Just recently noticed this IOM workshop summary*. I've only very superficially glanced through it, but it seems to cover some of the interesting microbial info that's been posted by others. (Emphasis added.)
Investigations of microbial ecology in a variety of organisms and contexts have begun to illuminate the properties of host-associated microorganisms. These observations have revealed a complex and dynamic network of interactions across the spectrum of host, microbe, and environmental niches that may influence states of health and disease. Alterations in the composition and dynamics of the human microbiome have been associated with a variety of complex diseases — including such chronic conditions as cardiovascular disease, obesity, and inflammatory bowel diseases. This ecologically-informed view is a paradigm shift away from the conventional "one-microbe, one-disease" perspective of infection and may lead to new insights and approaches to health maintenance, disease prevention, and treatment methods in humans, animals, and plants... [workshop summary webpage]
We postulate that the important factor in modern allergic and metabolic diseases might not be our decreased sampling of the microorganisms in food, air, water or soil, as has been postulated by the “hygiene hypothesis” (Strachan, 1989), but instead could reflect the loss of our ancestral microorganisms….
We believe that alterations in human macroecology have progressively affected the composition of our indigenous microbiota, which in turn has affected human physiology and, ultimately, disease risk.
The increases that have occurred in recent years in the prevalence of conditions such as obesity and asthma, as well as oesophageal disorders that are a consequence of reflux, have been so rapid that an environmental cause must be present (Eder et al., 2006; Flegal et al., 2007; Pohl and Welch, 2005). Is one of these causes the loss of one or more constituents of the indigenous microbiota? [p.116]