The present invention provides methods, compositions, and systems for producing cheese with S. thermophilus and a urease inhibitor, and for producing cottage cheese with S. thermophilus that is partially or completely deficient in its ability to release ammonia from urea. The present invention also provides methods, compositions, and systems for reducing the amount of open texture (e.g., slits, cracks, or fractures) in gassy cheeses, such as cheddar cheese.