RA and RA-ILD metagenome
Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular manifestation. The potential characterization of the gut mycobiome and virome in RA-ILD patients has been largely unexplored. Our goals were (1) to characterize the multi-kingdom characterization of the gut microbiota (including bacteriome, mycobiome, and virome) in patients with RA and (2) to compare the results with the gut microbiota of patients with RA-non-ILD, RA-ILD, and healthy controls. We carried out the whole-metagenome shotgun sequencing of the fecal samples from 60 RA patients (including 30 RA-ILD patients) and 40 matched healthy controls to investigate their gut microbiota composition. The gut bacteriome and mycobiome were explored using a reference-based approach, and the gut virome was profiled based on a non-redundant viral operational taxonomic unit (vOTU) catalogue. Our findings delineated the fecal bacteriome, mycobiome, and virome landscapes of the RA-ILD and RA-non-ILD gut microbiota and provided biomarkers that will aid in further mechanistic and clinical intervention research for treating and preventing RA and other autoimmune diseases.