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Adapting Gastrointestinal Organoids for Pathogen Infection and Single Cell Sequencing under Biosafety Level 3 (BSL-3) Conditions
Published on: September 10, 2021
Rapid evolution of the human gut virome
Samuel Minot1, Alexandra Bryson, Christel Chehoud
1Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Summary
The human gut virome is remarkably stable, with 80% of viral types persisting for 2.5 years. Rapid evolution of some viruses contributes to the unique viral communities found in each individual.
Area of Science:
- Microbiology
- Virology
- Genomics
Background:
- The human gut hosts a vast and diverse viral population, known as the virome.
- Metagenomic analysis reveals significant individual-specific variations in gut viral composition.
Purpose of the Study:
- To investigate the origin and evolutionary dynamics of the human gut virome.
- To analyze the long-term stability and variation within an individual's gut viral community.
Main Methods:
- Deep metagenomic sequencing of longitudinal fecal samples from one adult over 2.5 years.
- Assembly of viral sequences to identify and characterize viral genomes, primarily bacteriophages.
- Analysis of base substitution rates, mutation mechanisms, and genetic variation in different viral types.
Main Results:
- 478 distinct viral contigs, mostly novel bacteriophage genomes, were identified.
- 80% of identified viral types demonstrated long-term persistence throughout the 2.5-year study period.
- Temperate phages exhibited lower mutation rates, while lytic Microviridae showed high substitution rates, approaching species-level divergence.
Conclusions:
- The human gut virome is characterized by long-term stability of a core set of viral types.
- Rapid evolution, particularly in lytic bacteriophages, contributes significantly to the high interpersonal diversity of gut viruses.
- Mechanisms like diversity-generating retroelements and virus-encoded CRISPR arrays influence viral evolution within the gut environment.
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