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Study Examines Diet Influence on Gut Virome

NEW YORK (GenomeWeb News) – Viral communities in the human gut vary between individuals and are quite stable over time but can be coaxed into becoming more similar when individuals are placed on comparable diet plans, according to a study scheduled to appear online last night in Genome Research.

University of Pennsylvania researchers used metagenomic sequencing to assess the viral and bacterial communities in the guts of six individuals who were put on diets with varying amounts of fat and fiber for about a week. When they looked at the compositions of the viromes and overall microbiome in the gut of each individual over time, the researchers found that while gut viromes were quite different from one individual to the next, there was some convergence in the viromes of those given the same type of diet.

"The study provides a new window on the vast viral populations that live in the human gut, demonstrates that they vary radically between individuals, and shows that dietary changes can affect not just bacterial populations but also viral populations," senior author Frederic Bushman, a microbiologist at the University of Pennsylvania, said in a statement.

A number of studies have been done to explore the composition, establishment, and variability of the gut microbiome, as well as host factors that influence this microbial community and the microbiome's potential role in health and disease. Much of this research has focused on gut bacteria, though at least one prior study has found inter-personal variation and stability in the gut virome.

For the current study, Bushman and his colleagues investigated how diet affects the viral composition of the gut over time, using metagenomic sequencing to assess stool samples collected from six healthy, 18 to 40-year-old volunteers.

Researchers collected a stool sample from each participant on the first day of the study. After that, two of the individuals were put on a high-fat, low-fiber diet, three were placed a diet that was higher in fiber and low in fat, and one individual had an "ad-lib" diet.

Additional stool samples were collected about a day, six days, and a week after the diet plans began, and the investigators used filtration and density gradients to purify virus-like particles from each individual's pre- and post-diet stool samples.

After randomly amplifying virus-like particle DNA from each sample, they then sequenced the virus-like DNA by Roche 454 GS FLX Titanium shotgun sequencing. The team also isolated total DNA from the same samples to assess the gut bacterial communities, which were determined through 16S rDNA sequencing and shotgun sequencing.

From the 336 million bases of high quality virus-like particle sequence generated, the team assembled 7,175 contigs. Almost half of these contigs showed similarity to known bacteriophages families when the researchers compared the sequences and open reading frames in these contigs with several databases. They also identified genes involved in various aspects of bacterial infection, along with sequences representing viral CRISPRs and antibiotic resistance genes.

Overall, the gut viromes varied significantly from one individual to the next and stayed quite stable over course of the study, researchers reported. Even so, the viral communities in the guts of individuals placed on the same diet plan became somewhat more similar to one another over time, suggesting diet can influence the composition of the gut virome.

"We found that the predominant source of variation was differences among individuals," the study authors wrote, "but that significant changes in viral populations were detectable associated with switching to a defined diet and that convergence of viral populations was seen for individuals on similar diets."

"Considerable further study will be required to understand the acquisition of gut viral communities and the factors mediating the balance between long term stability and dynamic response to the environment," they concluded.

Sequence data from the gut virome study is being deposited to the NCBI Sequence Read Archive.

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