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Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts

Kosuke Fujimoto1, Yasumasa Kimura2, Masaki Shimohigoshi3

  • 1Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Division of Metagenome Medicine, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan.

Cell Host & Microbe
|July 12, 2020
PubMed

Insights

Bacteriophages (phages) show promise for eliminating gut pathogens. This study maps phage-host interactions in the human gut microbiome, aiding the development of targeted phage therapies against harmful bacteria.

Area of Science:

  • Microbiology
  • Virology
  • Genomics

Background:

  • Bacteriophages (phages) are viruses that infect bacteria and are being explored for targeted pathogen elimination.
  • Understanding phage-host interactions within the human gut microbiome is crucial for developing effective phage therapies.
  • Previous research has not fully elucidated the complex associations between phages and bacteria in the intestinal environment.

Purpose of the Study:

  • To characterize the intestinal viromes and bacteriomes in a cohort of healthy individuals.
  • To identify and map host bacteria-phage associations within the human gut.
  • To demonstrate the utility of this data for identifying phages and enzymes effective against specific pathogens like Clostridioides difficile.

Main Methods:

  • Collected fecal samples from 101 healthy Japanese individuals.
  • Performed metagenomic sequencing of both viral (viromes) and bacterial (bacteriomes) communities.
  • Analyzed genomic data to determine host bacteria-phage associations for both temperate and virulent phages.

Main Results:

  • Detailed mapping of host bacteria-phage associations in the human intestinal microbiome.
  • Identification of specific phages targeting Clostridioides difficile.
  • Validation of antibacterial enzyme activity in vitro and in vivo.

Conclusions:

  • Comprehensive metagenomic analysis provides essential insights into gut phage-host dynamics.
  • This data is vital for the development of precision phage therapies against intestinal pathobionts.
  • The study validates the potential of phage-based strategies for combating bacterial infections.
Keywords:
CRISPRClostridioides difficile infectionbacteriomebacteriophagehost bacteria-phage associationmetagenome analysisprophagevirome

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