Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2020, Volume and Issue: 70(11), P. 5972 - 6016

Published: Nov. 1, 2020

The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction predatory behaviour. Although this lineage is the fourth described phylum Proteobacteria , it rarely affiliates with other proteobacterial classes frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch encompassing Bdellovibrio- like predators was recently reclassified into separate class, Oligoflexia . Here we systematically explore phylogeny taxa currently assigned to these using 120 conserved single-copy marker genes well rRNA genes. overwhelming majority markers reject inclusion Instead, great recognized members are better classified four novel phylum-level lineages. We propose names Desulfobacterota phyl. nov. Myxococcota two phyla, based on oldest validly published each lineage, retain placeholder name SAR324 third pending formal description type material. Members represent which Bdellovibrionota priority literature general recognition genus Bdellovibrio. includes previously Thermodesulfobacteria reclassifications imply that ability vertically inherited rather than laterally acquired inferred. Our analysis also indicates independent acquisition behaviour phyla consistent their distinct modes action. This work represents stable reclassification most taxonomically challenging areas bacterial tree provides robust framework future ecological systematic studies.

Language: Английский

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IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D666 - D677

Published: Sept. 24, 2018

The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source include those generated by the DOE's Joint Genome Institute (JGI), submitted external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through IMG annotation pipeline then loaded into warehouse. IMG's web user interface provides a variety of analytical visualization tools for comparative analysis isolate genomes metagenomes in IMG. IMG/M allows open access to all warehouse, while its expert review (ER) (IMG/MER: https://img.jgi.doe.gov/mer/) registered users their private store workspace sharing further analysis. content has grown 60% since last report published 2017 NAR Database Issue. new more powerful search feature, statistical tools, supports metagenome binning.

Language: Английский

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DRAM for distilling microbial metabolism to automate the curation of microbiome function

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 48(16), P. 8883 - 8900

Published: July 22, 2020

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet specific reactions catalyzed by these biological engines are hard to decode due absence a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled Refined Annotation Metabolism), framework translate deluge microbiome-based genomic information into catalog microbial traits. To demonstrate applicability across diverse genomes, evaluated performance on defined, in silico soil community previously published human gut metagenomes. We show that accurately assigned contributions geochemical cycles automated partitioning carbohydrate metabolism at substrate levels. DRAM-v, mode DRAM, established rules identify virally-encoded auxiliary metabolic genes (AMGs), resulting categorization thousands putative AMGs from soils guts. Together DRAM-v provide critical profiling capabilities decipher mechanisms underpinning microbiome function.

Language: Английский

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A genomic catalog of Earth’s microbiomes

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(4), P. 499 - 509

Published: Nov. 9, 2020

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. expands known phylogenetic diversity bacteria archaea by 44% is broadly available for streamlined comparative analyses, interactive exploration, modeling bulk download. We demonstrate utility collection understanding secondary-metabolite biosynthetic potential resolving thousands new host linkages uncultivated viruses. resource underscores value genome-centric approaches revealing genomic properties microorganisms that affect ecosystem processes.

Language: Английский

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New insights from uncultivated genomes of the global human gut microbiome

Nature, Journal Year: 2019, Volume and Issue: 568(7753), P. 505 - 510

Published: March 13, 2019

The genome sequences of many species the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, geographically and phenotypically diverse humans. These provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over previously known phylogenetic diversity sequenced bacteria. On average, OTUs comprise 33% richness 28% abundance per individual, are enriched humans rural populations. A meta-analysis clinical gut-microbiome studies pinpointed numerous disease associations OTUs, have potential improve predictive models. Finally, our analysis revealed that uncultured undergone reduction has resulted loss certain biosynthetic pathways, may offer clues improving cultivation strategies future. Draft metagenomes populations enrich understanding identifying two thousand new taxa associations.

Language: Английский

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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(11), P. 1633 - 1644

Published: Feb. 23, 2023

Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. 4 explains ~20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome proves accurate than available alternatives on synthetic evaluations while also reliably quantifying with no cultured isolates. Application method to >24,500 metagenomes highlights previously undetected be strong biomarkers host conditions lifestyles mouse shows that even uncharacterized genetically profiled resolution single strains.

Language: Английский

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Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

Nature Microbiology, Journal Year: 2018, Volume and Issue: 3(7), P. 804 - 813

Published: June 8, 2018

Abstract Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as main suppliers of bioavailable this habitat. Although PCR amplicon surveys targeting nitrogenase reductase gene revealed existence diverse non-cyanobacterial diazotrophic populations, subsequent quantitative suggest that they generally occur low abundance. Here, we use state-of-the-art metagenomic assembly binning strategies to recover nearly one thousand non-redundant population genomes from TARA Oceans metagenomes. Among these, provide first genomic evidence for diazotrophs inhabiting waters open ocean, which correspond lineages within Proteobacteria and, most strikingly, Planctomycetes. Members latter phylum are prevalent aquatic systems, but never linked previously. Moreover, using genome-wide read recruitment, demonstrate discovered were not only widespread also remarkably abundant (up 0.3% reads a single population) both Pacific Ocean Atlantic northwest. Our results extend decades PCR-based surveys, substantiate importance heterotrophic bacteria ocean.

Language: Английский

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Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(10), P. 629 - 645

Published: Sept. 4, 2018

Language: Английский

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Tara Oceans: towards global ocean ecosystems biology

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(8), P. 428 - 445

Published: May 12, 2020

Language: Английский

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Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Cell, Journal Year: 2019, Volume and Issue: 179(5), P. 1068 - 1083.e21

Published: Nov. 1, 2019

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic genomic compositions, little is known about how transcriptomes vary globally. Here, we present a dataset 187 metatranscriptomes 370 metagenomes from 126 globally distributed sampling stations establish resource 47 million genes to study community-level across depth layers pole-to-pole. We examine gene expression changes community turnover as underlying mechanisms shaping along these axes environmental variation show individual contributions differ for multiple biogeochemically relevant processes. Furthermore, find relative contribution be significantly lower polar than non-polar waters hypothesize that regions, alterations activity response ocean warming will driven more by organismal composition regulatory mechanisms.Video AbstracteyJraWQiOiI4ZjUxYWNhY2IzYjhiNjNlNzFlYmIzYWFmYTU5NmZmYyIsImFsZyI6IlJTMjU2In0.eyJzdWIiOiI2ZDM3MTU3MTVlOWRjMjIwNjk3YmVlYTM4ZTFiYzA2NSIsImtpZCI6IjhmNTFhY2FjYjNiOGI2M2U3MWViYjNhYWZhNTk2ZmZjIiwiZXhwIjoxNjc5MzU4ODUzfQ.fR9n_CSDtj4NFNODQlYoh6-2hFK0eZLlkic_Tn2t6PReywCIRha7nJWNHEIa6TAVQq9D_kITAxjm7S04fAMziv-PQlBSfhL_LHBkD71WD64HFYZ-ET_4opJHSoEHKaf5frPuEEoZv_5n0WnuOl5fQlTHFURvD5f3GdcDiLnsUTIg_dKdeGl-KyXt6o9o5RDkcPiKgsNJkKAnw6nl263TvlMFG4WAW-wiQqbPBJCkmfoVvfMl1-qv6OMGso0eg7aFpbom6dqhlEZ4b4nBub03i9BEPccL7pf0G8bCICA2lqQB4j1ryqeK_zPImWClizV4XTOzLn7V-1MnIxPTsevMrg(mp4, (132.7 MB) Download video

Language: Английский

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