Canine 16S V4 microbiome Metagenome

Background: Canine perianal fistulas are painful ulcers or sinus tracts that disproportionately afflict German shepherd dogs and have been proposed as a spontaneous animal model of fistulizing Crohn's disease. Objectives of this study were to characterize the rectal microbiota and cutaneous microbiota, both lesional and non-lesional, in German shepherd dogs with perianal fistulas and to investigate longitudinal shifts associated with lesion resolution during immunomodulatory therapy.Eleven German shepherd dogs with perianal fistulas were evaluated and swabbed at 3 visits, 30 days apart, while undergoing standard treatment with cyclosporine and ketoconazole. Fifteen healthy German shepherd dogs were contemporaneously evaluated. Sites included the rectum, perianal skin, and axilla. The microbiome was evaluated following sequencing of the V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene.Results: Alpha diversity was not significantly different between healthy and affected dogs at each of the three body sites (P>0.5), but rectal and perianal beta diversity from affected dogs differed significantly from that of healthy dogs at day 0 (P = 0.004). Similar microbial community composition was noted from the rectum and perianal skin. Lower initial relative abundance of Prevotella spp. from the rectum and perianal skin and higher relative abundance of Staphylococcus spp. from the perianal skin were noted for dogs with perianal fistulas as compared with healthy dogs. Rectal and perianal relative abundance of Prevotella spp. increased and perianal Staphylococcus spp. relative abundance decreased in affected dogs over time, coincident with lesion resolution. Staphylococcus relative abundance was higher from the axilla (non-lesional) skin of dogs with perianal fistulas as compared with healthy dogs.Conclusions: Changes in lesional cutaneous and rectal microbiota occur in German shepherd dogs with perianal fistulas, and appear to shift over time during immunomodulatory therapy, coincident with lesion resolution. Further work is needed to clarify the role of the cutaneous and enteric microbiota in the pathogenesis of canine perianal fistulas, and whether manipulation of microbial populations may ameliorate disease. Cutaneous dysbiosis may not be limited to lesional sites, suggesting that barrier defects or a more widespread dysfunctional immune response to microbes may exist in in German shepherd dogs with perianal fistulas.