I think fermentation might be good for you because it kills off harmful microbes but also I think the fermenters are a type of fungus at least in brewing it is and fungus's are high in nutrients and very good at concentrating it. So imagine that it is more they have converted hard to digest or absorb nutrients from the plants in a more accessible form. Although I am not 100% on that just going off my knowledge and what I read.
I have got a bit carried way with posting about gut bacteria :S. The field of research is relatively new and like all science is only right until proved wrong some is based off my own experience some not. Take what I am saying with a pinch of sea salt (better for you) and if you think it makes sense to you great, if it doesn't then check the facts or feel free to ignore

. I hope it is interesting and helpful.
Well gut bacteria is a fascinating subject if your a microbiologist like me lol. Yeast is a fungus and the alcohol it produces is to kill off other microbes that compete with it for food. Ever wondered why alcohol is good for sterilising (70% is i think the best percentage for sterilising)? That is why

. Fortunately acohol absorbs mostly through your stomach lining otherwise you would get some upset bacteria i am sure.
It is an ecosystem in it's self and it keeps it's self in balance when you get upset stomach or the poo's what is mostly likely happened something has come along and upset that ecosystem. The bacteria and other microbes all regulate themselves and try to keep themselves in check so if a new "kid" comes on the block and doesn't mesh well with the others then it can cause problems. Imagine if you want the more science explanation, the new bacteria will secreate or produce a chemical toxic to you or the others and that will cause the gut bacteria to respond one of the best responses we have is to just clear everything out because your native bacteria should outnumber the new introduced ones they quickly bounce back and your fine after a while long as you don't keep introducing them. This will explain why if you go to new place and not used to water or food it can often give you the poo's because what actually happening is your introducing new things into your ecosystem and it hasn't found a way to live in balance with it.
I think a major contributor to gut bacteria health is what nutrution you feed them and the quality, think of them as your factory workers and you the factory. Their job is to break down the food and process it so it can be asborbed by the gut, they pay themselves with taking a cut of the food you bring in.
Problems probably arise when you eat food that favours a minority of the gut bacteria and they go it's christmas we got lots of food and so they multiple, you have effectively just given them a promotion. But of course your factory is running for years and all of a sudden you upset the balance, so it is going to cause trouble not so much they are bad it is they are out of balance. Also if you change your ph in gut can make things worse or better.
If you have ever been on antibiotics (unless straight into your blood stream) something they tend to forget to mention is your gut is going to go nuts, you get the poo's and terrible time, least I did the times I had them. That is because you have effectively declared chemical warfair on your gut bacteria and it can alter the balance and cause problems.
Also they are thinking that gut bacteria also plays a major role in metabolism of food and if you are particular good at putting weight on might be due to you having very efficient bacteria in your gut that give you a higher return (but it could be elsewhere). Also gut bacteria can be greatly different between parents and children, brothers and sisters. You might have more common gut bacteria profile with a stranger than people you known.
Gut bacteria (and other microbes) are so important that it is often referred to as the second genome, if you think about it we are partnership between us and our gut bacteria so it's no wonder that these little friends play such an important role in our day to day health.