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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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Cell, Год журнала: 2019, Номер 176(3), С. 649 - 662.e20

Опубликована: Янв. 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.

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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Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

Nature, Год журнала: 2019, Номер 574(7776), С. 117 - 121

Опубликована: Сен. 18, 2019

Язык: Английский

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The gut microbiome: Relationships with disease and opportunities for therapy

The Journal of Experimental Medicine, Год журнала: 2018, Номер 216(1), С. 20 - 40

Опубликована: Окт. 15, 2018

Over the past decade, our view of human-associated microbes has expanded beyond that a few species toward an appreciation diverse and niche-specialized microbial communities develop in human host with chronological age. The largest reservoir exists distal gastrointestinal tract, both lumen, where facilitate primary secondary metabolism, on mucosal surfaces, they interact immune cell populations. While local microbial-driven immunomodulation gut is well described, more recent studies have demonstrated role for microbiome influencing remote organs hematopoietic function. Unsurprisingly, therefore, perturbation to composition function microbiota been associated chronic diseases ranging from inflammatory metabolic conditions neurological, cardiovascular, respiratory illnesses. Considerable effort currently focused understanding natural history development humans context health outcomes, parallel improving knowledge microbiome-host molecular interactions. These efforts ultimately aim effective approaches rehabilitate perturbed ecosystems as means restore or prevent disease. This review details modulating focus discusses strategies manipulating management prevention conditions.

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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The Role of Lung and Gut Microbiota in the Pathology of Asthma

Immunity, Год журнала: 2020, Номер 52(2), С. 241 - 255

Опубликована: Фев. 1, 2020

Язык: Английский

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The Gut Microbiota in the First Decade of Life

Trends in Microbiology, Год журнала: 2019, Номер 27(12), С. 997 - 1010

Опубликована: Авг. 29, 2019

Appreciation of the importance gut microbiome is growing, and it becoming increasingly relevant to identify preventive or therapeutic solutions targeting it. The composition function microbiota are relatively well described for infants (less than 3 years) adults, but have been largely overlooked in pre-school (3-6 primary school-age (6-12 children, as teenagers (12-18 years). Early reports suggested that infant would attain an adult-like structure at age years, recent studies development may take longer. This time key because there evidence suggest deviations this consequences later life. In review, we provide overview current knowledge concerning microbiota, its evolution, variation, response dietary challenges during first decade life with a focus on healthy children (up 12 from various populations around globe. should facilitate identification diet-based approaches individuals group, promote

Язык: Английский

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Prevotella diversity, niches and interactions with the human host

Nature Reviews Microbiology, Год журнала: 2021, Номер 19(9), С. 585 - 599

Опубликована: Май 28, 2021

Язык: Английский

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Impact of antibiotics on the human microbiome and consequences for host health

MicrobiologyOpen, Год журнала: 2022, Номер 11(1)

Опубликована: Янв. 13, 2022

It is well established that the gut microbiota plays an important role in host health and perturbed by several factors including antibiotics. Antibiotic-induced changes microbial composition can have a negative impact on reduced diversity, functional attributes of microbiota, formation, selection antibiotic-resistant strains making hosts more susceptible to infection with pathogens such as Clostridioides difficile. Antibiotic resistance global crisis increased use antibiotics over time warrants investigation into its effects health. In this review, we discuss adverse thus health, suggest alternative approaches antibiotic use.

Язык: Английский

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