To further investigate whether the observed alterations in BAL bacterial community composition in early RA patients was associated with phenotypic characteristics or metadata, we set out to describe the correlations between the relative abundance of taxa and (1) clinical disease activity (DAS28-ESR and CRP), (2) the local autoimmune response (BAL concentrations of ACPA and percentage of immune cells), and (3) the systemic immune response (serum concentrations of ACPA and RF) (Fig. 4 for genus; and Additional file 5: Figure S4 for OTUs). The gene discussed is ESR1; the disease is rheumatoid arthritis.