GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Bioinformatics, Год журнала: 2019, Номер 36(6), С. 1925 - 1927

Опубликована: Ноя. 14, 2019

The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient able to classify thousands of draft in parallel. Here we demonstrate accuracy by evaluating its performance a phylogenetically diverse set 10,156 metagenome-assembled genomes.

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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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Дек. 1, 2018

The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence contaminants—DNA sequences not truly present in sample. Contaminants come various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure identifies contaminants MGS data two widely reproduced patterns: appear at higher frequencies low-concentration samples are often found negative controls. Decontam classified amplicon sequence variants (ASVs) human oral dataset consistently with prior microscopic observations taxa inhabiting environment previous reports contaminant taxa. In metagenomics measurements dilution series, substantially reduced technical variation arising different protocols. application to recently published datasets corroborated extended their conclusions little evidence existed for indigenous placenta microbiome some low-frequency seemingly associated preterm birth were contaminants. improves quality by identifying removing DNA sequences. integrates easily existing workflows allows researchers generate more accurate profiles communities no additional cost.

Язык: Английский

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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Nature Biotechnology, Год журнала: 2017, Номер 35(8), С. 725 - 731

Опубликована: Авг. 1, 2017

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide adoption MISAG MIMAG will facilitate more robust comparative genomic analyses diversity.

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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Microbiome definition re-visited: old concepts and new challenges

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Язык: Английский

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Function and functional redundancy in microbial systems

Nature Ecology & Evolution, Год журнала: 2018, Номер 2(6), С. 936 - 943

Опубликована: Апрель 12, 2018

Язык: Английский

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A new genomic blueprint of the human gut microbiota

Nature, Год журнала: 2019, Номер 568(7753), С. 499 - 504

Опубликована: Фев. 11, 2019

The composition of the human gut microbiota is linked to health and disease, but knowledge individual microbial species needed decipher their biological roles. Despite extensive culturing sequencing efforts, complete bacterial repertoire remains undefined. Here we identify 1,952 uncultured candidate by reconstructing 92,143 metagenome-assembled genomes from 11,850 microbiomes. These substantially expand known collective microbiota, with a 281% increase in phylogenetic diversity. Although newly identified are less prevalent well-studied populations compared reference isolate genomes, they improve classification understudied African South American samples more than 200%. encode hundreds biosynthetic gene clusters possess distinctive functional capacity that might explain elusive nature. Our work expands diversity bacteria, which provides unprecedented resolution for taxonomic characterization intestinal microbiota.

Язык: Английский

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Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

Science, Год журнала: 2018, Номер 362(6416), С. 839 - 842

Опубликована: Окт. 19, 2018

CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 1400 amino acids) has been considered essential their specific DNA- or RNA-targeting activities. Here we present a set of from uncultivated archaea that contain Cas14, family exceptionally compact nucleases (400 700 acids). Despite small size, Cas14 capable targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Moreover, target recognition by triggers nonspecific cutting ssDNA molecules, an activity enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show multiple CRISPR-Cas14 evolved independently suggest potential evolutionary origin single-effector CRISPR-based immunity.

Язык: Английский

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A unified catalog of 204,938 reference genomes from the human gut microbiome

Nature Biotechnology, Год журнала: 2020, Номер 39(1), С. 105 - 114

Опубликована: Июль 20, 2020

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant from 4,644 prokaryotes. These encode >170 million protein sequences, which we collated in Protein (UHGP) catalog. The UHGP more than doubles number proteins comparison to those Integrated Gene Catalog. More 70% UHGG species lack cultured representatives, 40% annotations. Intraspecies genomic variation analyses revealed a large reservoir accessory genes single-nucleotide variants, many specific individual populations. collections will enable studies linking genotypes phenotypes microbiome. 200,000 prokaryotic they collated, providing comprehensive resources microbiome researchers.

Язык: Английский

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