Background: Due to disconnect between genetic predisposition and development of rheumatoid arthritis (RA), research into the potential role of the human microbiome in RA pathogenesis is essential. Initial questions explored in this study include: (1) is the RA microbiome less diverse than the healthy microbiome, (2) does disease influence dissimilarity in the gut microbiome, and (3) are any taxa over- or under- abundant, or unique to the RA gastrointestinal system?
Methods: Recruitment is ongoing at Royal North Shore Hospital, for an established RA group (n=22; mean age=59.95 ± 12.7) and the no-RA (‘healthy’) group (n=12; mean age=48 ± 14.5). Initially a subset of stool samples (RA=4; no-RA=3) was analysed. Extracted DNA was sent for 16s rRNA amplicon sequencing at the Australian Genome Research Facility (AGRF). Samples were processed with a QIIME2 pipeline using the cutadapt and DADA2 plugins. Diversity analyses were performed using the core metrics function. Taxonomy was assigned using the q2-feature-classifier plugin and a Naïve Bayes classifier trained on the Silva database. PCR and absolute qPCR (standard curve) determined presence/absence of Prevotella copri in stool samples.
Findings and Conclusion: A microbiome analyses pipeline has now been established and optimized using a subset of data [RA (n=4) and no-RA (n=3)], with quality control of both samples and data performed. While no significant difference in richness (p-value = 0.7), evenness (p-value = 0.5) or beta-diversity metrics (q-value = 0.9) between groups was identified, this may be accounted for due to the low statistical power of the initial analyses, and presence of confounding factors. Data must be explored in more detail with a larger cohort; these analyses are currently underway with results forthcoming. P. copri was confirmed in the stool samples of 2 RA and No-RA (n = 4) participants.