Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

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

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GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

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

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A complete domain-to-species taxonomy for Bacteria and Archaea

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

Published: April 27, 2020

Language: Английский

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

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

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GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Bioinformatics, Journal Year: 2022, Volume and Issue: 38(23), P. 5315 - 5316

Published: Oct. 11, 2022

Abstract Summary The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, growing size of GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts memory (∼320 GB) which limits its adoption ease use. Here, we present an update to that uses a divide-and-conquer approach where user genomes are initially placed into with family-level representatives followed placement appropriate class-level subtree comprising species representatives. This substantially reduces requirements while having minimal impact on classification. Availability implementation is implemented Python licenced under GNU General Public Licence v3.0. Source code documentation available at: https://github.com/ecogenomics/gtdbtk. Supplementary information data at Bioinformatics online.

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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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(11), P. 1633 - 1644

Published: Feb. 23, 2023

Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified at the species level. 4 explains ~20% reads in international human gut microbiomes >40% less-characterized environments such as rumen microbiome proves accurate than available alternatives on synthetic evaluations while also reliably quantifying with no cultured isolates. Application method to >24,500 metagenomes highlights previously undetected be strong biomarkers host conditions lifestyles mouse shows that even uncharacterized genetically profiled resolution single strains.

Language: Английский

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Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: May 21, 2021

Abstract Background In gut microbiome studies, the cultured microbial resource plays essential roles, such as helping to unravel functions and host-microbe interactions. Although several major studies have been performed elucidate human microbiota, up 70% of Unified Human Gastrointestinal Genome species not date. Large-scale isolation identification well availability public are imperative for further characterizing functions. Results this study, we constructed a Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn ) through cultivation 10,558 isolates from 31 sample mixtures 239 fresh fecal samples healthy Chinese volunteers, deposited 1170 strains representing 400 different in culture collections International Depository Authority long-term preservation access worldwide. Following rules Code Nomenclature Prokaryotes, 102 new were characterized denominated, while 28 genera 3 families proposed. hGMB represented over 80% common dominant global 16S rRNA gene amplicon data ( n = 11,647) 24 “most-wanted” “medium priority” taxa proposed by Microbiome Project. We total sequenced 115 genomes novel 13 previously known species. Further silico analysis revealed that newly 22 uncultured (UHGG) contributed representatives potentially “dark taxa” had discovered UHGG. The nonredundant catalogs generated covered 50% functionally genes (KEGG orthologs) largest approximately 10% “most wanted” unknown proteins FUnkFams database. Conclusions A publicly accessible (hGMB) was established contained represents expands resources genomic repository adding species, genera, families, microbes.

Language: Английский

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Massive expansion of human gut bacteriophage diversity

Cell, Journal Year: 2021, Volume and Issue: 184(4), P. 1098 - 1109.e9

Published: Feb. 1, 2021

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database, a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters (VCs) are not restricted to single species, across phylogenetically distinct species. Epidemiological analysis uncovered 280 VCs found at least 5 continents highly prevalent phage clade with features reminiscent p-crAssphage. This high-quality, large-scale catalog will improve future virome studies enable bacteriophages.

Language: Английский

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