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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Metal contamination and bioremediation of agricultural soils for food safety and sustainability

Nature Reviews Earth & Environment, Journal Year: 2020, Volume and Issue: 1(7), P. 366 - 381

Published: June 23, 2020

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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Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Jan. 22, 2018

Plastics, including poly(ethylene terephthalate) (PET), possess many desirable characteristics and thus are widely used in daily life. However, non-biodegradability, once thought to be an advantage offered by plastics, is causing major environmental problem. Recently, a PET-degrading bacterium, Ideonella sakaiensis, was identified suggested for possible use degradation and/or recycling of PET. the molecular mechanism PET not known. Here we report crystal structure I. sakaiensis PETase (IsPETase) at 1.5 Å resolution. IsPETase has Ser-His-Asp catalytic triad its active site contains optimal substrate binding accommodate four monohydroxyethyl terephthalate (MHET) moieties Based on structural site-directed mutagenesis experiments, detailed process into MHET, terephthalic acid, ethylene glycol suggested. Moreover, other candidates potentially having high activities based phylogenetic tree analysis 69 PETase-like proteins.

Language: Английский

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Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

Cell, Journal Year: 2018, Volume and Issue: 172(6), P. 1181 - 1197

Published: March 1, 2018

Language: Английский

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New CRISPR–Cas systems from uncultivated microbes

Nature, Journal Year: 2016, Volume and Issue: 542(7640), P. 237 - 241

Published: Dec. 22, 2016

Language: Английский

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Archaea and the origin of eukaryotes

Nature Reviews Microbiology, Journal Year: 2017, Volume and Issue: 15(12), P. 711 - 723

Published: Nov. 10, 2017

Language: Английский

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Biodegradation of PET: Current Status and Application Aspects

ACS Catalysis, Journal Year: 2019, Volume and Issue: 9(5), P. 4089 - 4105

Published: April 8, 2019

Most petroleum-derived plastics, as exemplified by poly(ethylene terephthalate) (PET), are chemically inactive and highly resistant to microbial attack. The accumulation of plastic waste results in environmental pollution threatens ecosystems, referred the "microplastic issue". Recently, PET hydrolytic enzymes (PHEs) have been identified we reported degradation a consortium its bacterial resident, Ideonella sakaiensis. Bioremediation may thus provide an alternative solution recycling waste. mechanism into benign monomers hydrolase mono(2-hydroxyethyl) terephthalic acid (MHET) from I. sakaiensis has elucidated; nevertheless, biodegradation require additional development for commercialization owing low catalytic activity these enzymes. Here, introduce degrading microorganisms involved, along with evolution PHEs address issues that hamper enzymatic degradation. Potential applications also discussed.

Language: Английский

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