Colonoscopy screening considerations

What are the down sides of going in for a colonoscopy. I hear that the prep for colonoscopy results in most of the gut bacteria getting wiped out and can cause side effects for long term. Is it wise to go for a colonoscopy as suggested by the GI doctor as a first step for long term constipation or should other options like fiber increase , natural remedies be tried first? Thanks for taking the time to answer the question.