Methods and compositions are provided for evaluating a subject for chronic immune disease, including predicting whether a subject is susceptible to a chronic immune disease, diagnosing whether a subject has a chronic immune disease and/or determining a treatment for a subject suffering from a chronic immune disease. Aspects of the methods include obtaining an intestinal bacterial assessment for the subject and using the assessment to provide the evaluation. In addition, reagents and kits thereof that find use in practicing the subject methods are provided. Furthermore, methods of treating a subject for a chronic immune disease are provided.
