Some posts I have made on these topics on the Curious Cat Science Blog: Waste from Gut Bacteria Helps Host Control Weight (2008) - Tracking the Ecosystem Within Us (2007) - People Have More Bacterial Cells than Human Cells (2007) - Microbes Flourish In Healthy People (2010) - Human Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic (2013)
Here is a recent article looking at variation in human microbiome.
Burgers and fries have nearly killed our ancestral micro biome.
A group of Italian microbiologists had compared the intestinal microbes of young villagers in Burkina Faso with those of children in Florence, Italy. The villagers, who subsisted on a diet of mostly millet and sorghum, harbored far more microbial diversity than the Florentines, who ate a variant of the refined, Western diet. Where the Florentine microbial community was adapted to protein, fats, and simple sugars, the Burkina Faso microbiome was oriented toward degrading the complex plant carbohydrates we call fiber.
The Western microbiome, the community of microbes scientists thought of as “normal” and “healthy,” the one they used as a baseline against which to compare “diseased” microbiomes, might be considerably different than the community that prevailed during most of human evolution.
a remarkable and somewhat quixotic effort has begun to catalog and possibly preserve, before they disappear, the microbes of people who live in environments thought to resemble humanity’s past—people whose microbiomes may approximate an ancestral state. Researchers are motoring down rivers in the Amazon, off-roading in the East African savanna, hiking into the mountain villages of Papua New Guinea. They see themselves as rushing to catalog an ecosystem that may soon disappear.
“It’s really our last chance to harvest a lot of these microbes from around the world,” Rob Knight, a microbiologist at the University of California, San Diego, told me. “We have to do it before it’s too late—and it’s very nearly too late.”
It is a very good idea to learn much more about this area. And it is also wise to learn what microbes we have co-evolved with for so long - before that information is lost.