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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Unified rational protein engineering with sequence-based deep representation learning

Nature Methods, Journal Year: 2019, Volume and Issue: 16(12), P. 1315 - 1322

Published: Oct. 21, 2019

Language: Английский

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Fusobacterium nucleatum — symbiont, opportunist and oncobacterium

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 17(3), P. 156 - 166

Published: Dec. 13, 2018

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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A computational framework to explore large-scale biosynthetic diversity

Nature Chemical Biology, Journal Year: 2019, Volume and Issue: 16(1), P. 60 - 68

Published: Nov. 25, 2019

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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Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Feb. 19, 2019

Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected intestine of other animals. Because they had not been cultured until recently classification is still ambiguous, interaction with their host was difficult to study confusion exists regarding sequence data annotation.We investigated by combining from large-scale 16S rRNA gene analysis functional taxonomic studies metagenomic species.A total 685 species inferred full-length clustering. While many could be assigned ecological habitats (93,045 samples analyzed), most commonly identified (average 20% relative abundance nine co-occurring species). Shotgun metagenomics allowed reconstruction 59 molecular species, which 34 were representative gene-derived clusters. In addition, cultivation efforts isolating five strains representing three including two novel taxa. Genome revealed that spp. functionally distinct neighboring families versatile respect complex carbohydrate degradation.We provide on diversity, ecology, description bacterial S24-7, for name Muribaculaceae proposed.

Language: Английский

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Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Feb. 26, 2018

The 16S ribosomal RNA gene is the most widely used marker in microbial ecology. Counts of sequence variants, often PCR amplicons, are to estimate proportions bacterial and archaeal taxa communities. Because different organisms contain copy numbers (GCNs), variant counts biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods based on sequenced genomes, order correct these biases. However, accuracy those predictions has not independently assessed. Here, we systematically evaluate predictability across clades, ∼ 6,800 public genomes several methods. Further, assess predicted by three published (PICRUSt, CopyRighter, PAPRICA) over a wide range 635 communities from varied environments. We find that regardless method tested, could only be accurately limited fraction taxa, namely closely moderately related representatives (≲15% divergence rRNA gene). Consistent this observation, all considered exhibit low predictive when evaluated against completely some cases explaining less than 10% variance. Substantial disagreement was also observed between (R2<0.5) majority tested nearest taxon index (NSTI) communities, i.e., average distance genome, strong predictor agreement GCN prediction non-animal-associated samples, but moderate animal-associated samples. recommend correcting microbiome surveys default, unless OTUs sufficiently or need true OTU warrants additional noise introduced, so community profiles remain interpretable comparable studies.

Language: Английский

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Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

Microbial Genomics, Journal Year: 2021, Volume and Issue: 7(11)

Published: Nov. 5, 2021

Command-line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command-line pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and, nonetheless, fast Bakta conducts comprehensive workflow including detection small proteins taking into account replicon metadata. The coding sequences is accelerated via an alignment-free sequence identification approach that in addition facilitates precise assignment public database cross-references. Annotation are exported GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files, as JSON facilitating automated downstream analysis. We other rapid contemporary both targeted taxonomically broad benchmarks isolates metagenomic-assembled demonstrated outperforms terms functional annotations, categories cross-references, whilst providing comparable wall-clock runtimes. implemented Python 3 runs MacOS Linux systems. It freely available under GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version https://bakta.computational.bio.

Language: Английский

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