Thank you very much for posting this question, which reminded me to dig out research I have done over 6 years ago and made into a book (but never published it). At that time, there was very little interest in soil microorganisms, and I reckon few people would have read the book. But, now it seems the time has come to show that the presence of these soil organisms are the only real reasons for the body to heal, or when they are not supplied, to cause diseases. Those people living in remote, rural farming areas in Africa, Asia, and South America, and also don't use pesticides, hardly ever suffer from the degenerative disease epidemics overwhelming modern societies. The fruits and vegetables they eat are packed with soil-based microbes, keeping the immune systems strong and the digstive systems efficent.
It always better to get these microbes from foods. But if that isn't possible, yes, the next best option would be to supplement them. There are no safety issues, since these organisms pro-life and are anti-disease oriented.
There is a good health website where you can read more about them (see link 1 below)and actually a product that contains them. There is another site, link 2, where you can get similar products and even learn how to make your own soil become enriched with these organisms.