It was a 2 week study, and diet was only changed for a week. The time period was probably long enough for existing microbes to decline due to environmental chan

It was a 2 week study, and diet was only changed for a week. The time period was probably long enough for existing microbes to decline due to environmental changes, but not long enough for new microbes that favor the new conditions to move in. If you've ever dramatically changed your diet, you'll know a week is not long enough for the resulting GI upset to subside. It often takes a month or longer.