High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Ноя. 26, 2018

A fundamental question in microbiology is whether there continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this by facilitating high resolution taxonomic analysis thousands genomes from diverse phylogenetic lineages. To scale to available and beyond, we present FastANI, a new method estimate ANI using alignment-free approximate sequence mapping. FastANI accurate for both finished draft up three orders magnitude faster compared alignment-based approaches. We leverage compute pairwise values all prokaryotic the NCBI database. Our results reveal discontinuity, with 99.8% total 8 billion genome pairs analyzed conforming >95% intra-species <83% inter-species values. This discontinuity manifested without most frequently sequenced species, robust historic additions databases.

Язык: Английский

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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Nature Biotechnology, Год журнала: 2018, Номер 36(10), С. 996 - 1004

Опубликована: Авг. 27, 2018

Язык: Английский

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A new view of the tree of life

Nature Microbiology, Год журнала: 2016, Номер 1(5)

Опубликована: Апрель 11, 2016

The tree of life is one the most important organizing principles in biology(1). Gene surveys suggest existence an enormous number branches(2), but even approximation full scale has remained elusive. Recent depictions have focused either on nature deep evolutionary relationships(3-5) or known, well-classified diversity with emphasis eukaryotes(6). These approaches overlook dramatic change our understanding life's resulting from genomic sampling previously unexamined environments. New methods to generate genome sequences illuminate identity organisms and their metabolic capacities, placing them community ecosystem contexts(7,8). Here, we use new data over 1,000 uncultivated little known organisms, together published sequences, infer a dramatically expanded version life, Bacteria, Archaea Eukarya included. depiction both global overview snapshot within each major lineage. results reveal dominance bacterial diversification underline importance lacking isolated representatives, substantial evolution concentrated radiation such organisms. This highlights lineages currently underrepresented biogeochemical models identifies radiations that are probably for future analyses.

Язык: Английский

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Nature Microbiology, Год журнала: 2017, Номер 2(11), С. 1533 - 1542

Опубликована: Сен. 11, 2017

Abstract Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances sequencing throughput and computational techniques that allow for cultivation-independent recovery genomes from metagenomes. Here, we report reconstruction 7,903 bacterial archaeal >1,500 public All are estimated to be ≥50% complete nearly half ≥90% with ≤5% contamination. These increase genome trees >30% provide first representatives 17 three candidate phyla. We also recovered 245 Patescibacteria superphylum (also known as Candidate Phyla Radiation) find relative this group varies substantially different protein marker sets. The scale quality data set demonstrate recovering metagenomes provides an expedient path forward exploring dark matter.

Язык: Английский

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Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

Frontiers in Microbiology, Год журнала: 2020, Номер 11

Опубликована: Апрель 7, 2020

The class

Язык: Английский

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Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Ноя. 6, 2019

Abstract The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing the full only recently become realistic prospect. Here, we use in silico and experiments to critically re-evaluate potential provide taxonomic resolution at species strain level. We demonstrate that targeting variable regions with short-read platforms cannot achieve afforded by entire (~1500 bp) gene. further full-length are sufficiently accurate resolve subtle nucleotide substitutions (but not insertions/deletions) exist between intragenomic copies In consequence, argue modern approaches must necessarily account variation copies. particular, appropriate treatment copy variants communities

Язык: Английский

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Unusual biology across a group comprising more than 15% of domain Bacteria

Nature, Год журнала: 2015, Номер 523(7559), С. 208 - 211

Опубликована: Июнь 15, 2015

Язык: Английский

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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Окт. 24, 2016

Abstract The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central Earth’s biogeochemical cycles. However, little is known about how complex in such environments are structured, and inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics aquifer sediments groundwater, reconstruct 2,540 draft-quality, near-complete complete strain-resolved genomes represent the majority bacterial phyla as well 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity representing 36% organisms detected system used document distribution pathways coexisting organisms. Consistent with prior findings indicating metabolic handoffs simple consortia, find few within community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages selected for, altering linkages among major

Язык: Английский

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Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

Nature Medicine, Год журнала: 2019, Номер 25(6), С. 968 - 976

Опубликована: Июнь 1, 2019

Язык: Английский

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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, Год журнала: 2020, Номер 70(11), С. 5972 - 6016

Опубликована: Ноя. 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.

Язык: Английский

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