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, said method comprising:

• (a) determining in a bodily fluid sample collected from the subject a level of antibodies which recognize a bacterial lipoglycan-containing antigen,
• (b) comparing the level of the antibodies determined in step (a) to a control level of said antibodies, 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 level of the antibodies determined in step (a) is statistically significantly higher than the control level,
• wherein the lipoglycan-containing antigen is associated with Ruminococcus gnavus strain CC55 001C, HM-1056, and
• wherein the lipoglycan-containing antigen is the same as the lipoglycan-containing antigen obtained using a method selected from:
• (i) Method 1 comprising the steps:
• a. culturing Ruminococcus gnavus strain CC55 001C, HM-1056 at 37° C. under anaerobic conditions for 2-7 days, and
• b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;
• (ii) Method 2 comprising the steps:
• a. culturing Ruminococcus gnavus strain CC55 001C, HM-1056 in rich nutrient media at 37° C. under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days,
• b. pelleting bacteria by centrifugation,
• c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions,
• d. treating the extract obtained in step (c) with Proteinase K,
• e. incubating the treated extract obtained in step (d) at 55° C. for about 10 minutes,
• f. removing cell debris by centrifugation, and
• g. using the supernatant as an antigen preparation;
• or
• (iii) Method 3 comprising the steps:
• a. disrupting Ruminococcus gnavus strain CC55 001C, HM-1056 cells with a French press,
• b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant,
• c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase,
• d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and
• e. isolating lipoglycan-containing fractions.