Matcha has huge quantities of polyphenols — the naturally occurring compounds found in the tea plant that are thought to be responsible for some of the health effects conferred by a diet rich in fruit and vegetables. These polyphenols get broken down by our gut bacteria into bioactive, polyphenol-derived metabolites.
Not only do polyphenols increase counts of beneficial bacteria, they also inhibit growth of potentially pathogenic bacteria. And they do something similar to the bacteria in the mouth that cause plaque, which is one reason (among others) why dentists in Japan promote drinking matcha.