID: PMC5737865 DOI: 10.1093/gigascience/gix047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.
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Affiliation(s)
- Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | - Erwan Corre
- CNRS-UPMC, FR 2424, Station Biologique, Roscoff 29680, France
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy
| | - Folker Meyer
- Argonne National Laboratory, Argonne IL 60439, USA
| | - Alex Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Eric Pelletier
- Genoscope, CEA, Évry 91000, France.,CNRS/UMR-8030, Évry 91000, France.,Université Évry val d'Essonne, Évry 91000, France
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro," Bari 70126, Italy
| | - Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy
| | | | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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Kazamia E, Sutak R, Paz-Yepes J, Dorrell RG, Vieira FRJ, Mach J, Morrissey J, Leon S, Lam F, Pelletier E, Camadro JM, Bowler C, Lesuisse E. Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms. Sci Adv 2018; 4:eaar4536. [PMID: 29774236 PMCID: PMC5955625 DOI: 10.1126/sciadv.aar4536] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/29/2018] [Indexed: 05/20/2023]
Abstract
Phytoplankton growth is limited in vast oceanic regions by the low bioavailability of iron. Iron fertilization often results in diatom blooms, yet the physiological underpinnings for how diatoms survive in chronically iron-limited waters and outcompete other phytoplankton when iron becomes available are unresolved. We show that some diatoms can use siderophore-bound iron, and exhibit a species-specific recognition for siderophore types. In Phaeodactylum tricornutum, hydroxamate siderophores are taken up without previous reduction by a high-affinity mechanism that involves binding to the cell surface followed by endocytosis-mediated uptake and delivery to the chloroplast. The affinity recorded is the highest ever described for an iron transport system in any eukaryotic cell. Collectively, our observations suggest that there are likely a variety of iron uptake mechanisms in diatoms besides the well-established reductive mechanism. We show that iron starvation-induced protein 1 (ISIP1) plays an important role in the uptake of siderophores, and through bioinformatics analyses we deduce that this protein is largely diatom-specific. We quantify expression of ISIP1 in the global ocean by querying the Tara Oceans atlas of eukaryotic genes and show a link between the abundance and distribution of diatom-associated ISIP1 with ocean provinces defined by chronic iron starvation.
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Affiliation(s)
- Elena Kazamia
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Javier Paz-Yepes
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Joe Morrissey
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Sébastien Leon
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
| | - France Lam
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, CNRS, Univ Evry, Univ Paris-Saclay, 91000 Evry, France
| | - Jean-Michel Camadro
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole normale supérieure, Ecole normale supérieure, CNRS, INSERM, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
- Corresponding author. (E.L.); (C.B.)
| | - Emmanuel Lesuisse
- Université Paris Diderot (Paris 07), Centre National de la Recherche Scientifique, Institut Jacques Monod, F-75013 Paris, France
- Corresponding author. (E.L.); (C.B.)
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Pelletier E, Billot E. Consultation pluridisciplinaire d’aide à la reprise de travail après un cancer. ARCH MAL PROF ENVIRO 2018. [DOI: 10.1016/j.admp.2018.03.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 2017; 35:1069-1076. [PMID: 28967887 DOI: 10.1038/nbt.3960] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
Abstract
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Eric Pelletier
- CEA - Institut François Jacob - Genoscope, Evry, France.,CNRS UMR-8030, Evry, France.,Université Evry Val d'Essonne, Evry, France
| | | | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Melanie Tramontano
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rajna Hercog
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris-Elias Jung
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthew R Hayward
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jillian R M Brown
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Michelle Daigneault
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.,Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruth Ann Luna
- Texas Children's Hospital, Feigin Center, Houston, Texas, USA
| | | | - Jana Junick
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Philippe Langella
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Céline Orvain
- CEA - Institut François Jacob - Genoscope, Evry, France
| | - Kiran Raosaheb Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Søren Persson
- Unit of Foodborne Infections, Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Delphine Saulnier
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Bhagirath Singh
- Centre for Human Immunology, Department of Microbiology & Immunology and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Kathleen Slezak
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Liping Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Joel Dore
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
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39
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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Vannier T, Leconte J, Seeleuthner Y, Mondy S, Pelletier E, Aury JM, de Vargas C, Sieracki M, Iudicone D, Vaulot D, Wincker P, Jaillon O. Survey of the green picoalga Bathycoccus genomes in the global ocean. Sci Rep 2016; 6:37900. [PMID: 27901108 PMCID: PMC5128809 DOI: 10.1038/srep37900] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 11/03/2016] [Indexed: 01/23/2023] Open
Abstract
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.
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Affiliation(s)
- Thomas Vannier
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Jade Leconte
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Yoann Seeleuthner
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Samuel Mondy
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Eric Pelletier
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Jean-Marc Aury
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michael Sieracki
- National Science Foundation, 4201 Wilson Blvd., Arlington, VA 22230, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Daniel Vaulot
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Olivier Jaillon
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
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41
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Pelletier E, Daigle JM, Defay F, Major D, Guertin MH, Brisson J. Frequency and Determinants of a Short-Interval Follow-up Recommendation After an Abnormal Screening Mammogram. Can Assoc Radiol J 2016; 67:322-329. [PMID: 27209218 DOI: 10.1016/j.carj.2015.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/28/2015] [Accepted: 11/10/2015] [Indexed: 11/17/2022] Open
Abstract
PURPOSE After imaging assessment of an abnormal screening mammogram, a follow-up examination 6 months later is recommended to some women. Our aim was to identify which characteristics of lesions, women, and physicians are associated to such short-interval follow-up recommendation in the Quebec Breast Cancer Screening Program. METHODS Between 1998 and 2008, 1,839,396 screening mammograms were performed and a total of 114,781 abnormal screens were assessed by imaging only. Multivariate analysis was done with multilevel Poisson regression models with robust variance and generalized linear mixed models. RESULTS A short-interval follow-up was recommended in 26.7% of assessments with imaging only, representing 2.3% of all screens. Case-mix adjusted proportion of short-interval follow-up recommendations varied substantially across physicians (range: 4%-64%). Radiologists with high recall rates (≥15%) had a high proportion of short-interval follow-up recommendation (risk ratio: 1.82; 95% confidence interval: 1.35-2.45) compared to radiologists with low recall rates (<5%). The adjusted proportion of short-interval follow-up was high (22.8%) even when a previous mammogram was usually available. CONCLUSIONS Short-interval follow-up recommendation at assessment is frequent in this Canadian screening program, even when a previous mammogram is available. Characteristics related to radiologists appear to be key determinants of short-interval follow-up recommendation, rather than characteristics of lesions or patient mix. Given that it can cause anxiety to women and adds pressure on the health system, it appears important to record and report short-interval follow-up and to identify ways to reduce its frequency. Short-interval follow-up recommendations should be considered when assessing the burden of mammography screening.
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Affiliation(s)
- Eric Pelletier
- Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Québec City, Québec, Canada.
| | - Jean-Marc Daigle
- Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Québec City, Québec, Canada
| | - Fannie Defay
- Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Québec City, Québec, Canada
| | - Diane Major
- Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Québec City, Québec, Canada
| | - Marie-Hélène Guertin
- Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Québec City, Québec, Canada
| | - Jacques Brisson
- Bureau d'information et d'études en santé des populations, Institut national de santé publique du Québec, Québec City, Québec, Canada; Centre de recherche du Centre hospitalier universitaire de Québec, Département de médecine sociale et préventive, Université Laval, Québec City, Québec, Canada
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42
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Senterre C, Levêque A, Pelletier E, Rochette L, St-Laurent D, Rahme E. 564 Surveillance of suicide using administrative health databases: a study in Québec and in Belgium. Inj Prev 2016. [DOI: 10.1136/injuryprev-2016-042156.564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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43
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Hofvind S, Bennett R, Brisson J, Lee W, Pelletier E, Flugelman A, Geller B. Authors' response to Ravaioli et al. J Med Screen 2016; 24:56. [PMID: 27430535 DOI: 10.1177/0969141316649407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Solveig Hofvind
- 1 Department of Screening, Cancer Registry of Norway, Oslo, Norway
| | - Rachel Bennett
- 2 Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jacques Brisson
- 3 Centre de Recherche du, CHU de Quebec and Centre des Maladies du Sein Deschenes-Fabia, Hospital du Saint-Sacrement, Quebec, Canada
| | - Warwick Lee
- 4 Discipline Medical Radiation Sciences, the University of Sydney, Lidcombe, NSW, Australia
| | | | - Anath Flugelman
- 6 CHS National Cancer Control Center, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Berta Geller
- 7 Department of Family Medicine, University of Vermont, Burlington, VT, USA
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Hofvind S, Bennett RL, Brisson J, Lee W, Pelletier E, Flugelman A, Geller B. Audit feedback on reading performance of screening mammograms: An international comparison. J Med Screen 2016; 23:150-9. [DOI: 10.1177/0969141315610790] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/17/2015] [Indexed: 01/16/2023]
Abstract
Objective Providing feedback to mammography radiologists and facilities may improve interpretive performance. We conducted a web-based survey to investigate how and why such feedback is undertaken and used in mammographic screening programmes. Methods The survey was sent to representatives in 30 International Cancer Screening Network member countries where mammographic screening is offered. Results Seventeen programmes in 14 countries responded to the survey. Audit feedback was aimed at readers in 14 programmes, and facilities in 12 programmes. Monitoring quality assurance was the most common purpose of audit feedback. Screening volume, recall rate, and rate of screen-detected cancers were typically reported performance measures. Audit reports were commonly provided annually, but more frequently when target guidelines were not reached. Conclusion The purpose, target audience, performance measures included, form and frequency of the audit feedback varied amongst mammographic screening programmes. These variations may provide a basis for those developing and improving such programmes.
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Affiliation(s)
- S Hofvind
- Department of Screening, Cancer Registry of Norway, Oslo, Norway
| | - RL Bennett
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - J Brisson
- Centre de Recherche du, CHU de Québec and Centre des Maladies du Sein Deschênes-Fabia, Hôpital du Saint-Sacrement, Quebec, Canada
| | - W Lee
- Discipline Medical Radiation Sciences, The University of Sydney, Lidcombe, NSW, Australia
| | - E Pelletier
- Institut National de santé Publique du Québec, Canada
| | - A Flugelman
- CHS National Cancer Control Center, Lady Davis Carmel Medical Center, Haifa, Israel
| | - B Geller
- Department of Family Medicine, University of Vermont, Burlington, VT, USA
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45
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Cailhol L, Pelletier E, Rochette L, Villeneuve E, Laporte L, David P, Lesage A. Prevalence, mortality and healthcare utilization of cluster B personality disorders in Quebec: A province cohort study, 2001–2012. Eur Psychiatry 2016. [DOI: 10.1016/j.eurpsy.2016.01.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BackgroundCluster B personality disorder (PD) is a highly prevalent mental health condition in general population (1 to 6% depending on the subtype and study). Patients affected are known to be heavier users of both mental and medical healthcare than other clinical conditions such as depression. Few studies have highlighted their elevated mortality rate compared to general population.MethodsThe estimates were produced using data from the integrated monitoring system for chronic disease of Quebec. It provides annual and life prevalence, mortality rate, years of and healthcare utilization profile Quebec inhabitants.ResultsA total of 7,995,963 people were included in the study. The life prevalence of cluster B PD is 2.6%. The mean years of lost life is 13 for men and 9 for women when they are compared to general population. The 3 most important causes of death are: suicide (20.4%), cardiovascular diseases (19.1%) and cancers (18.6%). The standardized mortality ratio (SMR) for each medical condition is superior in cluster B personality disorders than general population. The most important SMR is for suicide (male: 10.2 and female: 21). In the year 2011–2012, 78% had consulted a general practitioner, 62% a psychiatrist, 41% were admitted in an emergency department and 21% were hospitalized.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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46
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Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussières L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M, Ville Y. Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma. Prenat Diagn 2016; 35:471-6. [PMID: 25643828 DOI: 10.1002/pd.4561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 01/04/2015] [Accepted: 01/14/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVE By-the-book implementation of non-invasive prenatal test and clinical validation for trisomy 21. STUDY DESIGN Publicly funded prospective study of 225 cases. Women at risk for trisomy 21 > 1/250 based on combined ultrasound and serum markers during first or second trimester were eligible following an informed consent. The technique was established from the available literature and performed on 10 mL of venous blood collected prior to chorionic villus sampling or amniocentesis. Investigators were blinded to the fetal karyotype. Results were expressed in Z-scores of the percentage of each chromosome. RESULTS Among 976 eligible cases, 225 were processed: 8 were used for pretesting phase and 23 to build a reference set. One hundred thirty six euploid cases and 47 with trisomy 21 were then run randomly. Eleven cases yielded no result (4.8%). Z-scores were above 3 (7.58+/-2.41) for chromosome 21 in all 47 trisomies and in none of the euploid cases (0.11+/-1.0). Z-scores were within normal range for the other chromosomes in both groups. Using a cut-off of 3, sensitivity and specificity were of 100% 95% CI [94.1, 100] and 100% 95% CI [98, 100], respectively. CONCLUSION Non-invasive prenatal test for trisomy 21 is a robust strategy that can be translated from seminal publications. Publicly funded studies should refine its indications and cost-effectiveness in prenatal screening and diagnosis. © 2015 John Wiley & Sons, Ltd.
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Saint-Georges-Chaumet Y, Attaf D, Pelletier E, Edeas M. Targeting microbiota-mitochondria inter-talk: Microbiota control mitochondria metabolism. Cell Mol Biol (Noisy-le-grand) 2015; 61:121-124. [PMID: 26429302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
Our aim is to highlight the subtle relationship that exists between microbiota and mitochondria. Microbiota targets mitochondria by modulating the Reactive Oxygen Species (ROS) production and the mitochondrial activity through interactions with toxins, proteins or other metabolites released by gut microbiota. The intriguing relationship that exists between mitochondria and microbiota is strengthened by the probable prokaryotic origin of mitochondria. Emerging data implicates a role for ROS, nitric oxide, Short Chain Fatty Acids and hydrogen sulfide in the cross-talk between microbiota - mitochondria and REDOX signaling. Several studies have shown that microbiota act and modulate mitochondrial activity, and use it as a relay to strengthen host-microbiotal interaction. This modulation depends on the gut bacterial strain quality and diversity to increase its pathogenic versus beneficial effects. Furthermore, based on conclusions from new studies, it is possible that microbiota can directly interact with the host cell gene expression by favoring bacterial and mitochondrial DNA insertion in the nuclear genome. The emerging knowledge of mitochondria-microbiota interaction may be of great importance to better understand the mechanism of mitochondrial and metabolic diseases, and the syndromes associated with change in quality and quantity of microbiotal species. We suggest that microbiota via mitochondrial modulation influence cell homeostasis and metabolism. The challenge will be to find strategies to modulate the quality and diversity of microbiota rather than acting on microbiota metabolites and microbiota related factors. The medicine of tomorrow will be completely personalized. Firstly there will be a test to show the quality, quantity and diversity of microbiota, and secondly a preventive or therapeutic strategy will be administrated (probiotics, diet, prodrug or fecal transplantation). The era of digital medicine is here.
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Affiliation(s)
| | - D Attaf
- Microbiota platform-Biotech Biopole Microbiota Mitochondria task force Paris France
| | - E Pelletier
- Microbiota platform-Biotech Biopole Microbiota Mitochondria task force Paris France
| | - M Edeas
- Microbiota platform-Biotech Biopole Microbiota Mitochondria task force Paris France edeas@targeting—mitochondria.com
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Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 2015; 348:1261447. [PMID: 25999514 DOI: 10.1126/science.1261447] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.
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Affiliation(s)
- Emilie Villar
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France.
| | - Gregory K Farrant
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Michael Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laurence Garczarek
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sabrina Speich
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France. Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD) UMR 8539, Ecole Normale Supérieure, 24 Rue Lhomond, 75231 Paris Cedex 05, France
| | - Stéphane Audic
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lucie Bittner
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Bruno Blanke
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France
| | - Jennifer R Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Alison Chase
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - John R Dolan
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Fabrizio d'Ortenzio
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Jean-Pierre Gattuso
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Nicolas Grima
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France
| | - Lionel Guidi
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Christopher N Hill
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jean-Louis Jamet
- Université de Toulon, Laboratoire PROTEE-EBMA E.A. 3819, BP 20132, 83957 La Garde Cedex, France
| | - Hervé Le Goff
- CNRS, UMR 7159, Laboratoire d'Océanographie et du Climat LOCEAN, 4 Place Jussieu, 75005 Paris, France
| | - Cyrille Lepoivre
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Shruti Malviya
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Eric Pelletier
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Jean-Baptiste Romagnan
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sébastien Santini
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Atsuko Tanaka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Pierre Testor
- CNRS, UMR 7159, Laboratoire d'Océanographie et du Climat LOCEAN, 4 Place Jussieu, 75005 Paris, France
| | - Thomas Vannier
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Flora Vincent
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Céline Dimier
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Marc Picheral
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Sarah Searson
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France.
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Pascal Hingamp
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France.
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
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49
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Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TBH, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 2015; 4:e07966. [PMID: 26371554 PMCID: PMC4612132 DOI: 10.7554/elife.07966] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/14/2015] [Indexed: 01/06/2023] Open
Abstract
Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.
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Affiliation(s)
| | - Manuel Kleiner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ruby Ponnudurai
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Silke Wetzel
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Eric Pelletier
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- Metabolic Genomics Group, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- University of Évry-Val d'Essonne, Evry, France
| | - Valerie Barbe
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Dennis Fink
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Corinna Breusing
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Thorsten BH Reusch
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | | | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, Bremen, Germany
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50
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Thibault M, Michel MC, Varin F, Deschenes L, Pelletier E, Guevremont C, Berard G, Marcotte N, Turgeron M, Farand P, Froment D, Gaudreault P, Rajan R. 29: Descriptive Analysis of Paediatric Antimicrobial Prophylaxis in Surgery in Four University Teaching Hospitals. Paediatr Child Health 2015. [DOI: 10.1093/pch/20.5.e43b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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