Antibiotics can unbalance or completely eliminate ones intestinal flora. Antibiotics interfere with the growth and reproduction of bacteria, and the bacteria of the human intestine are not immune to most common antibiotics.The normal flora helps protect the body from invasion by harmful microorganisms. In humans, normal intestinal bacteria are also responsible for production of Vitamin K, which is necessary for normal blood clotting.
Human cells (intestinal or otherwise) are not killed by antibiotics because antibiotics attack or interfere with production of certain components of the bacterial cell wall, and animal cells do not have cell walls. As a consequence, the drugs can attack the bacteria exclusively, leaving the patient's cells unaffected.