Do we loose all good bacteris from the gut when preparing for colonoscopy?

Not at all: A 'prep' for a colonoscopy is designed to wash out the big visible chunks of stool that could interfere with visualizing the colon. Don't worry - the bacteria know how to survive and they will 'stick' to the lining of your colon. (I know it sounds gross but they are there to help you!) This is a routine procedure and I feel confident your colon health will be fine afterwards. I do recommend kefir