Transfer of modified fecal viromes improve blood glucose regulation and alleviates symptoms of metabolic dysfunction-associated fatty liver disease in an obesity male mouse model DOI Creative Commons
Xiaotian Mao,

Sabina Birgitte Larsen,

Line Fisker Zachariassen

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 20, 2023

Abstract Metabolic syndrome encompasses amongst other conditions like obesity, type-2 diabetes, and metabolic dysfunction associated fatty liver disease (MAFLD), which are all with gut microbiome (GM) dysbiosis. Fecal microbiota transplantation (FMT) has been explored to treat by restoring the GM. FMT is generally safe, but motivated case reports, accidental transfer of pathogenic bacteria remains a concern. As safer alternative, fecal virome (FVT, sterile-filtrated feces) advantage over in that mainly bacteriophages transferred FVT from lean male donors shown promise alleviating effects high-fat diet preclinical mouse study. However, still carries risk eukaryotic viral infections. To address this, we here apply recently developed modification methodologies inactivate or remove component while maintaining an active enteric bacteriophage community. Modified FVTs were compared unmodified saline animal model diet-induced obesity using C57BL/6N mice. In contrast obese control group, mice administered modified FVT, nearly depleted viruses (0.1%), exhibited enhanced blood glucose clearance, although without concurrent reduction weight gain. The improved pathology reduced proportions immune cells adipose tissue non-uniform response. GM analysis suggested bacteriophage-mediated modulation had influenced these outcomes. When optimized, this may pave way for developing safe bacteriophage-based therapies targeting through restoration.

Язык: Английский

A systematic analysis of marine lysogens and proviruses DOI Creative Commons
Yi Yi,

Shunzhang Liu,

Yali Hao

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 27, 2023

Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting over 12,000 bacterial archaeal genomes) Temperate Viral (MTVGD). At least 40% MPGD genomes contain one or more proviral sequences, indicating that they lysogens. The MTVGD includes 12,900 viral contigs putative proviruses, clustered into 10,897 genera. We show lysogens proviruses abundant ecosystems, particularly deep sea, differ from non-lysogens multiple features growth properties. reveal several virus-host interaction networks potential ecological relevance, identify appear be able infect (or transferred between) different classes phyla. Auxiliary metabolic genes enriched functions related carbohydrate metabolism. Finally, experimentally demonstrate impact prophage on transcriptome representative Shewanella bacterium. Our work contributes better understanding ecology their viruses.

Язык: Английский

Процитировано

23
Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle DOI Creative Commons
Danica T. Schmidtke, Angela Shang-Mei Hickey, Ivan Liachko

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 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.

Язык: Английский

Процитировано

13
Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments DOI Creative Commons
Hanpeng Liao, Chen Liu, Shungui Zhou

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 27, 2024

Язык: Английский

Процитировано

10
Life at the borderlands: microbiomes of interfaces critical to One Health DOI Creative Commons
Simon R. Law, Falko Mathes, Amy M. Paten

и другие.

FEMS Microbiology Reviews, Год журнала: 2024, Номер 48(2)

Опубликована: Фев. 28, 2024

Abstract Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and overall well-being ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with plant, animal, hosts, as well within soil environment. This review aims explore ecological, evolutionary, molecular processes governing establishment function microbiome–host relationships, specifically critical One Health—a transdisciplinary framework recognizes health outcomes people, animals, plants, tightly interconnected. Within context Health, core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms attachment, community succession, effect these have on host health. Finally, this catalogue recent advances microbiology ecology methods can used profile interfaces, particular attention multi-omic, advanced imaging, modelling approaches. These technologies for delineating general specific functions, mapping interconnectivity across varying spatial temporal scales, predictive frameworks guide development targeted microbiome-interventions deliver Health outcomes.

Язык: Английский

Процитировано

9
Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments DOI Creative Commons
Torben Sølbeck Rasmussen, Xiaotian Mao, Sarah Förster

и другие.

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Июль 1, 2024

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 hinder 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 (5/8, 7/8, 5/7, significantly load colonizing cells associated toxin A/B levels. There was potential elimination colonization, seven out eight 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 efficacy. Conclusions This proof-of-concept study shows specific modifications hold promise addressing related variability risks. Two strategies lead limiting colonization mice, solvent/detergent chemostat propagation emerging as promising approaches.

Язык: Английский

Процитировано

9
Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats DOI Creative Commons
Steven J. Biller, Matthew J. Ryan, Jasmine Li

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 3, 2025

Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, agents, phage satellites). The information enclosed these structures represents a substantial portion HGT potential available planktonic ecosystems, but whether some genes might be preferentially transported one type nanoparticle versus another unknown. Here we use long-read sequencing to compare genetic content EVs VLPs from oligotrophic North Pacific. Fractionated EV-enriched VLP-enriched subpopulations contain diverse surrounding microbial community, differ their capacity encoded functions. sequences carried by both particle types are enriched mobile elements (MGEs) as compared with other cellular chromosomal regions, highlight how this property enables novel MGE discovery. Examining Pelagibacter mobilome reveals >7200 distinct fragments MGEs, many differentially partitioned between VLPs. Together results suggest that distinctions contents contribute mode trajectory networks evolutionary dynamics natural habitats. Biller et al. fractionated ocean nanoparticles, showing pools thus may horizontal ocean.

Язык: Английский

Процитировано

1
Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species DOI Creative Commons
Yongyi Peng,

Zijian Lu,

Donald Pan

и другие.

The ISME Journal, Год журнала: 2023, Номер 17(10), С. 1774 - 1784

Опубликована: Авг. 12, 2023

Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial archaeal viruses. However, little is known about viral genetic features evolutionary patterns in these environments. Here, we examined the ecology of viruses across active extinct stages area Haima seeps South China Sea. A total 338 operational taxonomic units are identified linked 36 phyla. The dynamics host-virus interactions informed by antiviral defense systems 43 families found 487 microbial genomes. Cold predicted adaptive strategies persist this environment, including counter-defense systems, auxiliary metabolic genes, reverse transcriptases, alternative code assignments. Extremely low nucleotide diversity observed populations, being influenced factors host, sediment depth, stage. Most genes under strong purifying selection with trajectories that differ depending on whether or extinct. This work sheds light understanding environmental adaptation mechanisms sub-seafloor biosphere.

Язык: Английский

Процитировано

16
Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts DOI Creative Commons
L. Felipe Benites, Timothy G. Stephens, Julia Van Etten

и другие.

Communications Biology, Год журнала: 2024, Номер 7(1)

Опубликована: Апрель 9, 2024

Abstract Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate microbial biomass at these sites. Little is known about host-virus interactions environments. We analyzed virus community associated with algal mats three neighboring habitats (creek, endolithic, soil) Lemonade Creek, Yellowstone National Park (YNP), USA. find despite proximity, each habitat houses a unique collection of viruses, giant Megaviricetes, dominant all three. The early branching phylogenetic position genes encoded on metagenome assembled genomes (vMAGs) suggests YNP lineages are ancient origin and not due to multiple invasions from mesophilic habitats. existence genomic footprints adaptation thermophily vMAGs consistent this idea. geothermal sites originated ca. 1.5 Bya therefore relevant understanding biotic Earth.

Язык: Английский

Процитировано

7
Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake DOI Creative Commons
Zheng Yu, Zihao Gao, Shuai Wu

и другие.

Viruses, Год журнала: 2024, Номер 16(4), С. 590 - 590

Опубликована: Апрель 11, 2024

Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal roles. In this study, we selected Chaohu Lake, a representative eutrophic lake in China, our research site to explore community distribution, driving mechanisms, and potential functions of diverse viral communities, intricate virus–host interaction systems, overarching influence viruses global biogeochemical cycling.

Язык: Английский

Процитировано

7
Transfer of modified gut viromes improves symptoms associated with metabolic syndrome in obese male mice DOI Creative Commons
Xiaotian Mao,

Sabina Birgitte Larsen,

Line Fisker Zachariassen

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 3, 2024

Abstract Metabolic syndrome encompasses amongst other conditions like obesity and type-2 diabetes is associated with gut microbiome (GM) dysbiosis. Fecal microbiota transplantation (FMT) has been explored to treat metabolic by restoring the GM; however, concerns on accidentally transferring pathogenic microbes remain. As a safer alternative, fecal virome (FVT, sterile-filtrated feces) advantage over FMT in that mainly bacteriophages are transferred. FVT from lean male donors have shown promise alleviating effects of high-fat diet preclinical mouse study. However, still carries risk eukaryotic viral infections. To address this, recently developed methods applied for removing or inactivating viruses component FVT. Modified FVTs compared unmodified saline diet-induced model C57BL/6 N mice. Contrasted obese control, mice administered modified (nearly depleted viruses) exhibits enhanced blood glucose clearance but not weight loss. The improves liver pathology reduces proportions immune cells adipose tissue non-uniform response. GM analysis suggests bacteriophage-mediated modulation influences outcomes. Optimizing these approaches could lead development safe bacteriophage-based therapies targeting through restoration.

Язык: Английский

Процитировано

6