No, a “low carb” diet will not ruin the good bacteria in your gut unless you’re eating way too much cheese. The probiotics would be a good idea too. Also, “low carb” diets are not a good idea. Better to eat plenty of unrefined carbs like fruits and veggies for fiber. If you’re eating just protein or fat it’s not good for the kidneys, esp. long term. Dr. Atkins, who popularized the low carb diets died of a heart attack after all.