Could taking antibiotics for a prolonged amount of time severely harm or even worse kill off a large proportion of Gut Microbiota responsible entirely for digestion, Resulting in lifelong digestion problems similar to Crohn's Disease?
Yes. killing the normal flora of the colon will give chance to harmful bacteria to thrive and cause disease. One of the most common diseases that are a result of antibiotic use is Clostridium difficile infection. This disease is caused by a toxin releasing bacteria that can form spores. Antibiotics are ineffective agains spores, which is why this disease is hard to treat.
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Yes, even if you will not kill ALL the bacteria in your gut, you can mess up your flora pretty badly by using antibiotics for prolonged time.
For how long? It depends from person to person, from antibiotic to antibiotic.
Similar to Crohn's disease? Some symptoms like abdominal pain, diarrhoea and weight loss can occur in case of messed-up flora like in Crohn's disease (and many other diseases!).