Provided herein are kits, compositions, and methods for diagnosing and treating interstitial cystitis (IC) and/or interstitial cystitis/bladder pain syndrome (IC/BPS) based on finding lower levels of certain bacteria in a subject's stool sample (e.g., O. splanchnicus, F. prausnitzii, C. aerofaciens, E. sinensis, L. longoviformis, and R. intestinalis). In certain embodiments, then present invention provides probiotic formulations containing live bacteria (e.g., from O. splanchnicus, F. prausnitzii, C. aerofaciens, E. sinensis, L. longoviformis, and R. intestinalis).