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Meslier V, Menozzi E, David A, Morabito C, Lucas Del Pozo S, Famechon A, North J, Quinquis B, Koletsi S, Macnaughtan J, Mezabrovschi R, Ehrlich SD, Schapira AHV, Almeida M. Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics. Biomolecules 2023; 13:1505. [PMID: 37892187 PMCID: PMC10604855 DOI: 10.3390/biom13101505] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson's disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.
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Affiliation(s)
- Victoria Meslier
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Elisa Menozzi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Aymeric David
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Christian Morabito
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Sara Lucas Del Pozo
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Alexandre Famechon
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Janet North
- Research Department of Hematology, Cancer Institute, University College London (UCL), London WC1E 6BT, UK
| | - Benoit Quinquis
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Sofia Koletsi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Jane Macnaughtan
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Liver Failure Group, Institute for Liver and Digestive Health, University College London, London WC1E 6BT, UK
| | - Roxana Mezabrovschi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - S. Dusko Ehrlich
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Anthony H. V. Schapira
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Mathieu Almeida
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
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Andrikopoulos P, Aron-Wisnewsky J, Chakaroun R, Myridakis A, Forslund SK, Nielsen T, Adriouch S, Holmes B, Chilloux J, Vieira-Silva S, Falony G, Salem JE, Andreelli F, Belda E, Kieswich J, Chechi K, Puig-Castellvi F, Chevalier M, Le Chatelier E, Olanipekun MT, Hoyles L, Alves R, Helft G, Isnard R, Køber L, Coelho LP, Rouault C, Gauguier D, Gøtze JP, Prifti E, Froguel P, Zucker JD, Bäckhed F, Vestergaard H, Hansen T, Oppert JM, Blüher M, Nielsen J, Raes J, Bork P, Yaqoob MM, Stumvoll M, Pedersen O, Ehrlich SD, Clément K, Dumas ME. Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide. Nat Commun 2023; 14:5843. [PMID: 37730687 PMCID: PMC10511707 DOI: 10.1038/s41467-023-39824-4] [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: 11/02/2022] [Accepted: 06/30/2023] [Indexed: 09/22/2023] Open
Abstract
The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied "explainable" machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in 1,741 adult Europeans of the MetaCardis study. Here we show that next to age, kidney function is the primary variable predicting circulating TMAO, with microbiota composition and diet playing minor, albeit significant, roles. Mediation analysis suggests a causal relationship between TMAO and kidney function that we corroborate in preclinical models where TMAO exposure increases kidney scarring. Consistent with our findings, patients receiving glucose-lowering drugs with reno-protective properties have significantly lower circulating TMAO when compared to propensity-score matched control individuals. Our analyses uncover a bidirectional relationship between kidney function and TMAO that can potentially be modified by reno-protective anti-diabetic drugs and suggest a clinically actionable intervention for decreasing TMAO-associated excess cardiovascular risk.
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Affiliation(s)
- Petros Andrikopoulos
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Section of Genomic & Environmental Medicine, National Heart & Lung Institute, Imperial College London, London, UK.
| | - Judith Aron-Wisnewsky
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France
| | - Rima Chakaroun
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Antonis Myridakis
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Environmental Research Group, MRC Centre for Environment and Health, School of Public Health, Imperial College London, 86 Wood Lane, London, W12 0BZ, UK
| | - Sofia K Forslund
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Charité University Hospital, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Solia Adriouch
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
| | | | - Julien Chilloux
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Joe-Elie Salem
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France
| | - Fabrizio Andreelli
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France
| | - Eugeni Belda
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
- Sorbonne Université, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, F-93143, Bondy, France
| | - Julius Kieswich
- Diabetic Kidney Disease Centre, Renal Unit, Barts Health National Health Service Trust, The Royal London Hospital, London, UK
- Centre for Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kanta Chechi
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Section of Genomic & Environmental Medicine, National Heart & Lung Institute, Imperial College London, London, UK
| | - Francesc Puig-Castellvi
- European Genomics Institute for Diabetes, EGENODIA, INSERM U1283, CNRS UMR8199, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France
| | - Mickael Chevalier
- European Genomics Institute for Diabetes, EGENODIA, INSERM U1283, CNRS UMR8199, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France
| | | | - Michael T Olanipekun
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Renato Alves
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Gerard Helft
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France
- Institute of Cardiometabolism and Nutrition, ICAN, INSERM, 1166, Paris, France
| | - Richard Isnard
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France
| | - Lars Køber
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christine Rouault
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
| | - Dominique Gauguier
- INSERM UMR 1124, Université de Paris, 45 rue des Saint-Pères, 75006, Paris, France
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Jens Peter Gøtze
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Edi Prifti
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
- Sorbonne Université, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, F-93143, Bondy, France
| | - Philippe Froguel
- European Genomics Institute for Diabetes, EGENODIA, INSERM U1283, CNRS UMR8199, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Jean-Daniel Zucker
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France
- Sorbonne Université, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, F-93143, Bondy, France
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jean-Michel Oppert
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France
| | - Matthias Blüher
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, 03722, South Korea
| | - Muhammad M Yaqoob
- Diabetic Kidney Disease Centre, Renal Unit, Barts Health National Health Service Trust, The Royal London Hospital, London, UK
- Centre for Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Michael Stumvoll
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Gentofte University Hospital, Copenhagen, Denmark
| | - S Dusko Ehrlich
- Department of Clinical and Movement Neurosciences, University College London, London, NW3 2PF, UK
| | - Karine Clément
- Sorbonne Université, INSERM, Nutrition and obesities; systemic approaches (NutriOmics), Paris, France.
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France.
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Section of Genomic & Environmental Medicine, National Heart & Lung Institute, Imperial College London, London, UK.
- European Genomics Institute for Diabetes, EGENODIA, INSERM U1283, CNRS UMR8199, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France.
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
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Fan Y, Støving RK, Berreira Ibraim S, Hyötyläinen T, Thirion F, Arora T, Lyu L, Stankevic E, Hansen TH, Déchelotte P, Sinioja T, Ragnarsdottir O, Pons N, Galleron N, Quinquis B, Levenez F, Roume H, Falony G, Vieira-Silva S, Raes J, Clausen L, Telléus GK, Bäckhed F, Oresic M, Ehrlich SD, Pedersen O. The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Nat Microbiol 2023; 8:787-802. [PMID: 37069399 PMCID: PMC10159860 DOI: 10.1038/s41564-023-01355-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/03/2023] [Indexed: 04/19/2023]
Abstract
Anorexia nervosa (AN) is an eating disorder with a high mortality. About 95% of cases are women and it has a population prevalence of about 1%, but evidence-based treatment is lacking. The pathogenesis of AN probably involves genetics and various environmental factors, and an altered gut microbiota has been observed in individuals with AN using amplicon sequencing and relatively small cohorts. Here we investigated whether a disrupted gut microbiota contributes to AN pathogenesis. Shotgun metagenomics and metabolomics were performed on faecal and serum samples, respectively, from a cohort of 77 females with AN and 70 healthy females. Multiple bacterial taxa (for example, Clostridium species) were altered in AN and correlated with estimates of eating behaviour and mental health. The gut virome was also altered in AN including a reduction in viral-bacterial interactions. Bacterial functional modules associated with the degradation of neurotransmitters were enriched in AN and various structural variants in bacteria were linked to metabolic features of AN. Serum metabolomics revealed an increase in metabolites associated with reduced food intake (for example, indole-3-propionic acid). Causal inference analyses implied that serum bacterial metabolites are potentially mediating the impact of an altered gut microbiota on AN behaviour. Further, we performed faecal microbiota transplantation from AN cases to germ-free mice under energy-restricted feeding to mirror AN eating behaviour. We found that the reduced weight gain and induced hypothalamic and adipose tissue gene expression were related to aberrant energy metabolism and eating behaviour. Our 'omics' and mechanistic studies imply that a disruptive gut microbiome may contribute to AN pathogenesis.
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Affiliation(s)
- Yong Fan
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - René Klinkby Støving
- Center for Eating Disorders, Odense University Hospital, and Research Unit for Medical Endocrinology, Mental Health Services in the Region of Southern Denmark, Open Patient data Explorative Network (OPEN) and Clinical Institute, University of Southern Denmark, Odense, Denmark
| | | | | | | | - Tulika Arora
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Liwei Lyu
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, University of Copenhagen and Herlev-Gentofte University Hospital, Copenhagen, Denmark
| | - Evelina Stankevic
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Pierre Déchelotte
- INSERM U1073 Research Unit and TargEDys, Rouen University, Rouen, France
| | - Tim Sinioja
- School of Science and Technology, Örebro University, Örebro, Sweden
| | | | - Nicolas Pons
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | | | | | | | - Hugo Roume
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Gwen Falony
- Laboratory of Molecular bacteriology, Department of Microbiology and Immunology, Rega Institute Ku Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sara Vieira-Silva
- Laboratory of Molecular bacteriology, Department of Microbiology and Immunology, Rega Institute Ku Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jeroen Raes
- Laboratory of Molecular bacteriology, Department of Microbiology and Immunology, Rega Institute Ku Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Loa Clausen
- Department of Child and Adolescent Psychiatry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Gry Kjaersdam Telléus
- Unit for Psychiatric Research, Aalborg University Hospital, Aalborg, Denmark
- Department of Communication and Psychology, The Faculty of Social Sciences and Humanities, Aalborg University, Aalborg, Denmark
| | - Fredrik Bäckhed
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Matej Oresic
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - S Dusko Ehrlich
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
- Department of Clinical and Movement Neurosciences, University College London, London, UK
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.
- Department of Medicine, University of Copenhagen and Herlev-Gentofte University Hospital, Copenhagen, Denmark.
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4
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Etienne-Mesmin L, Meslier V, Uriot O, Fournier E, Deschamps C, Denis S, David A, Jegou S, Morabito C, Quinquis B, Thirion F, Plaza Oñate F, Le Chatelier E, Ehrlich SD, Blanquet-Diot S, Almeida M. In Vitro Modelling of Oral Microbial Invasion in the Human Colon. Microbiol Spectr 2023; 11:e0434422. [PMID: 36971547 PMCID: PMC10100946 DOI: 10.1128/spectrum.04344-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/05/2023] [Indexed: 03/29/2023] Open
Abstract
Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions. It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.
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Affiliation(s)
- Lucie Etienne-Mesmin
- UMR 454 UCA-INRAE Microbiologie Environnement DIgestif et Santé (MEDIS), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Victoria Meslier
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | - Ophélie Uriot
- UMR 454 UCA-INRAE Microbiologie Environnement DIgestif et Santé (MEDIS), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Elora Fournier
- UMR 454 UCA-INRAE Microbiologie Environnement DIgestif et Santé (MEDIS), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charlotte Deschamps
- UMR 454 UCA-INRAE Microbiologie Environnement DIgestif et Santé (MEDIS), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sylvain Denis
- UMR 454 UCA-INRAE Microbiologie Environnement DIgestif et Santé (MEDIS), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Aymeric David
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | - Sarah Jegou
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | - Christian Morabito
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | - Benoit Quinquis
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | - Florence Thirion
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | | | | | - S. Dusko Ehrlich
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
| | - Stéphanie Blanquet-Diot
- UMR 454 UCA-INRAE Microbiologie Environnement DIgestif et Santé (MEDIS), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathieu Almeida
- Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France
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5
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Xu Q, Wu C, Zhu Q, Gao R, Lu J, Valles-Colomer M, Zhu J, Yin F, Huang L, Ding L, Zhang X, Zhang Y, Xiong X, Bi M, Chen X, Zhu Y, Liu L, Liu Y, Chen Y, Fan J, Sun Y, Wang J, Cao Z, Fan C, Ehrlich SD, Segata N, Qin N, Qin H. Author Correction: Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nat Aging 2022; 2:680. [PMID: 37253873 DOI: 10.1038/s43587-022-00258-0] [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] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Qian Xu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Renyuan Gao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianquan Lu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | | | - Jian Zhu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Fang Yin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Linsheng Huang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lulu Ding
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiaohui Zhang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yonghui Zhang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiao Xiong
- Realbio Genomics Institute, Shanghai, China
| | | | - Xiang Chen
- Realbio Genomics Institute, Shanghai, China
| | - Yefei Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lin Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongqiang Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongshen Chen
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jian Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Yan Sun
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jun Wang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Zhan Cao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunsun Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - S Dusko Ehrlich
- MGP MetaGenoPolis, INRAE, Université Paris-Saclay, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Nan Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
- Realbio Genomics Institute, Shanghai, China.
| | - Huanlong Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
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6
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Xu Q, Wu C, Zhu Q, Gao R, Lu J, Valles-Colomer M, Zhu J, Yin F, Huang L, Ding L, Zhang X, Zhang Y, Xiong X, Bi M, Chen X, Zhu Y, Liu L, Liu Y, Chen Y, Fan J, Sun Y, Wang J, Cao Z, Fan C, Ehrlich SD, Segata N, Qin N, Qin H. Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nat Aging 2022; 2:438-452. [PMID: 37118062 DOI: 10.1038/s43587-022-00193-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/16/2022] [Indexed: 04/30/2023]
Abstract
A better understanding of the biological and environmental variables that contribute to exceptional longevity has the potential to inform the treatment of geriatric diseases and help achieve healthy aging. Here, we compared the gut microbiome and blood metabolome of extremely long-lived individuals (94-105 years old) to that of their children (50-79 years old) in 116 Han Chinese families. We found extensive metagenomic and metabolomic remodeling in advanced age and observed a generational divergence in the correlations with socioeconomic factors. An analysis of quantitative trait loci revealed that genetic associations with metagenomic and metabolomic features were largely generation-specific, but we also found 131 plasma metabolic quantitative trait loci associations that were cross-generational with the genetic variants concentrated in six loci. These included associations between FADS1/2 and arachidonate, PTPA and succinylcarnitine and FLVCR1 and choline. Our characterization of the extensive metagenomic and metabolomic remodeling that occurs in people reaching extreme ages may offer new targets for aging-related interventions.
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Affiliation(s)
- Qian Xu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Renyuan Gao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianquan Lu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | | | - Jian Zhu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Fang Yin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Linsheng Huang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lulu Ding
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiaohui Zhang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yonghui Zhang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiao Xiong
- Realbio Genomics Institute, Shanghai, China
| | | | - Xiang Chen
- Realbio Genomics Institute, Shanghai, China
| | - Yefei Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lin Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongqiang Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongshen Chen
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jian Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Yan Sun
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jun Wang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Zhan Cao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunsun Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - S Dusko Ehrlich
- MGP MetaGenoPolis, INRAE, Université Paris-Saclay, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Nan Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
- Realbio Genomics Institute, Shanghai, China.
| | - Huanlong Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
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7
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Talmor-Barkan Y, Bar N, Shaul AA, Shahaf N, Godneva A, Bussi Y, Lotan-Pompan M, Weinberger A, Shechter A, Chezar-Azerrad C, Arow Z, Hammer Y, Chechi K, Forslund SK, Fromentin S, Dumas ME, Ehrlich SD, Pedersen O, Kornowski R, Segal E. Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease. Nat Med 2022; 28:295-302. [PMID: 35177859 DOI: 10.1038/s41591-022-01686-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [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: 03/01/2021] [Accepted: 01/06/2022] [Indexed: 12/29/2022]
Abstract
Complex diseases, such as coronary artery disease (CAD), are often multifactorial, caused by multiple underlying pathological mechanisms. Here, to study the multifactorial nature of CAD, we performed comprehensive clinical and multi-omic profiling, including serum metabolomics and gut microbiome data, for 199 patients with acute coronary syndrome (ACS) recruited from two major Israeli hospitals, and validated these results in a geographically distinct cohort. ACS patients had distinct serum metabolome and gut microbial signatures as compared with control individuals, and were depleted in a previously unknown bacterial species of the Clostridiaceae family. This bacterial species was associated with levels of multiple circulating metabolites in control individuals, several of which have previously been linked to an increased risk of CAD. Metabolic deviations in ACS patients were found to be person specific with respect to their potential genetic or environmental origin, and to correlate with clinical parameters and cardiovascular outcomes. Moreover, metabolic aberrations in ACS patients linked to microbiome and diet were also observed to a lesser extent in control individuals with metabolic impairment, suggesting the involvement of these aberrations in earlier dysmetabolic phases preceding clinically overt CAD. Finally, a metabolomics-based model of body mass index (BMI) trained on the non-ACS cohort predicted higher-than-actual BMI when applied to ACS patients, and the excess BMI predictions independently correlated with both diabetes mellitus (DM) and CAD severity, as defined by the number of vessels involved. These results highlight the utility of the serum metabolome in understanding the basis of risk-factor heterogeneity in CAD.
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Affiliation(s)
- Yeela Talmor-Barkan
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviv A Shaul
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Nir Shahaf
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Bussi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Shechter
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Chava Chezar-Azerrad
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ziad Arow
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yoav Hammer
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kanta Chechi
- Genomic and Environmental Medicine, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- School of Public Health, Faculty of Medicine, Imperial College London, Medical School Building, St Mary's Hospital, London, UK
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- MCharité University Hospital, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Sebastien Fromentin
- University College London, Department of Clinical and Movement Neurosciences, London, UK
| | - Marc-Emmanuel Dumas
- Genomic and Environmental Medicine, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- European Genomics Institute for Diabetes, UMR1283/8199 INSERM, CNRS, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France
| | - S Dusko Ehrlich
- University College London, Department of Clinical and Movement Neurosciences, London, UK
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ran Kornowski
- Department of Cardiology, Rabin Medical Center, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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8
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Petersen AØ, Julienne H, Hyötyläinen T, Sen P, Fan Y, Pedersen HK, Jäntti S, Hansen TH, Nielsen T, Jørgensen T, Hansen T, Myers PN, Nielsen HB, Ehrlich SD, Orešič M, Pedersen O. Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species. Sci Rep 2021; 11:13252. [PMID: 34168163 PMCID: PMC8225906 DOI: 10.1038/s41598-021-91482-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 02/08/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
Knowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.
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Affiliation(s)
- Anders Ø Petersen
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Hanna Julienne
- Department of Computational Biology-USR 3756 CNRS, Institut Pasteur, 75015, Paris, France
| | | | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Yong Fan
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Helle Krogh Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Clinical Microbiomics A/S, Fruebjergvej 3 , 2100 , Copenhagen, Denmark
| | - Sirkku Jäntti
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Torben Jørgensen
- Department of Public Health, Faculty of Health and Medical Sciences , University of Copenhagen , Blegdamsvej 3B , 2200 , Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Niels Jernes Vej 10, 9200 , Aalborg East, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Pernille Neve Myers
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - H Bjørn Nielsen
- Clinical Microbiomics A/S, Fruebjergvej 3 , 2100 , Copenhagen, Denmark
| | - S Dusko Ehrlich
- Department of Computational Biology-USR 3756 CNRS, Institut Pasteur, 75015, Paris, France
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- School of Medical Sciences, Örebro University, 702 81, Örebro, Sweden
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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9
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Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F. Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nat Commun 2020; 11:6448. [PMID: 33349634 PMCID: PMC7752903 DOI: 10.1038/s41467-020-20412-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Antonio Molinaro
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden.,Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre Bel Lassen
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France.,Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France
| | - Marcus Henricsson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Hao Wu
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Solia Adriouch
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Eugeni Belda
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France.,Integromics Unit, Institute of Cardiometabolism and Nutrition, 75013, Paris, France
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Per-Olof Bergh
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Christine Rouault
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Sébastien André
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Florian Marquet
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Fabrizio Andreelli
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Joe-Elie Salem
- Assistance Publique Hôpitaux de Paris, Clinical Investigation Center Paris East, 75013, Paris, France
| | - Karen Assmann
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Jean-Philippe Bastard
- Assistance Publique Hôpitaux de Paris, Biochemistry and Hormonology Department, Tenon Hospital, 75020, Paris, France
| | - Sofia Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany
| | | | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Nicolas Pons
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Edi Prifti
- Integromics Unit, Institute of Cardiometabolism and Nutrition, 75013, Paris, France.,Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, 93143, Bondy, France
| | - Benoit Quinquis
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Hugo Roume
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Helle Krogh Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Christian Lewinter
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Nadja B Sønderskov
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | | | - Lars Køber
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jean-Daniel Zucker
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, 93143, Bondy, France
| | - Pilar Galan
- Sorbonne Paris Cité Epidemiology and Statistics Research Centre (CRESS), U1153 Inserm, U1125, Inra, Cnam, University of Paris 13, Nutritional Epidemiology Research Team (EREN), 93017, Bobigny, France
| | - Marc-Emmanuel Dumas
- Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.,Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, SW3 6KY, UK
| | - Jeroen Raes
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France.,Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jean-Michel Oppert
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France
| | - Ivica Letunic
- Biobyte Solutions GmbH, Bothestr. 142, 69117, Heidelberg, Germany
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41128, Gothenburg, Sweden
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - S Dusko Ehrlich
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Judith Aron-Wisnewsky
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France.,Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France
| | - Karine Clément
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France. .,Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France.
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark. .,Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
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10
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Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nat Commun 2020; 11:5881. [PMID: 33208748 PMCID: PMC7676231 DOI: 10.1038/s41467-020-19589-w] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [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: 09/02/2019] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism. Gut microbial metabolism of nutrients contributes to metabolic diseases, and the histidine metabolite imidazole propionate (ImP) is produced by type 2 diabetes (T2D) associated microbiome. Here the authors report that circulating ImP levels are increased in subjects with prediabetes or T2D in three European populations, and this increase associates with altered gut microbiota rather than dietary histidine.
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Affiliation(s)
- Antonio Molinaro
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden.,Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre Bel Lassen
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France.,Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France
| | - Marcus Henricsson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Hao Wu
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Solia Adriouch
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Eugeni Belda
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France.,Integromics Unit, Institute of Cardiometabolism and Nutrition, 75013, Paris, France
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Per-Olof Bergh
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Christine Rouault
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Sébastien André
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Florian Marquet
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Fabrizio Andreelli
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Joe-Elie Salem
- Assistance Publique Hôpitaux de Paris, Clinical Investigation Center Paris East, 75013, Paris, France
| | - Karen Assmann
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France
| | - Jean-Philippe Bastard
- Assistance Publique Hôpitaux de Paris, Biochemistry and Hormonology Department, Tenon Hospital, 75020, Paris, France
| | - Sofia Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany
| | | | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Nicolas Pons
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Edi Prifti
- Integromics Unit, Institute of Cardiometabolism and Nutrition, 75013, Paris, France.,Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, 93143, Bondy, France
| | - Benoit Quinquis
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Hugo Roume
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Helle Krogh Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Christian Lewinter
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Nadja B Sønderskov
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | | | - Lars Køber
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Jean-Daniel Zucker
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, 93143, Bondy, France
| | - Pilar Galan
- Sorbonne Paris Cité Epidemiology and Statistics Research Centre (CRESS), U1153 Inserm, U1125, Inra, Cnam, University of Paris 13, Nutritional Epidemiology Research Team (EREN), 93017, Bobigny, France
| | - Marc-Emmanuel Dumas
- Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.,Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, SW3 6KY, UK
| | - Jeroen Raes
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France.,Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jean-Michel Oppert
- Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France
| | - Ivica Letunic
- Biobyte Solutions GmbH, Bothestr. 142, 69117, Heidelberg, Germany
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41128, Gothenburg, Sweden
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - S Dusko Ehrlich
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Judith Aron-Wisnewsky
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France.,Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France
| | - Karine Clément
- INSERM, Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, Paris, France. .,Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Nutrition department, CRNH Ile de France, Paris, France.
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, 413 45, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark. .,Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
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11
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Plaza Oñate F, Le Chatelier E, Almeida M, Cervino ACL, Gauthier F, Magoulès F, Ehrlich SD, Pichaud M. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. Bioinformatics 2020; 35:1544-1552. [PMID: 30252023 PMCID: PMC6499236 DOI: 10.1093/bioinformatics/bty830] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/29/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022] Open
Abstract
Motivation Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters. Results We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses. Availability and implementation The binary is freely available for non-commercial users at www.enterome.com/downloads. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Florian Plaza Oñate
- Enterome, 94-96 Avenue Ledru Rollin, Paris, France
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
- To whom correspondence should be addressed. E-mail:
| | | | - Mathieu Almeida
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Franck Gauthier
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Frédéric Magoulès
- CentraleSupélec, Université Paris Saclay, 9 rue Joliot Curie, Gif-sur-Yvette, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
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12
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Farin W, Oñate FP, Plassais J, Bonny C, Beglinger C, Woelnerhanssen B, Nocca D, Magoules F, Le Chatelier E, Pons N, Cervino ACL, Ehrlich SD. Impact of laparoscopic Roux-en-Y gastric bypass and sleeve gastrectomy on gut microbiota: a metagenomic comparative analysis. Surg Obes Relat Dis 2020; 16:852-862. [PMID: 32360114 DOI: 10.1016/j.soard.2020.03.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 10/24/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Bariatric surgery is an effective therapeutic procedure for morbidly obese patients. The 2 most common interventions are sleeve gastrectomy (SG) and laparoscopic Roux-en-Y gastric bypass (LRYGB). OBJECTIVES The aim of this study was to compare microbiome long-term microbiome after SG and LRYGB surgery in obese patients. SETTING University Hospital, France; University Hospital, United States; and University Hospital, Switzerland. METHODS Eighty-nine and 108 patients who underwent SG and LRYGB, respectively, were recruited. Stools were collected before and 6 months after surgery. Microbial DNA was analyzed with shotgun metagenomic sequencing (SOLiD 5500 xl Wildfire). MSPminer, a novel innovative tool to characterize new in silico biological entities, was used to identify 715 Metagenomic Species Pan-genome. One hundred forty-eight functional modules were analyzed using GOmixer and KEGG database. RESULTS Both interventions resulted in a similar increase of Shannon's diversity index and gene richness of gut microbiota, in parallel with weight loss, but the changes of microbial composition were different. LRYGB led to higher relative abundance of aero-tolerant bacteria, such as Escherichia coli and buccal species, such as Streptococcus and Veillonella spp. In contrast, anaerobes, such as Clostridium, were more abundant after SG, suggesting better conservation of anaerobic conditions in the gut. Enrichment of Akkermansia muciniphila was also observed after both surgeries. Function-level changes included higher potential for bacterial use of supplements, such as vitamin B12, B1, and iron upon LRYGB. CONCLUSION Microbiota changes after bariatric surgery depend on the nature of the intervention. LRYGB induces greater taxonomic and functional changes in gut microbiota than SG. Possible long-term health consequences of these alterations remain to be established.
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Affiliation(s)
| | - Florian Plaza Oñate
- Data Science, Enterome, Paris, France; Université Paris-Saclay, Jouy en Josas, France
| | | | | | - Christoph Beglinger
- Department of Biomedicine, University of Basel and Department of Research, St. Claraspital, Basel, Switzerland
| | - Bettina Woelnerhanssen
- Department of Biomedicine, University of Basel and Department of Research, St. Claraspital, Basel, Switzerland
| | - David Nocca
- Digestive Surgery, Saint-Eloi University Hospital of Montpellier, Montpellier, France
| | | | | | | | | | - S Dusko Ehrlich
- Université Paris-Saclay, Jouy en Josas, France; Centre for Host Microbiome Interaction, Dental Institute, King's College London, London, United Kingdom
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13
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Cox SR, Lindsay JO, Fromentin S, Stagg AJ, McCarthy NE, Galleron N, Ibraim SB, Roume H, Levenez F, Pons N, Maziers N, Lomer MC, Ehrlich SD, Irving PM, Whelan K. Effects of Low FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial. Gastroenterology 2020; 158:176-188.e7. [PMID: 31586453 DOI: 10.1053/j.gastro.2019.09.024] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS There is limited evidence that a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduces gut symptoms in quiescent inflammatory bowel disease (IBD). We performed a randomized, controlled trial to investigate the effects of a low FODMAP diet on persistent gut symptoms, the intestinal microbiome, and circulating markers of inflammation in patients with quiescent IBD. METHODS We performed a single-blind trial of 52 patients with quiescent Crohn's disease or ulcerative colitis and persistent gut symptoms at 2 large gastroenterology clinics in the United Kingdom. Patients were randomly assigned to groups that followed a diet low in FODMAPs (n = 27) or a control diet (n = 25), with dietary advice, for 4 weeks. Gut symptoms and health-related quality of life were measured using validated questionnaires. Stool and blood samples were collected at baseline and end of trial. We assessed fecal microbiome composition and function using shotgun metagenomic sequencing and phenotypes of T cells in blood using flow cytometry. RESULTS A higher proportion of patients reported adequate relief of gut symptoms following the low FODMAP diet (14/27, 52%) than the control diet (4/25, 16%, P=.007). Patients had a greater reduction in irritable bowel syndrome severity scores following the low FODMAP diet (mean reduction of 67; standard error, 78) than the control diet (mean reduction of 34; standard error, 50), although this difference was not statistically significant (P = .075). Following the low FODMAP diet, patients had higher health-related quality of life scores (81.9 ± 1.2) than patients on the control diet (78.3 ± 1.2, P = .042). A targeted analysis revealed that in stool samples collected at the end of the study period, patients on the low FODMAP diet had significantly lower abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Faecalibacterium prausnitzii than patients on control diet. However, microbiome diversity and markers of inflammation did not differ significantly between groups. CONCLUSIONS In a trial of the low FODMAP diet vs a control diet in patients with quiescent IBD, we found no significant difference after 4 weeks in change in irritable bowel syndrome severity scores, but significant improvements in specific symptom scores and numbers reporting adequate symptom relief. The low FODMAP diet reduced fecal abundance of microbes believed to regulate the immune response, compared with the control diet, but had no significant effect on markers of inflammation. We conclude that a 4-week diet low in FODMAPs is safe and effective for managing persistent gut symptoms in patients with quiescent IBD. www.isrctn.com no.: ISRCTN17061468.
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Affiliation(s)
- Selina R Cox
- Department of Nutritional Sciences, King's College London, London, United Kingdom
| | - James O Lindsay
- Barts Health NHS Trust, Department of Gastroenterology, Royal London Hospital, London, United Kingdom; Blizard Institute, Queen Mary University of London, Centre for Immunobiology, London, United Kingdom
| | - Sébastien Fromentin
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Andrew J Stagg
- Blizard Institute, Queen Mary University of London, Centre for Immunobiology, London, United Kingdom
| | - Neil E McCarthy
- Blizard Institute, Queen Mary University of London, Centre for Immunobiology, London, United Kingdom
| | - Nathalie Galleron
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Samar B Ibraim
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Hugo Roume
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Florence Levenez
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Nicolas Pons
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Nicolas Maziers
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Miranda C Lomer
- Department of Nutritional Sciences, King's College London, London, United Kingdom; Department of Nutrition and Dietetics, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - S Dusko Ehrlich
- Metagénopolis, Institut National de la Recherche Agronomique, Université Paris-Saclay, Paris, France
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College London, London, United Kingdom.
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14
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Fadlallah J, El Kafsi H, Sterlin D, Juste C, Parizot C, Dorgham K, Autaa G, Gouas D, Almeida M, Lepage P, Pons N, Le Chatelier E, Levenez F, Kennedy S, Galleron N, de Barros JPP, Malphettes M, Galicier L, Boutboul D, Mathian A, Miyara M, Oksenhendler E, Amoura Z, Doré J, Fieschi C, Ehrlich SD, Larsen M, Gorochov G. Microbial ecology perturbation in human IgA deficiency. Sci Transl Med 2019; 10:10/439/eaan1217. [PMID: 29720448 DOI: 10.1126/scitranslmed.aan1217] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 12/07/2017] [Accepted: 03/12/2018] [Indexed: 12/14/2022]
Abstract
Paradoxically, loss of immunoglobulin A (IgA), one of the most abundant antibodies, does not irrevocably lead to severe infections in humans but rather is associated with relatively mild respiratory infections, atopy, and autoimmunity. IgA might therefore also play covert roles, not uniquely associated with control of pathogens. We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. Metagenomic analysis highlights an expected pathobiont expansion but a less expected depletion in some typically beneficial symbionts. Gut colonization by species usually present in the oropharynx is also reminiscent of spatial microbiota disorganization. IgM only partially rescues IgA deficiency because not all typical IgA targets are efficiently bound by IgM in the intestinal lumen. Together, IgA appears to play a nonredundant role at the forefront of the immune/microbial interface, away from the intestinal barrier, ranging from pathobiont control and regulation of systemic inflammation to preservation of commensal diversity and community networks.
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Affiliation(s)
- Jehane Fadlallah
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France
| | - Hela El Kafsi
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France
| | - Delphine Sterlin
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, 75013 Paris, France
| | - Catherine Juste
- UMR1319 Micalis, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Christophe Parizot
- Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, 75013 Paris, France
| | - Karim Dorgham
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France
| | - Gaëlle Autaa
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France
| | - Doriane Gouas
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France
| | - Mathieu Almeida
- Center for Bioinformatics and Computational Biology, University of Maryland, Paint Branch Road, College Park, MD 20742, USA
| | - Patricia Lepage
- UMR1319 Micalis, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Nicolas Pons
- INRA, US1367 MetaGenoPolis, 78350 Jouy en Josas, France
| | | | | | - Sean Kennedy
- INRA, US1367 MetaGenoPolis, 78350 Jouy en Josas, France
| | | | - Jean-Paul Pais de Barros
- INSERM, LNC UMR866, University Bourgogne Franche-Comté, F-21000 Dijon, France.,LIPoprotéines et Santé prévention & Traitement des maladies Inflammatoires et du Cancer (LipSTIC) LabEx, Fondation de Coopération Scientifique Bourgogne-Franche Comté, F-21000 Dijon, France
| | - Marion Malphettes
- Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Lionel Galicier
- Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - David Boutboul
- Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.,INSERM U1126, Université Paris Diderot Paris 7, 75010 Paris, France
| | - Alexis Mathian
- Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Service de Médecine Interne 2, Institut E3M, 75013 Paris, France
| | - Makoto Miyara
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, 75013 Paris, France
| | - Eric Oksenhendler
- Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.,Université Paris Diderot Paris 7, EA3518, 75010 Paris, France
| | - Zahir Amoura
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Service de Médecine Interne 2, Institut E3M, 75013 Paris, France
| | - Joel Doré
- UMR1319 Micalis, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France.,INRA, US1367 MetaGenoPolis, 78350 Jouy en Josas, France
| | - Claire Fieschi
- Département d'Immunologie Clinique, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.,INSERM U1126, Université Paris Diderot Paris 7, 75010 Paris, France
| | - S Dusko Ehrlich
- INRA, US1367 MetaGenoPolis, 78350 Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Martin Larsen
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, 75013 Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses-Paris (CIMI-Paris), 75013 Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, 75013 Paris, France
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15
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Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJY, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. Correction: Amendments: Author Correction: A catalog of the mouse gut metagenome. Nat Biotechnol 2019; 37:102. [DOI: 10.1038/nbt0119-102a] [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: 11/09/2022]
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16
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Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol 2018; 4:112-123. [PMID: 30478291 DOI: 10.1038/s41564-018-0292-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/11/2018] [Indexed: 12/21/2022]
Abstract
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens.
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Affiliation(s)
- Etienne Ruppé
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France. .,IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.
| | - Amine Ghozlane
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - Julien Tap
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Danone Nutricia Research, Palaiseau, France
| | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Nicolas Maziers
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | | | - Irene Clares
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Teresa M Coque
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Luis Máiz
- Unit for Cystic Fibrosis, Ramon y Cajal University Hospital, Madrid, Spain
| | - Tiphaine Goulenok
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Victoire de Lastours
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Nawal Amor
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Bruno Fantin
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Ingrid Wieder
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malbert Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xinglin Zhang
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandre G de Brevern
- INSERM UMR_S 1134, Paris Diderot University, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles, INTS, GR-Ex, Paris, France
| | - Jean-Michel Batto
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Hervé M Blottière
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Pierre Léonard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Véronique Léjard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Aline Letur
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Levenez
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Kevin Weiszer
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Haimet
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Joël Doré
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Sean P Kennedy
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Centre of Host Microbiome Interactions, King's College, London, UK
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17
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Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB. A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links. Nat Protoc 2018; 13:2781-2800. [DOI: 10.1038/s41596-018-0064-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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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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19
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Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. Erratum: Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2017; 545:116. [DOI: 10.1038/nature22318] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AMD, de Evgrafov MCR, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O, Sommer MOA, Ehrlich SD, Sicheritz-Pontén T, Brunak S, Nielsen HB. Transcriptional interactions suggest niche segregation among microorganisms in the human gut. Nat Microbiol 2016; 1:16152. [PMID: 27564131 DOI: 10.1038/nmicrobiol.2016.152] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/22/2016] [Indexed: 11/09/2022]
Abstract
The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species1. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species2,3. To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans. In 102 significantly interacting species pairs, the transcriptional changes led to a reduced expression of orthologous functions between the coexisting species. Specific species-species transcriptional interactions were enriched for functions important for H2 and CO2 homeostasis, butyrate biosynthesis, ATP-binding cassette (ABC) transporters, flagella assembly and bacterial chemotaxis, as well as for the metabolism of carbohydrates, amino acids and cofactors. The analysis gives the first insight into the microbial community-wide transcriptional interactions, and suggests that the regulation of gene expression plays an important role in species adaptation to coexistence and that niche segregation takes place at the transcriptional level.
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Affiliation(s)
- Damian Rafal Plichta
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,Clinical-Microbiomics A/S, DK-2200 Copenhagen, Denmark
| | - Agnieszka Sierakowska Juncker
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Marcelo Bertalan
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Elizabeth Rettedal
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Laurent Gautier
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,Department of Systems Biology, DTU Multi-Assay Core, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Encarna Varela
- Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain
| | - Chaysavanh Manichanh
- Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain
| | - Charlène Fouqueray
- INRA, Institut National de la Recherche Agronomique, Metagenopolis, Cedex 78350 Jouy en Josas, France
| | - Florence Levenez
- INRA, Institut National de la Recherche Agronomique, Metagenopolis, Cedex 78350 Jouy en Josas, France.,MGP, MetaGenoPolis, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Joël Doré
- MGP, MetaGenoPolis, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.,MICALIS, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France
| | - Ana Manuel Dantas Machado
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | | | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Faculty of Health Sciences, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Torben Jørgensen
- Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Research Centre for Prevention and Health, Capital region, Glostrup Hospital, DK-2600 Glostrup, Denmark.,Faculty of Medicine, Aalborg University, DK-9220 Aalborg, Denmark
| | - Peer Bork
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Francisco Guarner
- Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - S Dusko Ehrlich
- MGP, MetaGenoPolis, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.,MICALIS, INRA, Université Paris-Saclay, Cedex 78350 Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London SE1 9RT, UK
| | - Thomas Sicheritz-Pontén
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Søren Brunak
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - H Bjørn Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.,Clinical-Microbiomics A/S, DK-2200 Copenhagen, Denmark
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21
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Ruppé E, Le Chatelier E, Pons N, Andremont A, Ehrlich SD. Dissemination of the mcr-1 colistin resistance gene. Lancet Infect Dis 2016; 16:290-1. [PMID: 26973305 DOI: 10.1016/s1473-3099(16)00066-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/25/2016] [Indexed: 11/17/2022]
Affiliation(s)
- Etienne Ruppé
- Genomic Research Laboratory, Geneva University Hospitals, Geneva 1205, Switzerland.
| | | | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy en Josas, France
| | - Antoine Andremont
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France; INSERM, IAME, UMR 1137, F-75018 Paris, France; Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy en Josas, France; Centre of Host Microbiome Interactions, King's college, London, UK
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22
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Ren W, Xun Z, Wang Z, Zhang Q, Liu X, Zheng H, Zhang Q, Zhang Y, Zhang L, Wu C, Zheng S, Qin N, Ehrlich SD, Li Y, He X, Xu T, Chen T, Chen F. Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis. Sci Rep 2016; 6:24481. [PMID: 27080513 PMCID: PMC4832241 DOI: 10.1038/srep24481] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 12/14/2015] [Accepted: 03/30/2016] [Indexed: 12/20/2022] Open
Abstract
Halitosis is a common symptom mainly caused by microbial activities in the oral cavity. Here, we used 16S rRNA gene pyrosequencing and metagenomic sequencing to examine oral microbial compositions and their functional variations in children with halitosis. We found that the tongue coating of subjects with halitosis had greater bacterial richness than those of healthy subjects. The relative abundance and prevalence of Leptotrichia wadei and Peptostreptococcus stomatis were higher in tongue coating samples from children with halitosis than those from children without halitosis; Prevotella shahii had higher relative abundance and prevalence in saliva samples from children with halitosis. We present the first comprehensive evaluation of the co-occurrence networks of saliva and tongue coating communities under healthy and halitosis conditions, and investigated patterns of significant differences between these communities. Moreover, we observed that bacterial genes associated with responses to infectious diseases and terpenoid and polyketide metabolism were enriched in subjects with halitosis, but not in healthy subjects. Hydrogen sulphide (H2S)-related metabolic pathways suggested that there was higher microbial production and less usage of H2S in subjects with halitosis. Thus, the mechanism of halitosis was implied for the first time via metagenomic sequencing.
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Affiliation(s)
- Wen Ren
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Zhe Xun
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Zicheng Wang
- Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Qun Zhang
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Xuenan Liu
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Hui Zheng
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yifei Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | | | - Chunyan Wu
- Realbio Genomics Institute, Shanghai, China
| | - Shuguo Zheng
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Nan Qin
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - 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 Bridge, London, UK
| | - Yihong Li
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, USA
| | - Xuesong He
- School of Dentistry, University of California Los Angeles, Los Angeles, USA
| | - Tao Xu
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Ting Chen
- Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China.,Programs in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, USA
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
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23
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Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2015; 528:262-266. [PMID: 26633628 PMCID: PMC4681099 DOI: 10.1038/nature15766] [Citation(s) in RCA: 1332] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 10/05/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Kristoffer Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gwen Falony
- Center for the Biology of Disease, VIB, Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Emmanuelle Le Chatelier
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Edi Prifti
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Sara Vieira-Silva
- Center for the Biology of Disease, VIB, Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Valborg Gudmundsdottir
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helle K Pedersen
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Anita Yvonne Voigt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit , University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajna Hercog
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Paul Igor Costea
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jens Roat Kultima
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | - Florence Levenez
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Joël Dore
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - H Bjørn Nielsen
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeroen Raes
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Jun Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, China.,Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China.,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong
| | - S Dusko Ehrlich
- MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France.,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, United Kingdom
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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24
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Qin N, Zheng B, Yao J, Guo L, Zuo J, Wu L, Zhou J, Liu L, Guo J, Ni S, Li A, Zhu Y, Liang W, Xiao Y, Ehrlich SD, Li L. Influence of H7N9 virus infection and associated treatment on human gut microbiota. Sci Rep 2015; 5:14771. [PMID: 26490635 PMCID: PMC4614822 DOI: 10.1038/srep14771] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022] Open
Abstract
Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut.
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Affiliation(s)
- Nan Qin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Jian Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Lihua Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Jian Zuo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Lingjiao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Jiawei Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Lin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Jing Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Shujun Ni
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Ang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Yixin Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Weifeng Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, 78350, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
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25
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Affiliation(s)
- Nan Qin
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | | | - Jing Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou,
| | - Edi Prifti
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas,
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, .,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK
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26
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Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJY, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. A catalog of the mouse gut metagenome. Nat Biotechnol 2015; 33:1103-8. [PMID: 26414350 DOI: 10.1038/nbt.3353] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/20/2015] [Indexed: 12/28/2022]
Abstract
We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.
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Affiliation(s)
- Liang Xiao
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Qiang Feng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Suisha Liang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Si Brask Sonne
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhongkui Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Xinmin Qiu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Xiaoping Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Hua Long
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Jianfeng Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Dongya Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Chuan Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhiwei Fang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Joyce Chou
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Jacob Glanville
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Qin Hao
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dorota Kotowska
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Colding
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Donghai Wu
- Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Jao Yiu Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiaoyi Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Junhua Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Huijue Jia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhou Lan
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Piotr Dworzynski
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - H Bjørn Nielsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Joël Doré
- Institut National de la Recherche Agronomique (Microbiologie de l'Alimentation au Service de la Santé), Jouy en Josas, France.,Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France
| | | | - S Dusko Ehrlich
- Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, UK
| | - John C Lin
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Manimozhiyan Arumugam
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jun Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China
| | - Lise Madsen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Karsten Kristiansen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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27
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Brahe LK, Le Chatelier E, Prifti E, Pons N, Kennedy S, Hansen T, Pedersen O, Astrup A, Ehrlich SD, Larsen LH. Specific gut microbiota features and metabolic markers in postmenopausal women with obesity. Nutr Diabetes 2015; 5:e159. [PMID: 26075636 PMCID: PMC4491860 DOI: 10.1038/nutd.2015.9] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 03/27/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut microbial gene richness and specific bacterial species are associated with metabolic risk markers in humans, but the impact of host physiology and dietary habits on the link between the gut microbiota and metabolic markers remain unclear. The objective of this study was to identify gut metagenomic markers associated with estimates of insulin resistance, lipid metabolism and inflammation in obesity, and to explore whether the associations between metagenomic and metabolic markers persisted after adjustment for body fat, age and habitual dietary intake. METHODS Faecal DNA from 53 women with obesity was analysed through quantitative metagenomic sequencing and analysis, and a systematic search was performed for bacterial genes associated with estimates of insulin resistance, inflammation and lipid metabolism. Subsequently, the correlations between metagenomic species and metabolic markers were tested by linear regression models, with and without covariate adjustment. RESULTS One hundred and fourteen metagenomic species correlated with metabolic markers (P<0.001) including Akkermansia muciniphila, Bilophila wadsworthia, Bifidobacterium longum and Faecalibacterium prausnitzii, but also species not previously associated with metabolic markers including Bacteroides faecis and Dorea longicatena. The majority of the identified correlations between bacterial species and metabolic markers persisted after adjustment for differences in body fat, age and dietary macronutrient composition; however, the negative correlation with insulin resistance observed for B. longum and F. prausnitzii appeared to be modified by the intake of dietary fibre and fat, respectively. CONCLUSIONS This study shows that several gut bacterial species are linked to metabolic risk markers in obesity, also after adjustment for potential confounders, such as long-term diet composition. The study supports the use of gut metagenomic markers for metabolic disease prediction and warrants further investigation of causality.
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Affiliation(s)
- L K Brahe
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - E Le Chatelier
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - E Prifti
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - N Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - S Kennedy
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - T Hansen
- Novo Nordisk Foundation Centre for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - O Pedersen
- Novo Nordisk Foundation Centre for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - A Astrup
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - S D Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - L H Larsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
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28
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Sirota M, Willemsen G, Sundar P, Pitts SJ, Potluri S, Prifti E, Kennedy S, Ehrlich SD, Neuteboom J, Kluft C, Malone KE, Cox DR, de Geus EJC, Boomsma DI. Effect of genome and environment on metabolic and inflammatory profiles. PLoS One 2015; 10:e0120898. [PMID: 25853885 PMCID: PMC4390246 DOI: 10.1371/journal.pone.0120898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022] Open
Abstract
Twin and family studies have established the contribution of genetic factors to variation in metabolic, hematologic and immunological parameters. The majority of these studies analyzed single or combined traits into pre-defined syndromes. In the present study, we explore an alternative multivariate approach in which a broad range of metabolic, hematologic, and immunological traits are analyzed simultaneously to determine the resemblance of monozygotic (MZ) twin pairs, twin-spouse pairs and unrelated, non-cohabiting individuals. A total of 517 participants from the Netherlands Twin Register, including 210 MZ twin pairs and 64 twin-spouse pairs, took part in the study. Data were collected on body composition, blood pressure, heart rate, and multiple biomarkers assessed in fasting blood samples, including lipid levels, glucose, insulin, liver enzymes, hematological measurements and cytokine levels. For all 51 measured traits, pair-wise Pearson correlations, correcting for family relatedness, were calculated across all the individuals in the cohort. Hierarchical clustering techniques were applied to group the measured traits into sub-clusters based on similarity. Sub-clusters were observed among metabolic traits and among inflammatory markers. We defined a phenotypic profile as the collection of all the traits measured for a given individual. Average within-pair similarity of phenotypic profiles was determined for the groups of MZ twin pairs, spouse pairs and pairs of unrelated individuals. The average similarity across the full phenotypic profile was higher for MZ twin pairs than for spouse pairs, and lowest for pairs of unrelated individuals. Cohabiting MZ twins were more similar in their phenotypic profile compared to MZ twins who no longer lived together. The correspondence in the phenotypic profile is therefore determined to a large degree by familial, mostly genetic, factors, while household factors contribute to a lesser degree to profile similarity.
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Affiliation(s)
- Marina Sirota
- Rinat-Pfizer, South San Francisco, California, United States of America
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Purnima Sundar
- Rinat-Pfizer, South San Francisco, California, United States of America
| | - Steven J. Pitts
- Rinat-Pfizer, South San Francisco, California, United States of America
| | - Shobha Potluri
- Rinat-Pfizer, South San Francisco, California, United States of America
| | - Edi Prifti
- INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy-en-Josas, France
| | - Sean Kennedy
- INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy-en-Josas, France
| | - S. Dusko Ehrlich
- INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy-en-Josas, France
| | | | | | | | - David R. Cox
- Rinat-Pfizer, South San Francisco, California, United States of America
| | - Eco J. C. de Geus
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, Netherlands
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Plaza Onate F, Batto JM, Juste C, Fadlallah J, Fougeroux C, Gouas D, Pons N, Kennedy S, Levenez F, Dore J, Ehrlich SD, Gorochov G, Larsen M. Quality control of microbiota metagenomics by k-mer analysis. BMC Genomics 2015; 16:183. [PMID: 25887914 PMCID: PMC4373121 DOI: 10.1186/s12864-015-1406-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 06/20/2014] [Accepted: 02/26/2015] [Indexed: 01/04/2023] Open
Abstract
Background The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case–control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue. Results We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from “empty” ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets. Conclusions We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Plaza Onate
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France.
| | | | - Catherine Juste
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. .,UMR1319 Micalis, INRA, Jouy-en-Josas, France.
| | - Jehane Fadlallah
- Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. .,Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France.
| | - Cyrielle Fougeroux
- Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France.
| | - Doriane Gouas
- Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. .,Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France.
| | - Nicolas Pons
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France.
| | - Sean Kennedy
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France.
| | - Florence Levenez
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. .,UMR1319 Micalis, INRA, Jouy-en-Josas, France.
| | - Joel Dore
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. .,UMR1319 Micalis, INRA, Jouy-en-Josas, France.
| | - S Dusko Ehrlich
- INRA, Institut National de la Recherche Agronomique, US1367 MetaGenoPolis, 78350, Jouy en Josas, France. .,UMR1319 Micalis, INRA, Jouy-en-Josas, France.
| | - Guy Gorochov
- Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. .,Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. .,Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France.
| | - Martin Larsen
- Sorbonne Universités, UPMC Univ Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Hôpital Pitié-Salpêtrière, 83 bd. de l'Hôpital, 75013, Paris, France. .,Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié-Salpêtrière, F-75013, Paris, France. .,Inserm UMR-S1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France.
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30
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Juste C, Kreil DP, Beauvallet C, Guillot A, Vaca S, Carapito C, Mondot S, Sykacek P, Sokol H, Blon F, Lepercq P, Levenez F, Valot B, Carré W, Loux V, Pons N, David O, Schaeffer B, Lepage P, Martin P, Monnet V, Seksik P, Beaugerie L, Ehrlich SD, Gibrat JF, Van Dorsselaer A, Doré J. Bacterial protein signals are associated with Crohn's disease. Gut 2014; 63:1566-77. [PMID: 24436141 PMCID: PMC4173658 DOI: 10.1136/gutjnl-2012-303786] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls. DESIGN We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. RESULTS Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. CONCLUSIONS This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis.
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Affiliation(s)
| | - David P Kreil
- Chair of Bioinformatics, Boku University Vienna, Vienna, Austria,Department of Life Sciences, University of Warwick, Warwickshire, UK
| | | | - Alain Guillot
- Plate-forme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA, Gif-sur-Yvette, France
| | - Sebastian Vaca
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | | | - Peter Sykacek
- Chair of Bioinformatics, Boku University Vienna, Vienna, Austria
| | - Harry Sokol
- UMR1319 Micalis, INRA, Jouy-en-Josas, France,Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France
| | | | | | | | - Benoît Valot
- Plate-forme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA, Gif-sur-Yvette, France
| | - Wilfrid Carré
- UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France
| | - Valentin Loux
- UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France
| | | | - Olivier David
- UR341, Mathématiques et Informatique Appliquées (MIA), INRA, Jouy-en-Josas, France
| | - Brigitte Schaeffer
- UR341, Mathématiques et Informatique Appliquées (MIA), INRA, Jouy-en-Josas, France
| | | | - Patrice Martin
- UMR1313 GABI, Iso Cell Express (ICE), INRA, Jouy-en-Josas, France
| | | | - Philippe Seksik
- Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France
| | - Laurent Beaugerie
- Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France
| | | | | | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | - Joël Doré
- UMR1319 Micalis, INRA, Jouy-en-Josas, France
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31
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Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, Le Chatelier E, Yao J, Wu L, Zhou J, Ni S, Liu L, Pons N, Batto JM, Kennedy SP, Leonard P, Yuan C, Ding W, Chen Y, Hu X, Zheng B, Qian G, Xu W, Ehrlich SD, Zheng S, Li L. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014; 513:59-64. [PMID: 25079328 DOI: 10.1038/nature13568] [Citation(s) in RCA: 1330] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/09/2014] [Indexed: 02/07/2023]
Abstract
Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.
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Affiliation(s)
- Nan Qin
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]
| | - Fengling Yang
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]
| | - Ang Li
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]
| | - Edi Prifti
- 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2]
| | - Yanfei Chen
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]
| | - Li Shao
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]
| | - Jing Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | | | - Jian Yao
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Lingjiao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Jiawei Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Shujun Ni
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Lin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Jean Michel Batto
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Sean P Kennedy
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Pierre Leonard
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Chunhui Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Wenchao Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Yuanting Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Xinjun Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Beiwen Zheng
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Guirong Qian
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Wei Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - S Dusko Ehrlich
- 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | - Shusen Zheng
- 1] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China
| | - Lanjuan Li
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Consortium M, Weissenbach J, Ehrlich SD, Bork P. Addendum: Enterotypes of the human gut microbiome. Nature 2014. [DOI: 10.1038/nature13075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 2013; 10:1196-9. [PMID: 24141494 DOI: 10.1038/nmeth.2693] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/24/2013] [Indexed: 12/11/2022]
Abstract
To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.
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Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, Bork P, Wang J, Ehrlich SD, Pedersen O. Richness of human gut microbiome correlates with metabolic markers. Nature 2013; 500:541-6. [DOI: 10.1038/nature12506] [Citation(s) in RCA: 2791] [Impact Index Per Article: 253.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/26/2013] [Indexed: 02/07/2023]
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35
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Blottière HM, de Vos WM, Ehrlich SD, Doré J. Human intestinal metagenomics: state of the art and future. Curr Opin Microbiol 2013; 16:232-9. [DOI: 10.1016/j.mib.2013.06.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 06/14/2013] [Accepted: 06/24/2013] [Indexed: 12/12/2022]
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36
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Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P. Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res 2012; 41:687-99. [PMID: 23109554 PMCID: PMC3592452 DOI: 10.1093/nar/gks963] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [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] [Indexed: 12/02/2022] Open
Abstract
The nonessential regions in bacterial chromosomes are ill-defined due to incomplete functional information. Here, we establish a comprehensive repertoire of the genome regions that are dispensable for growth of Bacillus subtilis in a variety of media conditions. In complex medium, we attempted deletion of 157 individual regions ranging in size from 2 to 159 kb. A total of 146 deletions were successful in complex medium, whereas the remaining regions were subdivided to identify new essential genes (4) and coessential gene sets (7). Overall, our repertoire covers ∼76% of the genome. We screened for viability of mutant strains in rich defined medium and glucose minimal media. Experimental observations were compared with predictions by the iBsu1103 model, revealing discrepancies that led to numerous model changes, including the large-scale application of model reconciliation techniques. We ultimately produced the iBsu1103V2 model and generated predictions of metabolites that could restore the growth of unviable strains. These predictions were experimentally tested and demonstrated to be correct for 27 strains, validating the refinements made to the model. The iBsu1103V2 model has improved considerably at predicting loss of viability, and many insights gained from the model revisions have been integrated into the Model SEED to improve reconstruction of other microbial models.
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Affiliation(s)
- Kosei Tanaka
- INRA, UMR 1319 Micalis, AgroParisTech, UMR Micalis, Jouy-en-Josas F-78350, France
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, JunWang, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Consortium M, Weissenbach J, Ehrlich SD, Bork P. Erratum: Enterotypes of the human gut microbiome. Nature 2011. [DOI: 10.1038/nature10187] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature 2011; 473:174-80. [PMID: 21508958 DOI: 10.1038/nature09944] [Citation(s) in RCA: 4470] [Impact Index Per Article: 343.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 12/18/2010] [Indexed: 02/06/2023]
Abstract
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature 2011. [DOI: 78495111110.1038/nature09944' target='_blank'>'"<>78495111110.1038/nature09944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [78495111110.1038/nature09944','', 'S Dusko Ehrlich')">Reference Citation Analysis] [78495111110.1038/nature09944', 39)">What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
78495111110.1038/nature09944" />
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Abstract
A major challenge in the human metagenomics field is to identify associations of the bacterial genes and human phenotypes and act to modulate microbial populations in order to improve human health and wellbeing. MetaHIT project addresses this ambitious challenge by developing and integrating a number of necessary approaches within the context of the gut microbiome. Among the first results is the establishment of a broad catalog of the human gut microbial genes, which was achieved by an original application of the new generation sequencing technology. The catalog contains 3.3 million non-redundant genes, 150-fold more than the human genome equivalent and includes a large majority of the gut metagenomic sequences determined across three continents, Europe, America and Asia. Its content corresponds to some 1000 bacterial species, which likely represent a large fraction of species associated with humankind intestinal tract. The catalog enables development of the gene profiling approaches aiming to detect associations of bacterial genes and phenotypes. These should lead to the speedy development of diagnostic and prognostic tools and open avenues to reasoned approaches to the modulation of the individual's microbiota in order to optimize health and well-being.
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Affiliation(s)
- S Dusko Ehrlich
- Institut National de la Recherche Agronomique, MetaHIT coordinator, Microbiology and the Food Chain Division, Jouy-en-Josas, France.
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Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefèvre F, Doré J, Blottière HM. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLoS One 2010; 5. [PMID: 20927194 PMCID: PMC2948039 DOI: 10.1371/journal.pone.0013092] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [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: 01/15/2010] [Accepted: 09/09/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND/AIM The human intestinal microbiota plays an important role in modulation of mucosal immune responses. To study interactions between intestinal epithelial cells (IECs) and commensal bacteria, a functional metagenomic approach was developed. One interest of metagenomics is to provide access to genomes of uncultured microbes. We aimed at identifying bacterial genes involved in regulation of NF-κB signaling in IECs. A high throughput cell-based screening assay allowing rapid detection of NF-κB modulation in IECs was established using the reporter-gene strategy to screen metagenomic libraries issued from the human intestinal microbiota. METHODS A plasmid containing the secreted alkaline phosphatase (SEAP) gene under the control of NF-κB binding elements was stably transfected in HT-29 cells. The reporter clone HT-29/kb-seap-25 was selected and characterized. Then, a first screening of a metagenomic library from Crohn's disease patients was performed to identify NF-κB modulating clones. Furthermore, genes potentially involved in the effect of one stimulatory metagenomic clone were determined by sequence analysis associated to mutagenesis by transposition. RESULTS The two proinflammatory cytokines, TNF-α and IL-1β, were able to activate the reporter system, translating the activation of the NF-κB signaling pathway and NF-κB inhibitors, BAY 11-7082, caffeic acid phenethyl ester and MG132 were efficient. A screening of 2640 metagenomic clones led to the identification of 171 modulating clones. Among them, one stimulatory metagenomic clone, 52B7, was further characterized. Sequence analysis revealed that its metagenomic DNA insert might belong to a new Bacteroides strain and we identified 2 loci encoding an ABC transport system and a putative lipoprotein potentially involved in 52B7 effect on NF-κB. CONCLUSIONS We have established a robust high throughput screening assay for metagenomic libraries derived from the human intestinal microbiota to study bacteria-driven NF-κB regulation. This opens a strategic path toward the identification of bacterial strains and molecular patterns presenting a potential therapeutic interest.
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Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59-65. [PMID: 20203603 DOI: 10.1038/nature08821] [Citation(s) in RCA: 7128] [Impact Index Per Article: 509.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 12/23/2009] [Indexed: 11/09/2022]
Abstract
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
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Affiliation(s)
- S Dusko Ehrlich
- S. Dusko Ehrlich is the MetaHIT coordinator at the Institut National de la Recherche Agronomique (INRA), Unité de Génétique Microbienne, 78350 Jouy en Josas, France.
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Bidnenko E, Chopin A, Ehrlich SD, Chopin MC. Activation of mRNA translation by phage protein and low temperature: the case of Lactococcus lactis abortive infection system AbiD1. BMC Mol Biol 2009; 10:4. [PMID: 19173723 PMCID: PMC2661086 DOI: 10.1186/1471-2199-10-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [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: 04/20/2008] [Accepted: 01/27/2009] [Indexed: 01/09/2024] Open
Abstract
Background Abortive infection (Abi) mechanisms comprise numerous strategies developed by bacteria to avoid being killed by bacteriophage (phage). Escherichia coli Abis are considered as mediators of programmed cell death, which is induced by infecting phage. Abis were also proposed to be stress response elements, but no environmental activation signals have yet been identified. Abis are widespread in Lactococcus lactis, but regulation of their expression remains an open question. We previously showed that development of AbiD1 abortive infection against phage bIL66 depends on orf1, which is expressed in mid-infection. However, molecular basis for this activation remains unclear. Results In non-infected AbiD1+ cells, specific abiD1 mRNA is unstable and present in low amounts. It does not increase during abortive infection of sensitive phage. Protein synthesis directed by the abiD1 translation initiation region is also inefficient. The presence of the phage orf1 gene, but not its mutant AbiD1R allele, strongly increases abiD1 translation efficiency. Interestingly, cell growth at low temperature also activates translation of abiD1 mRNA and consequently the AbiD1 phenotype, and occurs independently of phage infection. There is no synergism between the two abiD1 inducers. Purified Orf1 protein binds mRNAs containing a secondary structure motif, identified within the translation initiation regions of abiD1, the mid-infection phage bIL66 M-operon, and the L. lactis osmC gene. Conclusion Expression of the abiD1 gene and consequently AbiD1 phenotype is specifically translationally activated by the phage Orf1 protein. The loss of ability to activate translation of abiD1 mRNA determines the molecular basis for phage resistance to AbiD1. We show for the first time that temperature downshift also activates abortive infection by activation of abiD1 mRNA translation.
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Affiliation(s)
- Elena Bidnenko
- Laboratoire de Génétique Microbienne, INRA, 78352 Jouy-en-Josas, France.
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Domingues S, McGovern S, Plochocka D, Santos MA, Ehrlich SD, Polard P, Chopin MC. The lactococcal abortive infection protein AbiP is membrane-anchored and binds nucleic acids. Virology 2008; 373:14-24. [DOI: 10.1016/j.virol.2007.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 10/19/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022]
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Lecointe F, Sérèna C, Velten M, Costes A, McGovern S, Meile JC, Errington J, Ehrlich SD, Noirot P, Polard P. Anticipating chromosomal replication fork arrest: SSB targets repair DNA helicases to active forks. EMBO J 2007; 26:4239-51. [PMID: 17853894 PMCID: PMC2230842 DOI: 10.1038/sj.emboj.7601848] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 08/10/2007] [Indexed: 11/08/2022] Open
Abstract
In bacteria, several salvage responses to DNA replication arrest culminate in reassembly of the replisome on inactivated forks to resume replication. The PriA DNA helicase is a prominent trigger of this replication restart process, preceded in many cases by a repair and/or remodeling of the arrested fork, which can be performed by many specific proteins. The mechanisms that target these rescue effectors to damaged forks in the cell are unknown. We report that the single-stranded DNA binding (SSB) protein is the key factor that links PriA to active chromosomal replication forks in vivo. This targeting mechanism determines the efficiency by which PriA reaches its specific DNA-binding site in vitro and directs replication restart in vivo. The RecG and RecQ DNA helicases, which are involved in intricate replication reactivation pathways, also associate with the chromosomal replication forks by similarly interacting with SSB. These results identify SSB as a platform for linking a 'repair toolbox' with active replication forks, providing a first line of rescue responses to accidental arrest.
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Affiliation(s)
- François Lecointe
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Céline Sérèna
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Marion Velten
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Audrey Costes
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Stephen McGovern
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Jean-Christophe Meile
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jeffrey Errington
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - S Dusko Ehrlich
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Philippe Noirot
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
| | - Patrice Polard
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, Jouy en Josas, France
- Unité de Génétique Microbienne, Laboratoire de Genetique Microbienne, INRA, Domaine de Vilvert, bat 440, Jouy en Josas 78352, France. Tel.: +33 1 34 65 25 13; Fax: +33 1 34 65 25 21; E-mail:
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Nicolas P, Bessières P, Ehrlich SD, Maguin E, van de Guchte M. Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract. BMC Evol Biol 2007; 7:141. [PMID: 17708761 PMCID: PMC1994166 DOI: 10.1186/1471-2148-7-141] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 08/20/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii) and yogurt (Lactobacillus delbrueckii ssp. bulgaricus), is ambiguous due to contradictory phenotypical and 16S rRNA based classifications. RESULTS Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract. CONCLUSION This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive horizontal gene transfer. The data give a first indication of the large extent of gene transfer that may take place in the gastrointestinal tract and its accumulated effect. For future studies, our results should encourage a careful weighing of data on phylogenetic tree topology, confidence and distribution to conclude on the absence or presence and extent of horizontal gene transfer.
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Affiliation(s)
- Pierre Nicolas
- INRA, Mathématique Informatique et Génome, UR1077, 78350 Jouy en Josas, France
| | - Philippe Bessières
- INRA, Mathématique Informatique et Génome, UR1077, 78350 Jouy en Josas, France
| | - S Dusko Ehrlich
- INRA, Génétique Microbienne, UR895, 78350 Jouy en Josas, France
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Chopin A, Deveau H, Ehrlich SD, Moineau S, Chopin MC. KSY1, a lactococcal phage with a T7-like transcription. Virology 2007; 365:1-9. [PMID: 17467024 DOI: 10.1016/j.virol.2007.03.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 03/12/2007] [Accepted: 03/23/2007] [Indexed: 11/20/2022]
Abstract
The virulent lactococcal phage KSY1 possesses a large elongated capsid (223 nm long, 45 nm wide) and a short tail (32 nm). This phage of the Podoviridae group (C3 morphotype) has a linear 79,232-bp double-stranded DNA genome, which encodes 131 putative proteins and 3 tRNAs. This is the first description of the genome of a phage of this morphotype. KSY1 possesses a T7-like transcription system, including an RNA polymerase and a series of specific promoters, showing sequence homology to other known T7-like RNA polymerase promoters. Late stages of KSY1 multiplication are resistant to rifampicin. Otherwise, KSY1 shares limited similarity with other Podoviridae phages. Fourteen KSY1 structural proteins were identified by SDS-PAGE analysis. Among these proteins, those forming the distal tail structure and likely involved in host recognition are encoded by a 5-kb genomic region of KSY1. This region consists of a mosaic of DNA segments highly homologous to DNA of other lactococcal phages, suggesting an horizontal gene transfer.
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Affiliation(s)
- Alain Chopin
- Laboratoire de Génétique Microbienne, INRA, 78352 Jouy-en-Josas, France.
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Jannière L, Canceill D, Suski C, Kanga S, Dalmais B, Lestini R, Monnier AF, Chapuis J, Bolotin A, Titok M, Le Chatelier E, Ehrlich SD. Genetic evidence for a link between glycolysis and DNA replication. PLoS One 2007; 2:e447. [PMID: 17505547 PMCID: PMC1866360 DOI: 10.1371/journal.pone.0000447] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 04/23/2007] [Indexed: 12/02/2022] Open
Abstract
Background A challenging goal in biology is to understand how the principal cellular functions are integrated so that cells achieve viability and optimal fitness in a wide range of nutritional conditions. Methodology/Principal Findings We report here a tight link between glycolysis and DNA synthesis. The link, discovered during an analysis of suppressors of thermosensitive replication mutants in bacterium Bacillus subtilis, is very strong as some metabolic alterations fully restore viability to replication mutants in which a lethal arrest of DNA synthesis otherwise occurs at a high, restrictive, temperature. Full restoration of viability by such alterations was limited to cells with mutations in three elongation factors (the lagging strand DnaE polymerase, the primase and the helicase) out of a large set of thermosensitive mutants affected in most of the replication proteins. Restoration of viability resulted, at least in part, from maintenance of replication protein activity at high temperature. Physiological studies suggested that this restoration depended on the activity of the three-carbon part of the glycolysis/gluconeogenesis pathway and occurred in both glycolytic and gluconeogenic regimens. Restoration took place abruptly over a narrow range of expression of genes in the three-carbon part of glycolysis. However, the absolute value of this range varied greatly with the allele in question. Finally, restoration of cell viability did not appear to be the result of a decrease in growth rate or an induction of major stress responses. Conclusions/Significance Our findings provide the first evidence for a genetic system that connects DNA chain elongation to glycolysis. Its role may be to modulate some aspect of DNA synthesis in response to the energy provided by the environment and the underlying mechanism is discussed. It is proposed that related systems are ubiquitous.
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Affiliation(s)
- Laurent Jannière
- Laboratoire de Génétique Microbienne, INRA, Jouy en Josas, France.
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Lapidus A, Goltsman E, Auger S, Galleron N, Ségurens B, Dossat C, Land ML, Broussolle V, Brillard J, Guinebretiere MH, Sanchis V, Nguen-The C, Lereclus D, Richardson P, Wincker P, Weissenbach J, Ehrlich SD, Sorokin A. Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem Biol Interact 2007; 171:236-49. [PMID: 17434157 DOI: 10.1016/j.cbi.2007.03.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 02/20/2007] [Accepted: 03/02/2007] [Indexed: 10/23/2022]
Abstract
The Bacillus cereus group represents sporulating soil bacteria containing pathogenic strains which may cause diarrheic or emetic food poisoning outbreaks. Multiple locus sequence typing revealed a presence in natural samples of these bacteria of about 30 clonal complexes. Application of genomic methods to this group was however biased due to the major interest for representatives closely related to Bacillus anthracis. Albeit the most important food-borne pathogens were not yet defined, existing data indicate that they are scattered all over the phylogenetic tree. The preliminary analysis of the sequences of three genomes discussed in this paper narrows down the gaps in our knowledge of the B. cereus group. The strain NVH391-98 is a rare but particularly severe food-borne pathogen. Sequencing revealed that the strain should be a representative of a novel bacterial species, for which the name Bacillus cytotoxis or Bacillus cytotoxicus is proposed. This strain has a reduced genome size compared to other B. cereus group strains. Genome analysis revealed absence of sigma B factor and the presence of genes encoding diarrheic Nhe toxin, not detected earlier. The strain B. cereus F837/76 represents a clonal complex close to that of B. anthracis. Including F837/76, three such B. cereus strains had been sequenced. Alignment of genomes suggests that B. anthracis is their common ancestor. Since such strains often emerge from clinical cases, they merit a special attention. The third strain, KBAB4, is a typical facultative psychrophile generally found in soil. Phylogenic studies show that in nature it is the most active group in terms of gene exchange. Genomic sequence revealed high presence of extra-chromosomal genetic material (about 530kb) that may account for this phenomenon. Genes coding Nhe-like toxin were found on a big plasmid in this strain. This may indicate a potential mechanism of toxicity spread from the psychrophile strain community. The results of this genomic work and ecological compartments of different strains incite to consider a necessity of creating prophylactic vaccines against bacteria closely related to NVH391-98 and F837/76. Presumably developing of such vaccines can be based on the properties of non-pathogenic strains such as KBAB4 or ATCC14579 reported here or earlier. By comparing the protein coding genes of strains being sequenced in this project to others we estimate the shared proteome, or core genome, in the B. cereus group to be 3000+/-200 genes and the total proteome, or pan-genome, to be 20-25,000 genes.
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Affiliation(s)
- Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA, USA
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