Autoimmune diseases have a multifactorial etiology, including genetic and environmental factors. Rheumatoid arthritis (RA) is a chronic auto inflammation of the joints, with a prevalence of about 1% in Western population. Treatment with live helminths or helminths’ secreted molecules in patients and in animal models have improved the clinical score in RA, multiple sclerosis, type I diabetes mellitus, and inflammatory bowel disease. We have constructed a novel chimeric compound of tuftsin and Phosphorylcholine (TPC). Recently, the critical involvement of the microbiome in the pathogenesis of autoimmune diseases has gained appreciation. The aim of the current study addresses the correlation between TPC therapeutic efficacy and the microbiome composition in a mouse model of collagen-induced arthritis (CIA). We show that the microbial composition changes with treatment and disease severity. Our results provide support for a microbial link in CIA and show the importance of the microbiome in the success of the treatment.