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Abstract
With evidence emerging that the microbiome has a role in the onset of many human diseases, including cancer, analyzing these microbial communities and their proteins (i.e., the metaproteome) has become a powerful research tool. The Trans-Proteomic Pipeline (TPP) is a free, comprehensive software suite that facilitates the analysis of mass spectrometry (MS) data. By utilizing available microbial proteomes, TPP can identify microbial proteins and species, with an acceptable peptide false-discovery rate (FDR). An application to a publicly available oral cancer dataset is presented as an example to identify the viral metaproteome on the oral cancer invasive tumor front. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Collection of data and resources Basic Protocol 2: Analysis of MS data using TPP Basic Protocol 3: Analysis of TPP output using R in RStudio.
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Affiliation(s)
- Steven He
- Applied Biosciences, Macquarie University, Sydney, NSW, Australia
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2
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Mazzantini D, Calvigioni M, Celandroni F, Lupetti A, Ghelardi E. Spotlight on the Compositional Quality of Probiotic Formulations Marketed Worldwide. Front Microbiol 2021; 12:693973. [PMID: 34354690 PMCID: PMC8329331 DOI: 10.3389/fmicb.2021.693973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
On the worldwide market, a great number of probiotic formulations are available to consumers as drugs, dietary supplements, and functional foods. For exerting their beneficial effects on host health, these preparations should contain a sufficient amount of the indicated living microbes and be pathogen-free to be safe. Therefore, the contained microbial species and their amount until product expiry are required to be accurately reported on the labels. While commercial formulations licensed as drugs are subjected to rigorous quality controls, less stringent regulations are generally applied to preparations categorized as dietary supplements and functional foods. Many reports indicated that the content of several probiotic formulations does not always correspond to the label claims in terms of microbial identification, number of living organisms, and purity, highlighting the requirement for more stringent quality controls by manufacturers. The main focus of this review is to provide an in-depth overview of the microbiological quality of probiotic formulations commercialized worldwide. Many incongruences in the compositional quality of some probiotic formulations available on the worldwide market were highlighted. Even if manufacturers carry at least some of the responsibility for these inconsistencies, studies that analyze probiotic products should be conducted following recommended and up-to-date methodologies.
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Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marco Calvigioni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.,Research Center Nutraceuticals and Food for Health-Nutrafood, University of Pisa, Pisa, Italy
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3
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Li F, Wang S, He Q, Zhang W, Guo D, Zhang Y, Hai W, Sun Y, Dong H, Hou W. Minerals Determined a Special Ecological Niche and Selectively Enriched Microbial Species from Bulk Water Communities in Hot Springs. Microorganisms 2021; 9:1020. [PMID: 34068582 DOI: 10.3390/microorganisms9051020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Minerals provide physical niches and supply nutrients or serve as electron donors/acceptors for microorganism survival and growth, and thus minerals and microbes co-evolved. Yet, little is known about how sediment minerals impact microbial community assembly in hot springs and to what extent mineralogical composition influences microbial community composition and diversity. Here the influences of minerals on thermophiles in Tengchong hot springs were revealed by network analysis of field samples, as well as in-situ microcosm experiments with minerals. A molecular ecological network was constructed based on high throughput sequencing data of 16S rRNA gene, with a combination of water geochemistry and sedimentary mineralogical compositions. Six modules were identified and this highly modular network structure represents the microbial preference to different abiotic factors, consequently resulting in niche partitioning in sedimentary communities in hot springs. Diverse mineralogical compositions generated special niches for microbial species. Subsequently, the in-situ microcosm experiments with four minerals (aragonite, albite, K-feldspar, and quartz) and spring water were conducted in a silicate-hosted alkaline spring (i.e., Gmq) and a carbonate-hosted neutral hot spring (i.e., Gxs) for 70 days. Different microbial preferences were observed among different mineral types (carbonate versus silicate). Aragonite microcosms in Gmq spring enriched archaeal genera Sulfophobococcus and Aeropyrum within the order Desulfurococcales by comparison with both in-situ water and silicate microcosms. Sulfophobococcus was also accumulated in Gxs aragonite microcosms, but the contribution to overall dissimilarity is much lower than that in Gmq spring. Besides, Caldimicrobium was a bacterial genus enriched in Gxs aragonite microcosms, in contrast to in-situ water and silicate microcosms, whereas Candidatus Kryptobacter and Thermus were more abundant in silicate microcosms. The differences in microbial accumulations among different mineral types in the same spring implied that mineral chemistry may exert extra deterministic selective pressure in drawing certain species from the bulk water communities, in addition to stochastic absorption on mineral surface. Taken together, our results highlight the special niche partitioning determined by mineralogical compositions and further confirm that minerals could be used as “fishing bait” to enrich certain rare microbial species.
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Kõljalg U, Nilsson HR, Schigel D, Tedersoo L, Larsson KH, May TW, Taylor AFS, Jeppesen TS, Frøslev TG, Lindahl BD, Põldmaa K, Saar I, Suija A, Savchenko A, Yatsiuk I, Adojaan K, Ivanov F, Piirmann T, Pöhönen R, Zirk A, Abarenkov K. The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa. Microorganisms 2020; 8:E1910. [PMID: 33266327 PMCID: PMC7760934 DOI: 10.3390/microorganisms8121910] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022] Open
Abstract
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
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Affiliation(s)
- Urmas Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Henrik R. Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Dmitry Schigel
- Global Biodiversity Information Facility, 2100 Copenhagen, Denmark; (D.S.); (T.S.J.)
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Karl-Henrik Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia;
| | - Andy F. S. Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK;
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | | | | | - Björn D. Lindahl
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden;
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Ave Suija
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Kristjan Adojaan
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Timo Piirmann
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Raivo Pöhönen
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Allan Zirk
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
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5
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Becraft ED, Wood JM, Cohan FM, Ward DM. Biogeography of American Northwest Hot Spring A/B '-Lineage Synechococcus Populations. Front Microbiol 2020; 11:77. [PMID: 32153516 PMCID: PMC7050468 DOI: 10.3389/fmicb.2020.00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/15/2020] [Indexed: 12/17/2022] Open
Abstract
Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B'-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by <50 km than among springs separated by >50 km, and springs separated by >800 km shared sequence variants only rarely. Phylogenetic analyses provided evidence for endemic lineages that could be related to geographic isolation and/or geochemical differences on regional scales. Ecotype Simulation 2 was used to predict putative ecotypes (ecologically distinct populations), and their membership, and canonical correspondence analysis was used to examine the geographical and geochemical bases for variation in their distribution. Across the range of Oregon and Yellowstone, geographical separation explained the largest percentage of the differences in distribution of ecotypes (9.5% correlated to longitude; 9.4% to latitude), with geochemical differences explaining the largest percentage of the remaining differences in distribution (7.4-9.3% correlated to magnesium, sulfate, and sulfide). Among samples within the Greater Yellowstone Ecosystem, geochemical differences significantly explained the distribution of ecotypes (6.5-9.3% correlated to magnesium, boron, sulfate, silicon dioxide, chloride, and pH). Nevertheless, differences in the abundance and membership of ecotypes in Yellowstone springs with similar chemistry suggested that allopatry may be involved even at local scales. Synechococcus populations have diverged both by physical isolation and physiochemical differences, and populations on surprisingly local scales have been evolving independently.
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Affiliation(s)
- Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States.,Department of Biology, University of North Alabama, Florence, AL, United States
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
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6
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Menchinelli G, Liotti FM, Fiori B, De Angelis G, D'Inzeo T, Giordano L, Posteraro B, Sabbatucci M, Sanguinetti M, Spanu T. Corrigendum: In vitro Evaluation of BACT/ALERT® VIRTUO®, BACT/ALERT 3D®, and BACTEC™ FX Automated Blood Culture Systems for Detection of Microbial Pathogens Using Simulated Human Blood Samples. Front Microbiol 2019; 10:2688. [PMID: 31807126 PMCID: PMC6883174 DOI: 10.3389/fmicb.2019.02688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/06/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Giulia Menchinelli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Flora Marzia Liotti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Barbara Fiori
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Scuola Provinciale Superiore di Sanità Claudiana, Bolzano, Italy
| | - Giulia De Angelis
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Tiziana D'Inzeo
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Liliana Giordano
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Istituto di Patologia e Semeiotica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Michela Sabbatucci
- Istituto Superiore di Sanità, Rome, Italy.,European Programme for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Maurizio Sanguinetti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Teresa Spanu
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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7
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Menchinelli G, Liotti FM, Fiori B, De Angelis G, D'Inzeo T, Giordano L, Posteraro B, Sabbatucci M, Sanguinetti M, Spanu T. In vitro Evaluation of BACT/ALERT® VIRTUO®, BACT/ALERT 3D®, and BACTEC™ FX Automated Blood Culture Systems for Detection of Microbial Pathogens Using Simulated Human Blood Samples. Front Microbiol 2019; 10:221. [PMID: 30837964 PMCID: PMC6389693 DOI: 10.3389/fmicb.2019.00221] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Blood culture (BC) is still the standard for diagnosing bloodstream infections (BSIs), especially those caused by bacteria and fungi. Infection-complicating sepsis or septic shock often occurs at BSI onset, making necessary to improve the diagnostic yield of positive BCs. Among the BC systems currently available, the BACT/ALERT® VIRTUO® (VIRTUO) system has been developed to shorten time to detection (TTD) of positive BCs. In this study, we assessed TTD for 330 clinically relevant species including 14 Gram-positive, 14 Gram-negative, and 5 yeast isolates in spiked human blood samples that were tested in parallel with VIRTUO BACT/ALERT® 3D (BTA3D) and BACTEC™ FX (BACTEC) systems. We inoculated 30 colony-forming unit (CFU) from each microbial suspension into BACT/ALERT® Plus or BACTEC™ Plus (aerobic/anaerobic or pediatric) BC bottles, and we used two different blood volumes to simulate, respectively, the BCs collected from adult and pediatric patients. Of 2,610 bottles tested, 2,600 (99.6%) signaled positive in the three systems. Only the BACTEC system did not detect Staphylococcus lugdunensis isolates in anaerobic bottles. Among adult simulated cultures, the median TTD was significantly shorter for aerobic/anaerobic bottles incubated in VIRTUO (11.6 h and 10.1 h) compared to bottles incubated in either BTA3D (13.3 and 12.3 h) or BACTEC (13.5 and 12.2 h) system. Among pediatric simulated cultures, the median TTD was significantly shorter for bottles incubated in VIRTUO (11.2 h) compared to bottles incubated in either the BTA3D (13.0 h) or BACTEC (12.5 h) system. Compared to BTA3D and/or BACTEC systems, VIRTUO allowed faster growth detection for most of the 33 microbial species tested. Notable examples were Salmonella spp. (7.4 h by VIRTUO vs. 10.1 h and 9.2 h by either BTA3D or BACTEC) and Streptococcus agalactiae (8.1 h by VIRTUO vs. 10.3 and 9.4 h by either BTA3D or BACTEC). The few notable exceptions included Stenotrophomonas maltophilia and some Candida species. Together, these findings confirm that VIRTUO has greater potential of improving the laboratory detection of bacteremia and fungemia than the progenitor BTA3D or the competitor BACTEC system.
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Affiliation(s)
- Giulia Menchinelli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Flora Marzia Liotti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Barbara Fiori
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Scuola Provinciale Superiore di Sanità Claudiana, Bolzano, Italy
| | - Giulia De Angelis
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Tiziana D'Inzeo
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Liliana Giordano
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Istituto di Patologia e Semeiotica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Maurizio Sanguinetti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Teresa Spanu
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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8
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Berry MA, White JD, Davis TW, Jain S, Johengen TH, Dick GJ, Sarnelle O, Denef VJ. Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes. Front Microbiol 2017; 8:365. [PMID: 28337183 PMCID: PMC5341627 DOI: 10.3389/fmicb.2017.00365] [Citation(s) in RCA: 48] [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] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/21/2017] [Indexed: 11/13/2022] Open
Abstract
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method’s constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis. We identified three Microcystis oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 Microcystis cultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in Microcystis oligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, Microcystis oligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Erie did not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, Microcystis oligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.
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Affiliation(s)
- Michelle A Berry
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
| | - Jeffrey D White
- Department of Biology, Framingham State University Framingham, MA, USA
| | - Timothy W Davis
- NOAA Great Lakes Environmental Research Laboratory Ann Arbor, MI, USA
| | - Sunit Jain
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Thomas H Johengen
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Orlando Sarnelle
- Department of Fisheries and Wildlife, Michigan State University East Lansing, MI, USA
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
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9
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Nowack S, Olsen MT, Schaible GA, Becraft ED, Shen G, Klapper I, Bryant DA, Ward DM. The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Front Microbiol 2015; 6:626. [PMID: 26175719 PMCID: PMC4484337 DOI: 10.3389/fmicb.2015.00626] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Closely related strains of thermophilic Synechococcus were cultivated from the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park (YNP). These strains have identical or nearly identical 16S rRNA sequences but are representative of separate, predicted putative ecotype (PE) populations, which were identified by using the more highly resolving psaA locus and which predominate at different vertical positions within the 1-mm-thick upper-green layer of the mat. Pyrosequencing confirmed that each strain contained a single, predominant psaA genotype. Strains differed in growth rate as a function of irradiance. A strain with a psaA genotype corresponding to a predicted PE that predominates near the mat surface grew fastest at high irradiances, whereas strains with psaA genotypes representative of predominant subsurface populations grew faster at low irradiance and exhibited greater sensitivity to abrupt shifts to high light. The high-light-adapted and low-light-adapted strains also exhibited differences in pigment content and the composition of the photosynthetic apparatus (photosystem ratio) when grown under different light intensities. Cells representative of the different strains had similar morphologies under low-light conditions, but under high-light conditions, cells of low-light-adapted strains became elongated and formed short chains of cells. Collectively, the results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.
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Affiliation(s)
- Shane Nowack
- Department of Mathematical Sciences, Montana State University, Bozeman MT, USA ; School of Environmental Sciences, University of Guelph, Guelph ON, Canada
| | - Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - George A Schaible
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park PA, USA
| | - Isaac Klapper
- Department of Mathematical Sciences, Montana State University, Bozeman MT, USA ; Department of Mathematics, Temple University, Philadelphia, PA USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park PA, USA ; Department of Chemistry and Biochemistry, Montana State University, Bozeman MT, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman MT, USA
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10
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Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz WS, Rusch DB, Cohan FM, Bryant DA, Ward DM. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Front Microbiol 2015; 6:604. [PMID: 26157428 PMCID: PMC4477158 DOI: 10.3389/fmicb.2015.00604] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
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Affiliation(s)
- Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Shane Nowack
- Department of Mathematical Sciences, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Kurt LaButti
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Joel Martin
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | | | | | | | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA ; Department of Chemistry and Biochemistry, Montana State University Bozeman, MT, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
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11
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Becraft ED, Wood JM, Rusch DB, Kühl M, Jensen SI, Bryant DA, Roberts DW, Cohan FM, Ward DM. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Front Microbiol 2015; 6:590. [PMID: 26157420 PMCID: PMC4475828 DOI: 10.3389/fmicb.2015.00590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/29/2015] [Indexed: 01/18/2023] Open
Abstract
Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.
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Affiliation(s)
- Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, MEUSA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
| | | | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSWAustralia
| | - Sheila I. Jensen
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, HellerupDenmark
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PAUSA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MTUSA
| | | | | | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
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