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

Megataxonomy and global ecology of the virosphere DOI Creative Commons
Eugene V. Koonin, Jens H. Kuhn, Valerian V. Dolja

et al.

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

Published: Jan. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Language: Английский

Citations

25
Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle DOI Creative Commons
Danica T. Schmidtke, Angela Shang-Mei Hickey, Ivan Liachko

et al.

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

Published: March 20, 2024

Summary The prototypic crAssphage ( Carjivirus communis ) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured its lifestyle uncharacterized. For last decade, has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain widespread success. Through genomic analyses culturing, we find uses a phage-plasmid persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, use plaque-free approach measure replication culture with Phocaeicola vulgatus, dorei, Bacteroides stercoris , revealing broad host range. We demonstrate persists hosts without causing major cell lysis events or integrating into chromosomes. ability switch between plasmid within wide range contributes prolific nature human microbiome.

Language: Английский

Citations

13
Factors Affecting Variation of the Human Gut Phageome DOI

Ciara A. Tobin,

Colin Hill, Andrey N. Shkoporov

et al.

Annual Review of Microbiology, Journal Year: 2023, Volume and Issue: 77(1), P. 363 - 379

Published: June 12, 2023

The gut microbiome is a dense and metabolically active consortium of microorganisms viruses located in the lower gastrointestinal tract human body. Bacteria their (phages) are most abundant members microbiome. Investigating biology interplay between two important if we to understand roles health disease. In this review, summarize recent advances resolving taxonomic structure ecological functions complex community phages gut-the phageome. We discuss how age, diet, geography can all have significant impact on phageome composition. note that alterations been observed several diseases such as inflammatory bowel disease, irritable syndrome, colorectal cancer, evaluate whether these changes directly or indirectly contribute disease etiology pathogenesis. also highlight lack standardization studying has contributed variation reported results.

Language: Английский

Citations

11
Gut phages and their interactions with bacterial and mammalian hosts DOI Creative Commons
Marshall Godsil, Nathaniel L. Ritz, Siddarth Venkatesh

et al.

Journal of Bacteriology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

ABSTRACT The mammalian gut microbiome is a dense and diverse community of microorganisms that reside in the distal gastrointestinal tract. In recent decades, bacterial members have been subject intense research. Less well studied large bacteriophages gut, which number billions viral particles per gram feces, consist considerable unknown “dark matter.” This gut-residing bacteriophages, called “phageome,” plays central role through predation transformation native bacteria, interactions with their hosts. this review, we will summarize what known about composition origins phageome, as its homeostasis host health. Furthermore, outline phages hosts, plot course for mechanistic study these systems.

Language: Английский

Citations

0
Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut DOI Creative Commons
Adrián Cortés‐Martín, Rémi Denise, Emma Guerin

et al.

Gut Microbes, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 4, 2024

The human gut microbiome plays a significant role in health and disease. viral component (virome) is predominantly composed of bacteriophages (phages) has received significantly less attention comparison to the bacteriome. This knowledge gap largely due challenges associated with isolation characterization novel phages, bioinformatic hurdles such as lack universal phage marker gene absence sufficient numbers homologs databases. Here, we describe from feces lytic siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, classified within newly proposed Sagittacolavirus genus. In silico biological this presented study. Key φPDS1 was antibiotic-driven selective enrichment bacterial host fecal fermenter. Despite producing plaques lacking genes lysogeny, demonstrates ability coexist liquid culture for multiple days without affecting abundance its host. Multiple studies have shown that changes can be linked various disease states, rendering phage-host pair their interactions particular interest.

Language: Английский

Citations

3
Genome Analysis of Epsilon CrAss-like Phages DOI Creative Commons
Igor V. Babkin, Artem Tikunov, Ivan K. Baykov

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(4), P. 513 - 513

Published: March 27, 2024

CrAss-like phages play an important role in maintaining ecological balance the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to epsilon crAss-like genomes was found. Comparative analysis indicated that divided into two putative genera, which were proposed be named Epsilonunovirus Epsilonduovirus; belongs former. The crAssE-Sib contains diversity-generating retroelement (DGR) cassette with all essential elements, including reverse transcriptase (RT) receptor binding protein (RBP) genes. RT GxxxSP motif its fourth domain instead of usual GxxxSQ found known bacterial DGRs. RBP encoded by other Epsilonunoviruses has unusual structure, no similar proteins addition, encode conserved prophage repressor anti-repressors could involved lysogenic-to-lytic cycle switches. Notably, DNA primase sequences not included monophyletic group formed primases phages. Therefore, substantially differ from phages, indicating need classify these separate family.

Language: Английский

Citations

3
Divergent Gut Microbiota: Archaeal and Bacterial Signatures Unveil Unique Patterns in Colombian Cyclists Compared to Weightlifters and Non‐Athletes DOI

J. V. Aya,

L. C. Vega,

Estefanía Muñoz

et al.

Advanced Biology, Journal Year: 2024, Volume and Issue: 8(6)

Published: March 28, 2024

Abstract Engagement in physical activity, across various sports, promotes a diverse microbiota active individuals. This study examines the gut of Colombian athletes, specifically weightlifters ( n = 16) and road cyclists 13), compared to non‐athletes 15). Using Kruskal–Wallis tests, activity level group non‐athletic individuals sports experience professional athletes is analyzed. The median age participants 24 years, comprising 25 men 19 women. collected using fecal samples. Participants provided these samples during their pre‐competitive stage, concentration phase occurring two weeks prior national competitions. timing chosen capture microbial composition period heightened preparation. Questionnaire responses assessments identify disparities among groups. Microbial analysis explores core microbiome, abundance, taxonomy Pavian, MicrobiomeAnalyst 2.0, GraPhlAn. ANCOM‐BC2 reveals differentially abundant species. Road exhibit decreased Bacteria increased Archaea abundance. Phylum‐level variations included Planctomycetes, Acidobacteria, Proteobacteria, while Bacteroidetes prevailed. Key families influencing are Bacteroidaceae, Muribaculaceae, Selenomonadaceae. Weightlifters unique viral archaeal community connections, showed specialized interplay influenced by endurance exercise. Correlation network emphasizes distinctive interactions within athlete groups, shedding light on impact activities health.

Language: Английский

Citations

3
Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil DOI
Leonardo Bachá, Marcelo de Assis Passos Oliveira, Felipe Schwahofer Landuci

et al.

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 968, P. 178778 - 178778

Published: Feb. 21, 2025

Language: Английский

Citations

0
Understanding the roles of viruses as key players in environmental dynamics and ecosystem functioning DOI Creative Commons
M. Abbasi, Masrure Alam

Discover Viruses., Journal Year: 2025, Volume and Issue: 2(1)

Published: April 17, 2025

Language: Английский

Citations

0
Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome DOI Creative Commons
Yaxiang Wang, Chao Wei, Zhe Chen

et al.

Frontiers in Veterinary Science, Journal Year: 2025, Volume and Issue: 12

Published: April 22, 2025

Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of virome, show high abundance human and have attracted increasing interest. However, few studies been found pigs, distribution crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 phage genomes from 403 metagenomes publicly available a virome dataset constructed by ourselves. These were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that guts distributed four well-known family-level clusters (Alpha, Beta, Zeta, Delta) but absent Gamma Epsilon clusters. Genomic structure identified 149 vOTUs utilize alternative genetic codes. Gene blocks encoding replication assembly proteins varied Approximately 64.73% genes lacked functional annotations, highlighting gap understanding their potential. Numerous anti-CRISPR protein genomes, CAZymes encoded these primarily lysozymes. Host prediction indicated bacterial hosts belonged to Prevotella, Parabacteroides, UBA4372. We observed interactions between Prevotella copri might possible effect on fat deposition pigs. Finally, all detected exhibited low prevalence populations, suggesting heterogeneity compositions. This study provides resources novel insights for investigating phage-bacteria benefits research effects health production traits.

Language: Английский

Citations

0