Objective. Ankylosing spondylitis (AS) is a common highly heritable immune mediated arthropathy that occurs in genetically susceptible individuals exposed to an unknown but likely ubiquitous environmental trigger. There is a close relationship between the gut and SpA, exemplified in reactive arthritis patients where a typically self-limiting arthropathy follows either gastrointestinal or urogenital infection. Microbial involvement has been suggested in AS, however, no definitive link has been established. We sought to determine if the AS gut carries a distinct microbial signature, in comparison to healthy controls (HC). Methods. Microbial profiles from terminal ileal (TI) biopsies from subjects with recent-onset, TNF-antagonist naïve AS and HC, were generated using culture-independent 16S rRNA gene sequencing and analysis techniques. Results. Our results show the TI microbial communities of patients with AS differ significantly (P<0.001) from HC, driven by higher abundance of five families of bacteria Lachnospiraceae (P=0.001), Veillonellaceae (P=0.01), Prevotellaceae (P=0.004), Porphyromonadaceae (P=0.001), and Bacteroidaceae (P=0.001); two of which, Lachnospiracecae, and Prevotellaceace, have been strongly associated with colitis and CD. Conclusions. We show evidence for a discrete microbial signature in the TI of cases with AS compared to HC. The microbial composition was found to correlate with disease status and greater differences were observed between than within disease groups. These results are consistent with the hypothesis that genes associated with AS act at least in part through effects on the gut microbiome. This article is protected by copyright. All rights reserved.