Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Nature Biotechnology, Год журнала: 2019, Номер 37(8), С. 852 - 857

Опубликована: Июль 24, 2019

Язык: Английский

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PICRUSt2 for prediction of metagenome functions

Nature Biotechnology, Год журнала: 2020, Номер 38(6), С. 685 - 688

Опубликована: Июнь 1, 2020

Язык: Английский

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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Nature, Год журнала: 2019, Номер 569(7758), С. 655 - 662

Опубликована: Май 29, 2019

Abstract Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. colitis are complex diseases that heterogeneous at the clinical, immunological, molecular, genetic, microbial levels. Individual contributing factors have been focus of extensive research. As part Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles host activity during (up 24 time points each; in total 2,965 stool, biopsy, blood specimens). Here present results, provide a comprehensive view functional dysbiosis gut microbiome inflammatory activity. We demonstrate characteristic increase facultative anaerobes expense obligate anaerobes, as well disruptions transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, short-chain fatty acids), levels antibodies serum. Periods were also marked by increases temporal variability, with taxonomic, functional, biochemical shifts. Finally, integrative analysis identified microbial, biochemical, central this dysregulation. The study’s infrastructure resources, data, available through Bowel Disease Multi’omics Database ( http://ibdmdb.org ), most description date activities diseases.

Язык: Английский

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Gut microbiome structure and metabolic activity in inflammatory bowel disease

Nature Microbiology, Год журнала: 2018, Номер 4(2), С. 293 - 305

Опубликована: Ноя. 28, 2018

Язык: Английский

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Multivariable association discovery in population-scale meta-omics studies

PLoS Computational Biology, Год журнала: 2021, Номер 17(11), С. e1009442 - e1009442

Опубликована: Ноя. 16, 2021

It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata microbial community measurements, due in part their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often the form of count compositional measurements. Here we introduce an optimized combination novel established methodology assess multivariable association with complex population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations Linear Models), uses generalized linear mixed models accommodate a wide variety modern epidemiological studies, including cross-sectional longitudinal designs, well data types (e.g., counts relative abundances) without covariates repeated To construct this method, conducted large-scale evaluation broad range scenarios under which straightforward identification meta-omics associations can be challenging. These simulation studies reveal that 2’s model preserves statistical power presence measures multiple covariates, while accounting for nuances controlling false discovery. We also applied dataset from Integrative Human (HMP2) project which, addition reproducing results, revealed unique, integrated landscape inflammatory bowel diseases (IBD) across time points omics profiles.

Язык: Английский

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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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Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

Nature Genetics, Год журнала: 2019, Номер 51(4), С. 600 - 605

Опубликована: Фев. 18, 2019

Язык: Английский

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Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

Science, Год журнала: 2020, Номер 371(6529), С. 602 - 609

Опубликована: Дек. 10, 2020

New fecal microbiota for cancer patients The composition of the gut microbiome influences response to immunotherapies. Baruch et al. and Davar report first-in-human clinical trials test whether transplantation (FMT) can affect how metastatic melanoma respond anti–PD-1 immunotherapy (see Perspective by Woelk Snyder). Both studies observed evidence benefit in a subset treated patients. This included increased abundance taxa previously shown be associated with anti–PD-1, CD8 + T cell activation, decreased frequency interleukin-8–expressing myeloid cells, which are involved immunosuppression. These provide proof-of-concept ability FMT Science , this issue p. 602 595 ; see also 573

Язык: Английский

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The Integrative Human Microbiome Project

Nature, Год журнала: 2019, Номер 569(7758), С. 641 - 648

Опубликована: Май 29, 2019

Abstract The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, discoveries that link interactions between humans their microbiomes health-related outcomes. recently completed second phase, the Integrative Project, comprised studies of dynamic changes in microbiome host under three conditions: pregnancy preterm birth; inflammatory bowel diseases; stressors affect individuals with prediabetes. associated research begins elucidate mechanisms host–microbiome these conditions, provides unique data resources (at HMP Data Coordination Center), represents a paradigm for future multi-omic human microbiome.

Язык: Английский

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