Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis DOI Creative Commons
Michael J. Tisza, Richard E. Lloyd, Kristi L. Hoffman

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 29, 2023

Abstract Humans are colonized with commensal bacteria soon after birth, and, while this colonization is affected by lifestyle and other factors, bacterial proceeds through well-studied phases. However, less known about phage communities in early human development due to small study sizes, inability leverage large databases, lack of appropriate bioinformatics tools. In study, whole genome shotgun sequencing data from the TEDDY composed 12,262 longitudinal samples 887 children 4 countries, reanalyzed assess dynamics simultaneously. Reads these were mapped marker genes both a new database tens thousands taxa microbiomes. We uncover that each child hundreds different phages during years, more transitory than bacteria. Participants’ continually harbor species over time whereas diversification begins saturate. Phage improves ability for machine learning models discriminate country. Finally, populations individual-specific, striking patterns arose larger dataset, showing clear trends ecological succession amongst phages, which correlated well putative host Improved understanding phage-bacterial relationships may reveal means shape modulate microbiome its constituents improve health reduce disease, particularly vulnerable where antibiotic use and/or drastic measures not be advised.

Language: Английский

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models DOI Creative Commons
Guillermo Rangel-Piñeros, Alexandre Almeida, Martín Beracochea

et al.

PLoS Computational Biology, Journal Year: 2023, Volume and Issue: 19(8), P. e1011422 - e1011422

Published: Aug. 28, 2023

The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations sparked widespread interest in developing computational strategies that support comprehensive characterisation based sequencing data. Here we introduce VIRify, a new pipeline designed to provide user-friendly accurate functional taxonomic communities. VIRify identifies contigs prophages from metagenomic assemblies annotates them using collection profile hidden Markov models (HMMs). include our manually-curated HMMs, which serve as specific markers for wide range prokaryotic eukaryotic taxa are thus used reliably classify contigs. We tested two microbial mock communities, large metagenomics study, publicly available genomic sequences human gut. results showed could identify both viruses, provided classifications genus family rank with an average accuracy 86.6%. In addition, allowed detection classification viruses present 243 marine assemblies. Finally, use led expansion number taxonomically classified gut improvement outdated shallow classifications. Overall, demonstrate is novel powerful resource offers enhanced capability detect broad them.

Language: Английский

Citations

19
Infant gut DNA bacteriophage strain persistence during the first 3 years of life DOI Creative Commons
Yue Clare Lou,

LinXing Chen,

Adair L. Borges

et al.

Cell Host & Microbe, Journal Year: 2023, Volume and Issue: 32(1), P. 35 - 47.e6

Published: Dec. 13, 2023

Bacteriophages are key components of gut microbiomes, yet the phage colonization process in infant remains uncertain. Here, we establish a large sequence database and use strain-resolved analyses to investigate DNA succession infants throughout first 3 years life. Analysis 819 fecal metagenomes collected from 28 full-term 24 preterm their mothers revealed that early-life phageome richness increases over time reaches adult-like complexity by age 3. Approximately 9% early colonizers, which mostly maternally transmitted infect Bacteroides, persist for more prevalent than infants. Although rare, phages with stop codon reassignment likely non-recoded generally display an increase in-frame reassigned codons years. Overall, maternal seeding, reassignment, host CRISPR-Cas locus prevalence, diverse populations contribute stable viral colonization.

Language: Английский

Citations

17
Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads DOI Creative Commons
Manuel Bernabeu,

Elena Cabello-Yeves,

Eduard Flores Ventura

et al.

Current Opinion in Microbiology, Journal Year: 2024, Volume and Issue: 77, P. 102424 - 102424

Published: Jan. 21, 2024

Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well infant gut microbiome. Antibiotic exposure, mode of delivery breastfeeding practices modulate reservoir antibiotic resistance genes (ARGs). Vertical horizontal microbial gene transfer during early mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview current knowledge on in mother–infant dyad through vertical transmission highlight main gaps challenges area.

Language: Английский

Citations

6
Engineering Phages to Fight Multidrug-Resistant Bacteria DOI Creative Commons
Huan Peng, Irene A. Chen, Udi Qimron

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 16, 2024

Facing the global "superbug" crisis due to emergence and selection for antibiotic resistance, phages are among most promising solutions. Fighting multidrug-resistant bacteria requires precise diagnosis of bacterial pathogens specific cell-killing. Phages have several potential advantages over conventional antibacterial agents such as host specificity, self-amplification, easy production, low toxicity well biofilm degradation. However, narrow range, uncharacterized properties, risks from exponential replication evolution natural phages, currently limit their applications. Engineering can not only enhance range improve phage efficacy, but also confer new functions. This review first summarizes major engineering techniques including both chemical modification genetic engineering. Subsequent sections discuss applications engineered pathogen detection ablation through interdisciplinary approaches synthetic biology nanotechnology. We future directions persistent challenges in ongoing exploration control.

Language: Английский

Citations

5
Metagenomic investigation of viruses in green sea turtles (Chelonia mydas) DOI Creative Commons
Hongwei Li, Yuan Chen,

Zhongrong Xia

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: Jan. 22, 2025

Green sea turtles are listed on the International Union for Conservation of Nature’s Red List Threatened Species. Thus, conservation efforts, including investigation factors affecting health green turtles, critical. Viral communities play vital roles in maintaining animal health. In present study, shotgun metagenomics was used first time to survey viruses feces turtles. Most viral contigs were DNA that mainly belonged Caudoviricetes , followed by Crassvirales . Additionally, most not assigned any known family or genus, implying a large knowledge gap taxonomy turtle gut viruses. Host prediction showed connected two phyla: Bacteroidetes and Firmicutes Furthermore, KEGG enrichment analysis genes involved phage-associated metabolic pathways. Phylogenetic tree reconstruction Caudovirales terminase large-subunit (TerL) protein sequences phylogenetically distant. This study expands our understanding diversity particular, virome RNA fraction is exceedingly important investigating intestinal viromes; therefore, future studies could use metatranscriptomics

Language: Английский

Citations

0
Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages DOI
Yishay Pinto

Nature reviews. Immunology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 28, 2025

Language: Английский

Citations

0
Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut DOI Creative Commons

Ji-Woo Park,

Yeo-Eun Yun,

Jin Ah Cho

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 10, 2025

Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes six leafy green using virus-like particle (VLP) enrichment shotgun metagenome sequencing. On average, 9.2 × 107 viruses are present per gram tissue. The majority (93.1 ± 6.2%) these taxonomically unclassified. Virome compositions distinct among vegetable types exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) more dominant than temperate host fitness-benefiting AMGs. Analysis 1498 human fecal VLP metagenomes reveals that approximately 10% in gut virome, including commonly observed multiple studies. These gut-associated enriched short-term intake, depleted individuals immunologic disorders. Overall, this study elucidates ecological contribution fresh virome to diversity.

Language: Английский

Citations

0
Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater DOI
Xiaojie Yan, Yuan Xin, Liying Zhu

et al.

Water Research, Journal Year: 2025, Volume and Issue: unknown, P. 123627 - 123627

Published: April 1, 2025

Language: Английский

Citations

0
Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome DOI
Jamie Lopez Bernal,

Saria McKeithen-Mead,

Handuo Shi

et al.

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Lytic and temperate phage naturally coexist in a dynamic population model DOI Creative Commons
Ofer Kimchi, Yigal Meir, Ned S. Wingreen

et al.

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

Published: Jan. 1, 2024

When phage infect their bacterial hosts, they may either lyse the cell and generate a burst of new phage, or lysogenize bacterium, incorporating genome into it. Phage lysis/lysogeny strategies are assumed to be highly optimized, with optimal tradeoff depending on environmental conditions. However, in nature, radically different coexist same environment, preying bacteria. How can bacteria if one is more than other? Here, we address this conundrum within modeling framework, simulating population dynamics communities lysogens. We find that coexistence between natural outcome chaotic arise sufficiently diverse communities, which ensure no able absolutely dominate its competitors. Our results further suggest bet-hedging mechanism at level pan-genome, wherein obligate lytic (virulent) strains typically outcompete temperate strains, but also readily fluctuate extinction local community.

Language: Английский

Citations

3