Next-Generation Sequencing-Based Monitoring of Intestinal Bacteria and Bacteriophages Following Fecal Microbiota Transplantation in Inflammatory Bowel Diseases DOI Creative Commons
Oleg V. Goloshchapov, О. Б. Щукина, Aleksey V. Kusakin

et al.

Pathogens, Journal Year: 2023, Volume and Issue: 12(12), P. 1438 - 1438

Published: Dec. 11, 2023

Inflammatory bowel diseases (IBD) and acute graft-versus-host disease (GVHD) are associated with persistent intestinal dysfunction preceded by gut bacterial dysbiosis. There limited data on bacteriophages in these conditions. The aim of the present work was to detect associations between dominant bacteria means 16S rRNA gene sequencing, some clinically significant viruses detected a customized primer panel for NGS-based study. clinical group included patients Crohn’s (IBD, n = 9), or GVHD (n 6) subjected fecal microbiota transplantation (FMT) from healthy donors. stool specimens were taken initially, 5 times post-FMT until day 120. Using NGS approach, we have found higher abundance Proteobacterota phylum GVHD, especially, at later terms post-FMT. Moreover, an early increase Klebsiella E. coli/Shigella along decreased relative content Faecalibacterium. Upon evaluation phageome, amount Caudoviricetes class GVHD. A correlation Proteobacteria Caudoviricetes, thus suggesting their association during period. amounts five phage species showed distinct correlations Enterococcus ratios different FMT. In conclusion, parallel use sequencing targeted viral is feasible useful option tracing specific strains microbiota. developed array primers may be extended other phages infecting relevant bacteria.

Language: Английский

CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing DOI Creative Commons
David Tavares Martins, Oscar Victor Cardenas-Alegría, Carlos Willian Dias Dantas

et al.

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 25, 2025

ABSTRACT Viruses are the most abundant biological entities in all ecosystems of world. Their ubiquity makes them suitable candidates for indicating fecal contamination rivers. Recently, a group Bacteroidetes bacteriophages named CrAssphages, which highly abundant, sensitive, and specific to human feces, were studied as potential viral biomarkers pollution water bodies. In this study, we evaluated presence, diversity, abundance viruses with focus on crAssphages via metagenomic analysis an Amazonian river conducted correlation analyses basis physicochemical georeferencing data. Several significant differences alpha diversity indexes observed among sample points, suggesting accumulation organisms mouth, whereas beta revealed divergence between replicates downstream point (IT4) when compared rest samples, possibly due increased impact at point. terms presence crAssphage, identified 61 crAssphage contigs distributed along Itacaiúnas River. Moreover, our correlations 19 population density, substantiating use these possible markers This study is first assess river, results Amazon. IMPORTANCE The Amazon biome one diverse world contains vast network; however, continuous advance urban centers toward aquatic bodies exacerbates discharge pollutants into Fecal contributes significantly pollution, application improved indicator essential evaluating quality. performed data test whether viable markers. Our both their showed relative density. These suggest quality assessment

Language: Английский

Citations

0
Dynamics of CRISPR-mediated virus–host interactions in the human gut microbiome DOI Creative Commons

Adrián López-Beltrán,

João Botelho, Jaime Iranzo

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying interactions among bacteria, plasmids, phages. Here, we used longitudinal metagenomic data from 130 healthy diseased individuals study how interplay parasites immunity reflects on dynamics human gut microbiome. Based coordinated 80 000 loci their targets, show that effectively modulates bacteriophage abundances gut. Acquisition typically leads a decrease abundance lytic phages but does not necessarily cause complete disappearance. Much smaller effects observed for lysogenic plasmids. Conversely, phage-CRISPR shape bacterial microdiversity producing weak selective sweeps benefit immune host lineages. We also distal (and chronologically older) regions CRISPR arrays enriched spacers potentially functional target crass-like local prophages. This suggests exposure reactivated prophages other endemic viruses is pressure drives maintenance long-lasting memory.

Language: Английский

Citations

3
Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage DOI Creative Commons
Patrick A. de Jonge, Bert‐Jan H. van den Born, Aeilko H. Zwinderman

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 27, 2024

Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and immune system. Most microbiome viruses bacteriophages, which exclusively infect bacteria. Until recently, most virome studies focused on low taxonomic resolution (e.g., viral operational units), hampering population-level analyses. We previously identified an expansive widespread bacteriophage lineage in inhabitants Amsterdam, Netherlands. Here, we study their biodiversity evolution various populations. Based a phylogeny using sequences from six genome databases, propose Candidatus order Heliusvirales. identify heliusviruses 82% 5441 individuals across 39 studies, nine metagenomes humans that lived Europe North America between 1000 5000 years ago. show large started to diversify when Homo sapiens first appeared some 300,000 Ancient peoples modern hunter-gatherers have distinct Ca. Heliusvirales populations lower richness than urbanized people. Urbanized people suffering type 1 2 diabetes, as well inflammatory bowel disease, higher healthy controls. thus conclude these ancient members thrived increasingly westernized lifestyles. based analyses authors new lineage, Heliusvirales, 5,441 1,000 5,000 ago, revealing associations diseases.

Language: Английский

Citations

3
Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes DOI Creative Commons
Suet‐Ying Kwan,

Caroline M. Sabotta,

Lorenzo R. Cruz

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(9)

Published: Aug. 22, 2024

Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of gut microbiome in MASLD, studies determining involvement phageome scarce. In this cross-sectional study, we characterized South Texas stool shotgun metagenomic sequencing 340 subjects, concurrently screened for steatosis transient elastography. Inter-individual variations were associated gender, country birth, diabetes, and steatosis. The phage signatures diabetes subsequently determined. Enrichment

Language: Английский

Citations

2
Stable coexistence between an archaeal virus and the dominant methanogen of the human gut DOI Creative Commons
Diana P. Baquero, Sofia Medvedeva, Camille Martin‐Gallausiaux

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 4, 2024

Language: Английский

Citations

2
Metagenomic Study Reveals Phage–Bacterial Interactome Dynamics in Gut and Oral Microbiota in Pancreatic Diseases DOI Open Access
Laura Vilà-Quintana, Esther Fort, Laura Pardo

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(20), P. 10988 - 10988

Published: Oct. 12, 2024

Individuals with pancreatic-related health conditions usually show lower diversity and different composition of bacterial viral species between the gut oral microbiomes compared to healthy individuals. We performed a thorough microbiome analysis, using deep shotgun sequencing stool saliva samples obtained from patients chronic pancreatitis (CP), pancreatic ductal adenocarcinoma (PDAC), controls (HCs).We observed similar microbiota at level in both PDAC HCs, among which most distinctive finding was that abundance oral-originated

Language: Английский

Citations

2
Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome DOI Creative Commons

Adrián López-Beltrán,

João Botelho, Jaime Iranzo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 23, 2024

Abstract Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying interactions among bacteria, plasmids, phages. Here, we used longitudinal metagenomic data from 130 healthy diseased individuals study how interplay parasites immunity reflects on dynamics human gut microbiome. Based coordinated 80,000 loci their targets, show that effectively modulates bacteriophage abundances gut. Acquisition typically leads a decrease abundance lytic phages, but does not necessarily cause complete disappearance. Much smaller effects observed for lysogenic phages plasmids. Conversely, phage-CRISPR shape bacterial microdiversity producing weak selective sweeps benefit immune host lineages. Interestingly, distal (and chronologically older) regions CRISPR arrays enriched spacers potentially functional target crass-like local prophages. This suggests exposure reactivated prophages other endemic viruses is pressure drives maintenance long-lasting memory.

Language: Английский

Citations

1
Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages DOI Creative Commons
Adrián Cortés‐Martín, Colin Buttimer,

Jessie L. Maier

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 17, 2024

Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies overcome these defences. Among most abundant crAss-like that infect members Bacteroidales, particular

Language: Английский

Citations

1
Characteristics of phage-plasmids and their impact on microbial communities DOI Creative Commons

Ruweyda Sayid,

Anne W.M. van den Hurk,

Daniela Rothschild-Rodriguez

et al.

Essays in Biochemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 29, 2024

Abstract Bacteria host various foreign genetic elements, most notably plasmids and bacteriophages (or phages). Historically, these two classes were seen as separate, but recent research has shown considerable interplay between them. Phage-plasmids (P-Ps) exhibit characteristics of both phages plasmids, allowing them to exist extrachromosomally within bacterial hosts also infect lyse bacteria phages. This dual functionality enables P-Ps utilize the modes transmission phage facilitating rapid dissemination material, including antibiotic resistance virulence genes, throughout populations. Additionally, have been found encode toxin-antitoxin CRISPR-Cas adaptive immune systems, which enhance survival under stress provide immunity against other elements. Despite a growing body literature on P-Ps, large gaps remain in our understanding their ecological roles environmental prevalence. review aims synthesise existing knowledge identify impacts microbial communities.

Language: Английский

Citations

1
Dynamic nature of viral and bacterial communities in human faeces DOI Creative Commons
Andrey N. Shkoporov,

Orla O’Regan,

L. J. Smith

et al.

iScience, Journal Year: 2023, Volume and Issue: 27(2), P. 108778 - 108778

Published: Dec. 29, 2023

Bacteriophages are a major component of the gut microbiome and believed to play role in establishment stabilization microbial communities by influencing taxonomic functional diversity. We show that activity lytic temperate phages can also significantly affect bacterial community structure model extended colonic retention. Intact fresh human feces were incubated anaerobically at 37°C without homogenization subjected metagenomic sequencing. observed subject-specific blooms collapses selected bacteriophage populations within some individuals. Most notable striking Prevotella accompanied increases specific bacteriophages. In number cases, we even shift from one "enterotype" another 48 h. These results confirm intact represents highly dynamic ecological system suggests retention time could have profound effect on composition, including significant impact

Language: Английский

Citations

3