The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

Cell Host & Microbe, Journal Year: 2020, Volume and Issue: 28(5), P. 724 - 740.e8

Published: Aug. 24, 2020

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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The human virome: assembly, composition and host interactions

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 19(8), P. 514 - 527

Published: March 30, 2021

Language: Английский

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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(7), P. 960 - 970

Published: June 24, 2021

Bacteriophages have important roles in the ecology of human gut microbiome but are under-represented reference databases. To address this problem, we assembled Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available stool metagenomes. Over 75% represent double-stranded DNA phages infect members Bacteroidia and Clostridia classes. Based on sequence clustering identified 54,118 candidate species, 92% which were not found existing The improves detection viruses metagenomes accounts for nearly 40% CRISPR spacers Bacteria Archaea. We also produced a 459,375 protein clusters to explore functional potential virome. This revealed tens thousands diversity-generating retroelements, use error-prone reverse transcription mutate target genes may be involved molecular arms race between their bacterial hosts.

Language: Английский

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Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review

Internal and Emergency Medicine, Journal Year: 2023, Volume and Issue: 19(2), P. 275 - 293

Published: July 28, 2023

Abstract The intestine is the largest interface between internal body and external environment. intestinal barrier a dynamic system influenced by composition of microbiome activity intercellular connections, regulated hormones, dietary components, inflammatory mediators, enteric nervous (ENS). Over years, it has become increasingly evident that maintaining stable crucial to prevent various potentially harmful substances pathogens from entering Disruption referred as 'leaky gut' or leaky gut wall syndrome seems be characterized release bacterial metabolites endotoxins, such lipopolysaccharide (LPS), into circulation. This condition, mainly caused infections, oxidative stress, high-fat diet, exposure alcohol chronic allergens, dysbiosis, appear highly connected with development and/or progression several metabolic autoimmune systemic diseases, including obesity, non-alcoholic fatty liver disease (NAFLD), neurodegeneration, cardiovascular disease, bowel type 1 diabetes mellitus (T1D). In this review, starting description mechanisms enable homeostasis analyzing relationship complex ecosystem pathological conditions, we explore role in driving inflammation, also shedding light on current future therapeutic interventions.

Language: Английский

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INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes

PHAGE, Journal Year: 2021, Volume and Issue: 2(4), P. 214 - 223

Published: Oct. 6, 2021

Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly past decade. Materials Methods: We developed an automated retrieval analysis system for (https://github.com/RyanCook94/inphared) to produce INfrastructure a PHAge REference Database (INPHARED) associated metadata. Results: As January 2021, 14,244 complete sequenced. The INPHARED data set is dominated by phages infect small bacterial genera, with 75% isolated on only 30 genera. There further bias, significantly more lytic (∼70%) than temperate (∼30%) within our database. Collectively, this results ∼54% originating from just three host much debate carriage antibiotic resistance genes their potential safety therapy, we searched putative genes. Frequency gene was found be higher again varied host. Conclusions: Given bias currently genomes, suggest fully understand diversity, efforts should made isolate sequence larger phages, particular greater diversity hosts.

Language: Английский

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Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

International Journal of Molecular Sciences, Journal Year: 2020, Volume and Issue: 21(8), P. 2668 - 2668

Published: April 11, 2020

The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well numerous disease etiologies. Dominated by bacteria, the also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in past two decades, these non-bacterial microorganisms, their functional roles, interaction one another or host immune system have not been widely explored. This review covers recent findings on communities gastrointestinal involvement health disease, particular focus pathophysiology inflammatory bowel disease.

Language: Английский

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Gut Microbiota Interact With the Brain Through Systemic Chronic Inflammation: Implications on Neuroinflammation, Neurodegeneration, and Aging

Frontiers in Immunology, Journal Year: 2022, Volume and Issue: 13

Published: April 7, 2022

It has been noticed in recent years that the unfavorable effects of gut microbiota could exhaust host vigor and life, yet knowledge theory are just beginning to be established. Increasing documentation suggests microbiota–gut–brain axis not only impacts brain cognition psychiatric symptoms but also precipitates neurodegenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s (PD), multiple sclerosis (MS). How blood–brain barrier (BBB), a machinery protecting central nervous system (CNS) from systemic circulation, allows risky factors derived translocated into seems paradoxical. For unique anatomical, histological, immunological properties underpinning its permeable dynamics, BBB regarded biomarker associated with neural pathogenesis. The permeability mice rats caused by GM dysbiosis raises question how metabolites change causes pathophysiology neuroinflammation neurodegeneration (NF&ND) aging, pivotal multidisciplinary field tightly immune chronic inflammation. If all, microbiota-induced inflammation (GM-SCI) mainly refers excessive mucosal immunity dysregulation, which is often influenced dietary components age, produced at interface intestinal (IB) or exacerbated after IB disruption, initiates various common diseases along dispersal routes, eventually impairs integrity cause NF&ND aging. To illustrate roles affected inflammatory “leaky” resulting their metabolites, we reviewed selected publications, including role barrier, influences on permeability, NF&ND, add depth bridging inflammation, plausible mechanism indispensable for corruption was highlighted; namely, maintenance cues cytokines, may help understand play major

Language: Английский

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The microbiome in inflammatory bowel diseases: from pathogenesis to therapy

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(5), P. 331 - 345

Published: June 29, 2020

ABSTRACT Inflammatory bowel disease (IBD) has become a global with accelerating incidence worldwide in the 21st century while its accurate etiology remains unclear. In past decade, gut microbiota dysbiosis consistently been associated IBD. Although many IBD-associated have not proven to be cause or an effect of IBD, it is often hypothesized that at least some alteration microbiome protective causative. this article, we selectively reviewed hypothesis supported by both association studies human and pathogenesis biological models. Specifically, potential bacterial pathways species against as well causative We also roles members mycobiome virome Lastly, covered current status therapeutic approaches targeting microbiome, which promising strategy alleviate cure inflammatory disease.

Language: Английский

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A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(23)

Published: June 3, 2021

Significance Mechanisms of many human chronic diseases involve abnormal action the immune system and/or altered metabolism. The microbiome, an important regulator metabolic and immune-related phenotypes, has been shown to be associated with or participate in development a variety diseases. Viruses bacteria (i.e., “phages”) are ubiquitous mysterious, several studies have that phages exert great control over behavior—and misbehavior—of their host bacteria. This study uses techniques discover analyze 45,000 viruses bodies. abundance 2,000 specific is found correlate common

Language: Английский

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