Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Сен. 6, 2022

Indigenous bacteriophage communities (virome) in the human gut have a huge impact on structure and function of bacterial (bacteriome), but virome variation at population scale is not fully investigated yet. Here, we analyse dsDNA Japanese 4D cohort 4198 deeply phenotyped individuals. By assembling metagenomic reads, discover thousands high-quality phage genomes including previously uncharacterised clades with different hosts than known major ones. The distribution host bacteria strong determinant for phages gut, diversity highly correlated anti-viral defence mechanisms bacteriome, such as CRISPR-Cas restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect structure, age, sex, lifestyle, diet, most which showed consistent associations both their predicted hosts. Among metadata categories, disease medication strongest effects structure. Overall, these results present basis to understand symbiotic viruses will facilitate medical industrial applications indigenous viruses.

Язык: Английский

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Alteration of the Gut Microbiome in Inflammatory Bowel Disease

Digestion, Год журнала: 2022, Номер 104(1), С. 16 - 23

Опубликована: Июль 28, 2022

Alteration of the gut microbial structure and function (dysbiosis) is associated with pathogenesis various disorders including inflammatory bowel disease (IBD).Under normal conditions, β-oxidation butyrate consumes oxygen in colonocytes maintains anaerobic environment lumen. Depletion butyrate-producing bacteria results glycolysis increases diffusion into lumen, leading to a luminal facultative anaerobe expansion. Dysbiosis IBD characterized by reduced abundance phylum Firmicutes (e.g., Faecalibacterium, Roseburia, Ruminococcus) an increase Proteobacteria Enterobacteriaceae). The overall mycobiome differs markedly patients, particularly Crohn's (CD), compared healthy individuals. An genus Candida major contributory factor alteration Japanese CD but Saccharomyces characteristic Western patients. virome, which mainly composed bacteriophages (phages), influences homeostasis pathogenic conditions via interaction bacterial community. Alterations virome have been suggested patients IBD. This may alter either immunogenicity bacteria, thus affecting bacteria-host interactions, or functions such as antibiotic resistance toxin synthesis.Advances DNA sequencing technology bioinformatics revolutionized our understanding microbiome gut.

Язык: Английский

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Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts

Cell Reports, Год журнала: 2022, Номер 38(2), С. 110204 - 110204

Опубликована: Янв. 1, 2022

The crAss-like phages are a diverse group of related viruses that includes some the most abundant human gut. To explore their diversity and functional role in population clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals Netherlands. We identify 1,556 phage genomes, including 125 species-level 32 genus-level clusters absent reference databases used. Analysis genomic features shows closely can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction hosts points primarily to bacteria phylum Bacteroidetes, consistent with previous reports. Finally, temporal stability over 4-year period associations between abundance several phenotypes, depletion inflammatory bowel disease patients.

Язык: Английский

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Opportunities and Challenges of Data-Driven Virus Discovery

Biomolecules, Год журнала: 2022, Номер 12(8), С. 1073 - 1073

Опубликована: Авг. 4, 2022

Virus discovery has been fueled by new technologies ever since the first viruses were discovered at end of 19th century. Starting with mechanical devices that provided evidence for virus presence in sick hosts, gradually transitioned into a sequence-based scientific discipline, which, nowadays, can characterize identity and explore viral diversity an unprecedented resolution depth. Sequencing are now being used routinely ever-increasing scales, producing avalanche novel sequences found multitude organisms environments. In this perspective article, we argue started to undergo another transformation prompted emergence approaches sequence data-centered primarily computational, setting them apart from previous technology-driven innovations. The data-driven approach is largely uncoupled collection processing biological samples, exploits availability massive amounts publicly freely accessible data sequencing archives. We discuss open challenges be solved order unlock full potential discovery, highlight benefits it bring classical (mostly molecular) virology molecular biology general.

Язык: Английский

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Signals triggering prophage induction in the gut microbiota

Molecular Microbiology, Год журнала: 2022, Номер 118(5), С. 494 - 502

Опубликована: Сен. 27, 2022

Compared to bacteria of the gut microbiota, bacteriophages are still poorly characterised, and their physiological importance is far less known. Temperate phages probably a major actor in gut, as it estimated that 80% intestinal lysogens, meaning they carrying prophages. In addition, prophage induction rates higher than vitro. However, studies on signals leading have essentially focused genotoxic agents with poor relevance for this environment. review, we sum up recent findings about able trigger gut. Three categories at play: those originating from interactions between microbes, human or animal host physiology external intakes. These results highlight diversity factors influencing start unveil ways by which microbiota composition may be modulated.

Язык: Английский

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Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence

Neural Regeneration Research, Год журнала: 2023, Номер 19(4), С. 833 - 845

Опубликована: Авг. 14, 2023

A growing body of evidence suggests that the gut microbiota contributes to development neurodegenerative diseases via microbiota-gut-brain axis. As a contributing factor, dysbiosis always occurs in pathological changes diseases, such as Alzheimer's disease, Parkinson's and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped reveal bidirectional communication between central nervous system enteric is facilitated by microbiota's diverse microorganisms, for both neuroimmune neuroendocrine systems. Here, we summarize bioinformatics analysis wet-biology validation metagenomics with an emphasis on multi-omics studies virome. The pathogen-associated signaling biomarkers identifying brain disorders potential therapeutic targets are also elucidated. Finally, discuss role diet, prebiotics, probiotics, postbiotics exercise interventions remodeling microbiome reducing symptoms diseases.

Язык: Английский

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Antibiotic resistance genes, mobile elements, virulence genes, and phages in cultivated ESBL-producing Escherichia coli of poultry origin in Kwara State, North Central Nigeria

International Journal of Food Microbiology, Год журнала: 2023, Номер 389, С. 110086 - 110086

Опубликована: Янв. 21, 2023

The paucity of information on the genomic diversity drug-resistant bacteria in most food-producing animals, including poultry Nigeria, has led to poor hazard characterization and lack critical control points safeguard public health. Hence, this study used whole genome sequencing (WGS) assess presence antibiotic resistance genes, mobile genetic elements, virulence phages Extended Spectrum Beta Lactamase producing Escherichia coli (ESBL - E. coli) isolates obtained from via EURL guideline 2017 Ilorin, Nigeria. prevalence ESBL was 10.5 % (n = 37/354). phenotypic susceptibility testing showed that all ESBL- were multi-drug resistant (MDR). in-silico analysis WGS raw-read data 11 purposively selected had a wide array ARGs conferred beta-lactam antibiotics, 8 other classes antibiotics (fluoroquinolones, foliate pathway antagonists, aminoglycoside, phenicol, tetracycline, epoxide, macrolides, rifamycin). All bacterial chromosome except two where plasmid-mediated quinolone (PMQR) detected. Two carried gyrAp.S83L mutation which confers certain fluoroquinolones. mobilome consisted several Col-plasmids predominant IncF plasmids belonged IncF64:A-:B27 sequence type. virulome genes function as adhesins, iron acquisition toxins, protectins. Intact found phageome representatives four families viruses: Myoviridae (62.5 %, n 5/8), Siphoviridae (37.5 3/8), Inoviridae (12.5 1), Podoviridae 1/8). harboured 1-5 intact no identified any phages. Although five phylogroup A, diverse they different serotype types. Our findings demonstrate high origin These harbor clinically relevant ARGs, may have detrimental zoonotic potentials human

Язык: Английский

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Phage-inclusive profiling of human gut microbiomes with Phanta

Nature Biotechnology, Год журнала: 2023, Номер 42(4), С. 651 - 662

Опубликована: Май 25, 2023

Язык: Английский

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The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Авг. 14, 2023

The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol conservation, are believed to be involved in host's dietary switch fibrous bamboo diet. However, their exact roles still largely unknown.In this study, we first comprehensively analyzed large number metagenomes pandas (n = 322), including 98 sequenced study with deep sequencing (Illumina) and third-generation (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), 148 which (36.27%) were near complete. most abundant MAG was classified as Streptococcus alactolyticus. A pairwise comparison meta-transcriptomes 14 feces revealed genes carbohydrate metabolism lower, but those protein greater abundance expression compared herbivores omnivores. Of note, S. alactolyticus positively correlated KEGG modules essential amino-acid biosynthesis. After being isolated from gavaged mice, significantly increased relative amino acids mice jejunum.The highlights unique metabolic profiles panda's microbiome. findings suggest that is an important player contributes adaptation by more involvement rather than metabolism. Video Abstract.

Язык: Английский

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The infant gut virome is associated with preschool asthma risk independently of bacteria

Nature Medicine, Год журнала: 2023, Номер 30(1), С. 138 - 148

Опубликована: Дек. 15, 2023

Язык: Английский

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