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

eLife, Год журнала: 2021, Номер 10

Опубликована: Май 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.

Язык: 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, Год журнала: 2021, Номер 50(D1), С. D785 - D794

Опубликована: Сен. 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.

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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Gut Microbiome: Profound Implications for Diet and Disease

Nutrients, Год журнала: 2019, Номер 11(7), С. 1613 - 1613

Опубликована: Июль 16, 2019

The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders colorectal cancer. Of increasing prevalence Western societies, these conditions carry a high burden care. Dietary patterns environmental factors have profound effect on shaping microbiota real time. Diverse populations intestinal bacteria mediate their beneficial effects through fermentation dietary fiber produce short-chain fatty acids, endogenous signals with roles lipid homeostasis reducing inflammation. Recent progress shows that individual's starting microbial profile is key determinant predicting response intervention live probiotics. complex challenging characterize. Enterotypes been proposed using metrics such as alpha species diversity, ratio Firmicutes Bacteroidetes phyla, relative abundance genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition bacterial are linked physiologic along different axes. We review diet quality, carbohydrate intake, fermentable FODMAPs, prebiotic maintaining healthy flora. implications discussed for various including obesity, diabetes, irritable bowel syndrome, inflammatory disease, depression, cardiovascular disease.

Язык: Английский

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The microbiome and human cancer

Science, Год журнала: 2021, Номер 371(6536)

Опубликована: Март 25, 2021

Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors immunotherapy, engineerable to treat metastases. Despite these findings, the number of microbes known directly cause carcinogenesis remains small. Critically evaluating building frameworks such evidence light modern biology is an important task. In this Review, we delineate between causal complicit trace common themes their influence through host's immune system, herein defined as immuno-oncology-microbiome axis. We further review intratumoral approaches manipulate gut or tumor microbiome while projecting next phase experimental discovery.

Язык: Английский

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DRAM for distilling microbial metabolism to automate the curation of microbiome function

Nucleic Acids Research, Год журнала: 2020, Номер 48(16), С. 8883 - 8900

Опубликована: Июль 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.

Язык: Английский

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A genomic catalog of Earth’s microbiomes

Nature Biotechnology, Год журнала: 2020, Номер 39(4), С. 499 - 509

Опубликована: Ноя. 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.

Язык: Английский

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New insights from uncultivated genomes of the global human gut microbiome

Nature, Год журнала: 2019, Номер 568(7753), С. 505 - 510

Опубликована: Март 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.

Язык: Английский

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Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer

Gastroenterology, Год журнала: 2019, Номер 158(2), С. 322 - 340

Опубликована: Окт. 3, 2019

Язык: Английский

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

Nature Biotechnology, Год журнала: 2023, Номер 41(11), С. 1633 - 1644

Опубликована: Фев. 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.

Язык: Английский

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