Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.

OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type. RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both α- and β-diversity between sample types (digesta, feces) than between treatments. β-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. β-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.