There are gluten-degrading enzymes found in Rothia species bacteria that are capable of breaking peptide bonds in -XPQ-, -QQP-, -PPF-, -LYP- and/or -PFP-containing peptides. These enzymes are acidic enzymes; they retain protease activity at acidic pH, eg., at 3.0, and have isoelectric points in a pH range of 2.0-7.0. Embodiments herein provide isolated enzyme compositions and probiotic compositions comprising at least one acidic gluten-degrading enzyme or a Rothia species bacteria. Also provided herein are methods of treatment of celiac disease or a related disorder, treatment of gluten-containing foodstuff, degrading and/or detoxifying gluten comprising the acidic gluten-degrading enzyme and/or compositions.