Adaptive strategies and ecological roles of phages in habitats under physicochemical stress

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(9), P. 902 - 916

Published: March 2, 2024

Language: Английский

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Lake salinization on the Qinghai–Tibetan Plateau alters viral community composition and lifestyles

Communications Earth & Environment, Journal Year: 2025, Volume and Issue: 6(1)

Published: Jan. 25, 2025

Language: Английский

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Hi-C metagenome sequencing reveals soil phage–host interactions

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 23, 2023

Bacteriophages are abundant in soils. However, the majority uncharacterized, and their hosts unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly phage-host relationships. Some have high centralities bacterial community co-occurrence networks, suggesting phage infections an important impact on soil interactions. We observe increased average viral copies per host (VPH) decreased transcriptional activity following a two-week soil-drying incubation, indicating increase lysogenic infections. Soil drying also alters observed range. A significant negative correlation between VPH abundance prior indicates more lytic result death inversely influence abundance. This study provides empirical evidence of phage-mediated population dynamics by capturing specific

Language: Английский

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Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

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

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Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 510 - 510

Published: March 2, 2024

Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, field metagenomics has emerged as powerful tool for studying microbial communities associated cereal crops and their impact on plant health growth. This chapter aims to provide comprehensive overview its enhancing food through exploration beneficial pathogenic interactions. Furthermore, we will examine how integration other tools can effectively address adverse effects security. For this purpose, discuss metagenomic data machine learning providing novel insights into dynamic interactions shaping plant-microbe relationships. We also shed light potential applications leveraging diversity epigenetic modifications improving crop resilience yield sustainability. Ultimately, revolutionized by harnessing between microbiota, paving way sustainable agricultural practices.

Language: Английский

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Beneath the surface: Unsolved questions in soil virus ecology

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109780 - 109780

Published: March 1, 2025

Language: Английский

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The role of rhizosphere phages in soil health

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(5)

Published: April 10, 2024

Abstract While the One Health framework has emphasized importance of soil microbiomes for plant and human health, one most diverse abundant groups—bacterial viruses, i.e. phages—has been mostly neglected. This perspective reviews significance phages health in rhizosphere explores their ecological evolutionary impacts on ecosystems. We first summarize our current understanding diversity roles terms nutrient cycling, top-down density regulation, pathogen suppression. then consider how drive bacterial evolution soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host fitness, selecting phage-resistant mutants with altered ecology due to trade-offs competitiveness virulence. Finally, we challenges avenues phage research ecosystems elucidate microbial ecosystem functioning future. conclude similar bacteria, likely play important connecting different compartments, affecting microbiome functions soils. From applied perspective, could offer novel approaches modulate optimize microbe–plant interactions enhance health.

Language: Английский

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From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 2, 2024

Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances technology have resulted the ability to easily collect large soil samples containing thousands unique taxa often poorly characterized. These reduce usefulness genome-resolved metagenomic (GRM) seen other fields microbiology, such as creation high quality assembled genomes adoption genome scale modeling approaches. The absence these resources restricts future research, limiting hypothesis generation predictive Creating publicly available databases MAGs, similar produced for microbiomes, has potential transform scientific insights about without requiring computational domain expertise binning.

Language: Английский

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Gut phages and their interactions with bacterial and mammalian hosts

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

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Analysis of metagenomic data

Nature Reviews Methods Primers, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 23, 2025

Language: Английский

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