No expert on the topic, though it really interests me. Have been drinking EM (http://en.wikipedia.org/wiki/Effective_microorganism) every day for the past 6 months which has improved my digestion a lot.

Thought this comment on the NPR article was really insightful:

There's so much more to developing a healthy microbiome than just eating yogurt and drinking kombucha, as many people like to claim. It starts at birth. As you travel through the birth canal, you come into contact with many different and important microorganisms through contact with your mother's vaginal fluids and even fecal matter. If you're born via C section, you're starting out at a disadvantage. Then breastfeeding is the next step. Mother's milk is where you get your next dose of a very broad spectrum of microorganisms. Then throughout life, as you come in contact with other people, you eat dirt, you hang around farm animals, etc, these are all mother nature's way of helping you develop that microbiome, which is essentially the core of your immune system. Eating is important too, and one of the biggest problems with our modern food system is that everything is pasteurized, cooked all the way through, sterilized, irradiated, etc. All of the healthy microorganisms that used to exist are being killed.

So the point here is that people need to rethink many of their lifestyle choices if they want to heal their guts. Every time you take an antibiotic, you likely suffer much collateral damage because you may be permanently killing beneficial species that you may never be exposed to again. They don't exist in yogurt or kombucha. Either that, or consider fecal bacteriotherapy (fecal transplants) since it seems to be one of the the most promising new approaches to healing microbiomes. ~Julie Latham

Totally non-scientific response to this, but I can say that after having to take antibiotics a few years back for a pretty bad sinus infection my digestive system has never completely recovered. I never had any sort of digestive issues that I can think of but have had numerous since then. I can't directly contribute it to the antibiotics, but it certainly seems to correlate.

Taking probiotics helped quite a bit, which I did a month or so after the antibiotics started causing these issues, but yeah, never completely felt 'better' since then. I guess this is yet another example of why/how over prescription of antibiotics is a bad thing.

>as you come in contact with other people, you eat dirt, you hang around farm animals, etc, these are all mother nature's way of helping you develop that microbiome

I find that way of personifying our environment counter productive. It's not mother nature's way of helping us, it's that we evolved over millions of years in this environment and to change that is to hinder ourselves. I find this a much more accurate and convincing way of arguing for a back to nature style of development and nutrition.