Multiomic spatial analysis reveals a distinct mucosa-associated virome

Area of Science:

• Microbiology
• Virology
• Gastroenterology

Background:

• The human gut virome is understudied, with most research using only fecal samples.
• Few studies integrate multiomic approaches to investigate phage-host interactions.

Purpose of the Study:

• To investigate virome-bacteriome interactions at the colonic mucosal-luminal interface in individuals with inflammatory bowel disease (IBD).
• To compare the virome composition between colonic tissue and stool samples.
• To explore viral gene transcription and prophage activation in IBD.

Main Methods:

• Combined metagenomics, metaviromics, and metatranscriptomics.
• Analyzed colonic mucosal-luminal interface samples from three IBD patients.
• Utilized viral protein prediction and deep sequencing.

Main Results:

• The mucosal viral population is distinct from the stool virome.
• Abundant crAss-like phages were detected in mucosal samples but not in stool.
• Identified viral gene transcription, prophage activation, and relationships between integrase and temperate phages in IBD subjects.
• Demonstrated the impact of deep sequencing on virus recovery.

Conclusions:

• Multiomic approaches reveal distinct viral populations and interactions at the colonic mucosa.
• Understanding the gut virome's role in IBD requires studying the mucosal environment.
• Deep sequencing is crucial for comprehensive virome analysis.