1
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Commichaux S, Luan T, Muralidharan HS, Pop M. Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes. PLoS Comput Biol 2024; 20:e1012343. [PMID: 39102435 PMCID: PMC11326629 DOI: 10.1371/journal.pcbi.1012343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 08/15/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. However, the 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other nearly-universal prokaryotic marker genes as the number of gene sequences increases in reference databases. This trend was strongly correlated with how represented a taxonomic group was in the database and indicates that, at the gene-level, the boundaries between many species might be fuzzy. Through our study, we argue that any approach that relies on a single marker to distinguish bacterial taxa is fraught even if some markers appear to be discriminative in current databases.
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Affiliation(s)
- Seth Commichaux
- Center for Food Safety and Nutrition, Food and Drug Administration, Laurel, Maryland, United States of America
| | - Tu Luan
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Harihara Subrahmaniam Muralidharan
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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2
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Roje B, Zhang B, Mastrorilli E, Kovačić A, Sušak L, Ljubenkov I, Ćosić E, Vilović K, Meštrović A, Vukovac EL, Bučević-Popović V, Puljiz Ž, Karaman I, Terzić J, Zimmermann M. Gut microbiota carcinogen metabolism causes distal tissue tumours. Nature 2024:10.1038/s41586-024-07754-w. [PMID: 39085612 DOI: 10.1038/s41586-024-07754-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Exposure to environmental pollutants and human microbiome composition are important predisposition factors for tumour development1,2. Similar to drug molecules, pollutants are typically metabolized in the body, which can change their carcinogenic potential and affect tissue distribution through altered toxicokinetics3. Although recent studies demonstrated that human-associated microorganisms can chemically convert a wide range of xenobiotics and influence the profile and tissue exposure of resulting metabolites4,5, the effect of microbial biotransformation on chemical-induced tumour development remains unclear. Here we show that the depletion of the gut microbiota affects the toxicokinetics of nitrosamines, which markedly reduces the development and severity of nitrosamine-induced urinary bladder cancer in mice6,7. We causally linked this carcinogen biotransformation to specific gut bacterial isolates in vitro and in vivo using individualized bacterial culture collections and gnotobiotic mouse models, respectively. We tested gut communities from different human donors to demonstrate that microbial carcinogen metabolism varies between individuals and we showed that this metabolic activity applies to structurally related nitrosamine carcinogens. Altogether, these results indicate that gut microbiota carcinogen metabolism may be a contributing factor for chemical-induced carcinogenesis, which could open avenues to target the microbiome for improved predisposition risk assessment and prevention of cancer.
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Affiliation(s)
- Blanka Roje
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Boyao Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eleonora Mastrorilli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ana Kovačić
- Public Health Institute of Split and Dalmatia County, Split, Croatia
| | - Lana Sušak
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Ivica Ljubenkov
- Department of Chemistry, University of Split Faculty of Science, Split, Croatia
| | - Elena Ćosić
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Katarina Vilović
- Department of Pathology, University Hospital of Split, Split, Croatia
| | - Antonio Meštrović
- Department of Gastroenterology, University Hospital of Split, Split, Croatia
| | | | | | - Željko Puljiz
- Department of Gastroenterology, University Hospital of Split, Split, Croatia
| | - Ivana Karaman
- Department of Pathology, University Hospital of Split, Split, Croatia
| | - Janoš Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia.
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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3
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Zhang H, Wei T, Li Q, Fu L, Li M, He L, Wang Y. Metagenomic 18S rDNA reads revealed zonation of eukaryotic communities in the Yongle blue hole. Front Microbiol 2024; 15:1420899. [PMID: 39135873 PMCID: PMC11317397 DOI: 10.3389/fmicb.2024.1420899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redox-layered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 μm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermo-halocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-μm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes.
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Affiliation(s)
- Hongxi Zhang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Taoshu Wei
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Qingmei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute Co., Ltd., Sansha, China
| | - Manjie Li
- Institute for Ocean Engineering, Shenzhen International Graduate School, Shenzhen, China
- Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lisheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Shenzhen, China
- Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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4
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Sánchez P, Coutinho FH, Sebastián M, Pernice MC, Rodríguez-Martínez R, Salazar G, Cornejo-Castillo FM, Pesant S, López-Alforja X, López-García EM, Agustí S, Gojobori T, Logares R, Sala MM, Vaqué D, Massana R, Duarte CM, Acinas SG, Gasol JM. Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition. Sci Data 2024; 11:154. [PMID: 38302528 PMCID: PMC10834958 DOI: 10.1038/s41597-024-02974-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
The Ocean microbiome has a crucial role in Earth's biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2-3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.
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Affiliation(s)
- Pablo Sánchez
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Felipe H Coutinho
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Massimo C Pernice
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Raquel Rodríguez-Martínez
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Guillem Salazar
- Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Stéphane Pesant
- EMBL's European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Xabier López-Alforja
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Ester María López-García
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
- Centre National de la Recherche Scientifique (CNRS), UMR5254, IPREM, Pau, France
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Ramiro Logares
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Maria Montserrat Sala
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Dolors Vaqué
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Silvia G Acinas
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Josep M Gasol
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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5
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Bueno de Mesquita CP, Hartman WH, Ardón M, Tringe SG. Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME COMMUNICATIONS 2024; 4:ycae040. [PMID: 38628812 PMCID: PMC11020224 DOI: 10.1093/ismeco/ycae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Wyatt H Hartman
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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6
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Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat Commun 2023; 14:3037. [PMID: 37264015 DOI: 10.1038/s41467-023-38502-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
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Affiliation(s)
- Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | | | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany
| | - Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Claudia Pogoreutz
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maggy M Nugues
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric Gilson
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Department of Medical Genetics, CHU Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, 8 rue de Prague, 75012, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
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7
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Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. MICROBIOME 2022; 10:212. [PMID: 36464731 PMCID: PMC9721005 DOI: 10.1186/s40168-022-01410-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both "known" and "unknown" species based on a set of select marker genes. RESULTS We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies. CONCLUSIONS We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs . Video Abstract.
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Affiliation(s)
- Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicolai Karcher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Quentin Clayssen
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Marisa Isabell Keller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel R. Mende
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
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