Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen DOI Creative Commons
Robert D. Stewart, Marc Auffret, Amanda Warr

et al.

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

Published: Feb. 22, 2018

Abstract The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded microbiome. Here we present 913 draft bacterial archaeal genomes assembled from over 800 Gb metagenomic sequence data derived 43 Scottish cattle, using both binning Hi-C-based proximity-guided assembly. Most these represent previously unsequenced strains species. contain 69,000 proteins predicted to be involved in carbohydrate metabolism, 90% which do not have good match public databases. Inclusion presented here improves read classification sevenfold against our own data, fivefold other publicly available datasets. Thus, dataset substantially coverage microbial databases represents valuable resource biomass-degrading enzyme discovery studies

Language: Английский

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database DOI Creative Commons
Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz

et al.

Bioinformatics, Journal Year: 2019, Volume and Issue: 36(6), P. 1925 - 1927

Published: Nov. 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.

Language: Английский

Citations

3848
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries DOI Creative Commons
Chirag Jain, Luis M. Rodriguez‐R, Adam M. Phillippy

et al.

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

Published: Nov. 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.

Language: Английский

Citations

3780
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life DOI
Donovan H. Parks, Maria Chuvochina, David W. Waite

et al.

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(10), P. 996 - 1004

Published: Aug. 27, 2018

Language: Английский

Citations

3027
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies DOI Creative Commons
Dongwan Kang, Feng Li, Edward Kirton

et al.

PeerJ, Journal Year: 2019, Volume and Issue: 7, P. e7359 - e7359

Published: July 26, 2019

We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated species. MetaBAT has become one the most popular tools largely due its computational efficiency and ease use, especially in experiments with a large number samples assembly. requires users choose parameters fine-tune sensitivity specificity. If those are not chosen properly, accuracy can suffer, assemblies poor quality. Here, we developed 2 overcome this problem. uses new adaptive algorithm eliminate manual parameter tuning. also performed extensive engineering optimization increase both memory efficiency. Comparing alternative over 100 real world shows superior computing speed. Binning typical assembly takes only few minutes commodity workstation. therefore recommend community adopts their experiments. is open source available at https://bitbucket.org/berkeleylab/metabat.

Language: Английский

Citations

2553
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 DOI Creative Commons
Francesco Beghini, Lauren J. McIver, Aitor Blanco‐Míguez

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: May 4, 2021

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest sequences now available. Compared current alternatives, MetaPhlAn 3 increases accuracy taxonomic profiling, HUMAnN improves that functional potential activity. These detected novel disease-microbiome links applications CRC (1262 metagenomes) IBD (1635 817 metatranscriptomes). Strain-level an additional 4077 StrainPhlAn PanPhlAn unraveled structure common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations cloud-deployable reproducible workflows, platform can help researchers deepen resolution, scale, multi-omic community studies.

Language: Английский

Citations

1397
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle DOI Creative Commons
Edoardo Pasolli, Francesco Asnicar, Serena Manara

et al.

Cell, Journal Year: 2019, Volume and Issue: 176(3), P. 649 - 662.e20

Published: Jan. 1, 2019

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% high quality) spanning body sites, ages, countries, lifestyles. recapitulated 4,930 species-level genome bins (SGBs), 77% without public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% well-assembled samples), expand underrepresented phyla, enriched non-Westernized populations (40% total SGBs). annotated 2.85 M genes SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). permit deeper analyses increase average mappability metagenomic reads from 67.76% 87.51% (median 94.26%) 65.14% 82.34% mouth. thus identify thousands yet-to-be-named species, pangenomes human-associated microbes, allow better exploitation technologies.

Language: Английский

Citations

1345
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy DOI Creative Commons
Donovan H. Parks, Maria Chuvochina, Christian Rinke

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D785 - D794

Published: Sept. 8, 2021

Abstract The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial 4316 archaeal genomes, 270% increase since introduction of in November, 2017. These are organized into 45 555 2339 species clusters which is 200% integration June, 2019. Here, we explore diversity perspective highlight importance metagenome-assembled expanding available genomic representation. We also discuss improvements to website allow tracking taxonomic changes, easy assessment genome assembly quality, identification assembled type material or used as representatives. Methodological updates policy changes made inception then described along with procedure update GTDB. conclude discussion on use average nucleotide identities pragmatic approach delineating species.

Language: Английский

Citations

1326
A complete domain-to-species taxonomy for Bacteria and Archaea DOI
Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil

et al.

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 38(9), P. 1079 - 1086

Published: April 27, 2020

Language: Английский

Citations

1172
A new genomic blueprint of the human gut microbiota DOI Creative Commons
Alexandre Almeida, Alex Mitchell, Miguel Boland

et al.

Nature, Journal Year: 2019, Volume and Issue: 568(7753), P. 499 - 504

Published: Feb. 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.

Language: Английский

Citations

1126
A unified catalog of 204,938 reference genomes from the human gut microbiome DOI Creative Commons
Alexandre Almeida, Stephen Nayfach, Miguel Boland

et al.

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(1), P. 105 - 114

Published: July 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.

Language: Английский

Citations

983