Methods and compositions for treating and diagnosing autoimmune diseases

A method for determining (i) whether a subject has systemic lupus erythematosus (SLE) and/or lupus nephritis or (ii) whether a subject diagnosed with SLE or incomplete lupus (ILE) is at an increased risk for developing lupus nephritis, progression of SLE, and/or complications of lupus comprising:

• a. determining in a gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Ruminococcus gnavus strain CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201;
• GenBank:
• AZJF00000000) or a strain from Lachnospiraceae family, wherein said strain has 16S rRNA with at least 95% sequence identity to the 16S rRNA of Ruminococcus gnavus strain C55_001C, HM-1056 over its entire length or at least 99% sequence identity to any single V region of the 16S rRNA of Ruminococcus gnavus strain C55_001C, HM-1056, or another bacterial strain that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants with Ruminococcus gnavus strain CC55_001C, HM-1056;
• b. comparing the abundance of bacteria determined in step (a) to a control abundance of said bacteria;
• and
• c. determining that the subject has SLE and/or lupus nephritis or is at an increased risk for developing lupus nephritis, progression of SLE, and/or complications of lupus if the abundance of bacteria determined in step (a) is statistically significantly higher than the control abundance.