• Science Saturday: How disease, diet, and genomics interact with gut virome

gut microbiome

Mayo Clinic researchers published a comprehensive analysis of the gut virome in Gastroenterology, showing how disease, diet and genomics interact with the gut virome in irritable bowel syndrome. This common disorder affects the intestine and manifests as abdominal pain associated with constipation, diarrhea or both.

The gut virome is one component of the microbiome (bacteria, fungi, viruses). It includes viruses that specifically attack bacteria (bacteriophages/phages) or those affecting humans (eukaryotic viruses. e.g., norovirus). Hence the gut virome can cause symptoms by direct effects on the gut or by shaping the composition and function of the gut bacteria, which then alter gut function. Purna Kashyap, M.B.B.S., the Bernard and Edith Waterman Co-Director for the Microbiome Program in Mayo Clinic's Center for Individualized Medicine Microbiome Program explains the virome's role is especially relevant in conditions where the microbiome is considered an essential factor in the development of disease and irritable bowel syndrome is one such condition.

Researchers take a step further by analyzing the virome

"Most present-day virome studies use metagenomic DNA sequencing as a starting point," says Dr. Kashyap. "However, this would miss a significant number of human gut pathogenic viruses (e.g., rotavirus, Norwalk virus, picornaviruses) that have RNA genomes."

Researchers analyzed the virome after enriching viral-like particles in the sample and converting RNA genomes to DNA. They combined this with multi-omics (a biological approach using multiple omics technologies), clinical and dietary data to understand how the virome fits within the context of health and disease.

Gut virome is stable and is associated with changes in gene expression in the gut

With data collected from healthy participants and different subsets of patients with irritable bowel syndrome, the researchers found that the gut virome was relatively stable over the 6-month study period. They also found the virome links with the expression of specific genes (the process of turning on a gene to produce RNA and eventually protein) linked to immune function in the intestine. Dr. Kashyap adds many plant genomes and an increasing number of known phages use RNA as their core genetic construct.

Gut bacteria and their metabolites have been found to regulate many of the mechanisms underlying irritable bowel syndrome. Still, there is little known about the gut virome, especially in different subsets of the condition, with symptoms of either constipation or diarrhea. In multi-omics analysis, researchers found a correlation between bacteriophages and gut bacterial composition and function. They also identified irritable bowel syndrome subset-specific changes in the bacteriophage population.

"This is important as bacteriophages may be responsible in part for shaping the gut bacterial population in these disease subsets and would also be important when considering probiotic therapy," says Dr. Kashyap. "If patients have bacteriophage that can kill the probiotic bacteria —  it may not be very effective — do we need to tailor probiotics to match the bacteriophage population?"

Read the rest of the article on the Center for Individualized Medicine blog.


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