The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls

• The fecal microbiota of cats with FIV infection differs from uninfected controls.
• FIV-infected cats had more Acidobacteria and Actinobacteria and fewer Fibrobacteres.
• Both community membership and structure differed between groups.
• There were no differences in richness, evenness or diversity.
• Various genera were more common in FIV-infected cats, including Lactobacillus.

Rectal swabs were collected from 31 cats, 16 with FIV infection and 15 uninfected controls, to evaluate and compare the rectal bacterial microbiota in cats with feline immunodeficiency virus (FIV) infection and uninfected controls. The rectal microbiota was characterized via next generation sequencing of 16S rRNA gene (V4 region) polymerase chain reaction products.Eighteen different phyla were identified. Firmicutes dominated in both groups, followed by Proteobacteria and Actinobacteria, but there were no significant differences between groups. When predominant orders are compared, FIV-infected cats had significant higher median relative abundances of Bifidobacteriales (P = 0.022), Lactobacillales (P = 0.022) and Aeromonadales (P = 0.043). No differences were identified in the 50 most common genera when adjusted for false discovery rate. There were significant differences in community membership (Jaccard index, unifrac P = 0.008, AMOVA P < 0.001) and community structure (Yue&Clayton index, unifrac P = 0.03, AMOVA P = 0.005) between groups. However, only one metacommunity (enterotype) was identified.The rectal microbiota differed between cats with FIV infection and uninfected controls. Some of the changes that were noted have been associated with ‘dysbiosis’ and proinflammatory states in other species, so it is possible that subclinical alteration in the intestinal microbiota could influence the health of FIV-infected cats. Evaluation of the reasons for microbiota alteration and the potential impact on cat health is required.