Drinking coffee contributes to the problem and not the other way around, its likely one of the reasons you are here in the first place. Its hard getting away from it cold turkey, but you will heal much faster without it from my experience.
Why do you drink it? If you want something that will promote digestion and perk you up, I recommend trying chamomile tea which is antifungal and promotes bowel movements. If you steep it longer than 8 mins, it will give you energy. Its also good for the liver.
Chickory coffee is also something to look at, its a a prebiotic that feeds the beneficial bacteria in the gut.
If you want to reverse the flora in your gut, it will be more difficult while consuming coffee.