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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Local and systemic mechanisms linking periodontal disease and inflammatory comorbidities

Nature reviews. Immunology, Journal Year: 2021, Volume and Issue: 21(7), P. 426 - 440

Published: Jan. 28, 2021

Language: Английский

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Gut microbiota in colorectal cancer: mechanisms of action and clinical applications

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2019, Volume and Issue: 16(11), P. 690 - 704

Published: Sept. 25, 2019

Language: Английский

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The microbiome and human cancer

Science, Journal Year: 2021, Volume and Issue: 371(6536)

Published: March 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.

Language: Английский

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

Gastroenterology, Journal Year: 2019, Volume and Issue: 158(2), P. 322 - 340

Published: Oct. 3, 2019

Language: Английский

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Rising incidence of early-onset colorectal cancer — a call to action

Nature Reviews Clinical Oncology, Journal Year: 2020, Volume and Issue: 18(4), P. 230 - 243

Published: Nov. 20, 2020

Language: Английский

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The rising tide of early-onset colorectal cancer: a comprehensive review of epidemiology, clinical features, biology, risk factors, prevention, and early detection

˜The œLancet. Gastroenterology & hepatology, Journal Year: 2022, Volume and Issue: 7(3), P. 262 - 274

Published: Jan. 26, 2022

Language: Английский

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Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis

Cell Host & Microbe, Journal Year: 2022, Volume and Issue: 30(3), P. 289 - 300

Published: March 1, 2022

Language: Английский

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The Intestinal Microbiota and Colorectal Cancer

Frontiers in Immunology, Journal Year: 2020, Volume and Issue: 11

Published: Nov. 30, 2020

The intestinal microbiota, composed of a large population microorganisms, is often considered "forgotten organ" in human health and diseases. Increasing evidence indicates that dysbiosis the microbiota closely related to colorectal cancer (CRC). roles for microorganisms initiated facilitated CRC process are becoming increasingly clear. Hypothesis models have been proposed illustrate complex relationship between CRC. Recent studies identified Streptococcus bovis, enterotoxigenic Bacteroides fragilis, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius as candidate pathogens. In this review, we summarized mechanisms involved microbiota-related carcinogenesis, including inflammation, pathogenic bacteria, their virulence factors, genotoxins, oxidative stress, bacterial metabolites, biofilm. We also described clinical values novel strategies preventing treating

Language: Английский

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Small molecule metabolites: discovery of biomarkers and therapeutic targets

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 20, 2023

Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks diseases. Metabolite signatures that have close proximity subject's phenotypic informative dimension, are useful for predicting diagnosis prognosis diseases as well monitoring treatments. The lack early biomarkers could poor serious outcomes. Therefore, noninvasive methods with high specificity selectivity desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool biomarker pathway analysis, revealing possible mechanisms human various deciphering therapeutic potentials. It help identify functional related variation delineate biochemical changes indicators pathological damage prior disease development. Recently, scientists established large number profiles reveal underlying networks target exploration in biomedicine. This review summarized analysis on potential value small-molecule candidate metabolites clinical events, may better diagnosis, prognosis, drug screening treatment. We also discuss challenges need be addressed fuel next wave breakthroughs.

Language: Английский

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