Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes DOI Creative Commons
David M. Robinson, Rachael M. Morgan‐Kiss, Zhong Wang

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 10, 2024

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic extreme habitats which dominated by microbial life. MDVs include glacial melt holes, streams, lakes, and soils, interconnected through the transfer energy flux inorganic organic material via wind hydrology. For first time, we provide new data on viral community structure function in metagenomics planktonic benthic mat communities Lakes Bonney Fryxell. Viral taxonomic diversity was compared across lakes ecological investigated characterizing auxiliary metabolic genes (AMGs) predicting hosts. Our suggest that differed between among sites: these differences were connected to host communities. AMGs associated with potential augmentation multiple biogeochemical processes host, most notably phosphorus acquisition, nitrogen sulfur oxidation, photosynthesis. genome abundances containing mats, indicating site specialization. Using procrustes analysis, also identified significant coupling bacterial (

Language: Английский

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments DOI Creative Commons
Torben Sølbeck Rasmussen, Xiaotian Mao, Sarah Förster

et al.

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

Published: March 17, 2023

ABSTRACT Background Fecal microbiota transplantation (FMT) and fecal virome (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) FMT or FVT hinders their wider clinical application less acute diseases. Methods To overcome these challenges, we developed methods to broaden FVT’s while maintaining efficacy increasing safety. Specifically, employed following approaches: 1) Chemostat-fermentation reproduce bacteriophage component remove viruses (FVT-ChP), 2) solvent-detergent treatment inactivate enveloped (FVT-SDT), 3) pyronin-Y inhibit RNA-virus replication (FVT-PyT). We assessed processed FVTs a C. infection mouse model compared them untreated (FVT-UnT), FMT, saline. Results FVT-SDT, FVT-UnT, FVT-ChP reduced incidence mice reaching humane endpoint (0/8, 2/7, 3/8, respectively) FVT-PyT, saline control (5/8, 7/8, 5/7, significantly load colonizing cells toxin A/B levels. There was potential elimination colonization, 7 out 8 treated FVT-SDT testing negative qPCR. In contrast, all other treatments exhibited continued presence . Moreover, results were supported by changes microbiome profiles, cecal cytokine levels histopathological findings. Assessment viral engraftment FMT/FVT host-phage correlations analysis suggested that phages likely an important contributing factor associated efficacy. Conclusions This proof-of-concept study show specific modifications hold promise addressing related variability risks. Two strategies lead limiting colonization mice, solvent/detergent chemostat-propagation emerging as promising approaches.

Language: Английский

Citations

4
Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae DOI
Yimin Ni, Ting Chu, Shuling Yan

et al.

Journal of General Virology, Journal Year: 2024, Volume and Issue: 105(3)

Published: March 6, 2024

Twenty complete genomes (29–63 kb) and 29 with an estimated completeness of over 90 % (30–90 were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered contribute to expansion viral taxonomy by introducing 46 potential new families. Except one virus, all others belong class Caudoviricetes . The exception is a member recently characterized group known as Gossevirus. Fifteen predicted be temperate. hosts appear involved various aspects nitrogen cycle, including fixation, oxidation denitrification. Two have host Flavobacterium Tepidimonas fonticaldi , respectively, matching CRISPR spacers protospacers. Our findings provide overview characterizing identifying specific from Harbor. Gossevirus-like virus uncovered emphasizes need further comprehensive isolation investigation polinton-like viruses.

Language: Английский

Citations

1
A diverse gut virome from Drosophila melanogaster DOI Creative Commons
Mina Ansari, Fabian Staubach,

Nurper Alacatli

et al.

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

Published: March 19, 2024

Abstract Drosophila melanogaster is not only one of the most important models antiviral immunity in invertebrates, but also a powerful model for research gut microbiome. Although recent studies have continued to improve our knowledge fly microbiota, viral component microbiome has remained unexplored. Here we explore using deep metagenomic DNA sequencing. We recovered 3035 phage sequences, resulting 167 Metagenome-Assembled Genomes. The majority these sequences are potentially novel bacteriophages from order Caudovirales , which mainly target major bacteria D. including Lactobacillus Acetobacter and Gluconobacter . Our functional annotation discovery auxiliary metabolic genes showed that potential influence microbial metabolism genetic information processing. identified evidence known pathogens Kallithea nudivirus, Vesanto bidna-like virus, Viltain densovirus, some were common studied populations. findings reveal complex diverse community microbiome, paving way study host-phage related natural communities.

Language: Английский

Citations

1
Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages DOI

Etan Dieppa-Colón,

Cody Martin, Karthik Anantharaman

et al.

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

Published: July 16, 2024

Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact community dynamics, ecology, and evolution. Efforts document diversity, host range, infection effects bacteriophage on cell metabolism extremely underexplored. Phages classified as virulent or temperate based their life cycles. Temperate phages adopt lysogenic mode infection, where genome integrates into forming a prophage. Prophages enable viral replication without lysis, often contribute novel beneficial traits genome. Current phage research predominantly focuses lytic phages, leaving significant gap knowledge regarding prophages, including biology, ecological roles.

Language: Английский

Citations

1
Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes DOI Creative Commons
David M. Robinson, Rachael M. Morgan‐Kiss, Zhong Wang

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 10, 2024

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic extreme habitats which dominated by microbial life. MDVs include glacial melt holes, streams, lakes, and soils, interconnected through the transfer energy flux inorganic organic material via wind hydrology. For first time, we provide new data on viral community structure function in metagenomics planktonic benthic mat communities Lakes Bonney Fryxell. Viral taxonomic diversity was compared across lakes ecological investigated characterizing auxiliary metabolic genes (AMGs) predicting hosts. Our suggest that differed between among sites: these differences were connected to host communities. AMGs associated with potential augmentation multiple biogeochemical processes host, most notably phosphorus acquisition, nitrogen sulfur oxidation, photosynthesis. genome abundances containing mats, indicating site specialization. Using procrustes analysis, also identified significant coupling bacterial (

Language: Английский

Citations

1