The relevance of the microbiome for disease is one of the very hot ares for research these days. I came across an article about how rheumatoid arthritis, an autoimmune disease, may be related to the bacteria living in our gut (see: Joint Pain, From the Gut). It's a long article and I encourage you to read the whole piece. I present below only an excerpt that interested me:
[A microbiome researcher] ...[says] that it appears that many of the bugs that live inside us have thrived by modulating the immune system to avoid being recognized...as invaders; in essence, these organisms train immune cells not to be trigger-happy. A microbiome with the wrong sorts of bugs, or the wrong ratio of bugs—a situation known as dysbiosis—may unbalance this immune system, causing immune cells to assault not only bacteria, but also the body itself. Microbes are especially influential in the gut, which houses two-thirds of the body’s immune cells. As the pathway for digestion, the gastrointestinal tract must deal with a constant stream of food-related foreign microbes, which must be monitored and, if they are harmful, destroyed. To do this, our intestines have developed an extensive immune system, whose effects reach far beyond the gut. Immune cells in the gut seem to be able to activate inflammatory cells throughout the body, including in joints.....Dozens of researchers are looking into a range of potential strategies to use bacteria as medicine for immune disorders. [One of them] thinks that eventually, it will be possible to treat arthritis by adjusting the microbiome.
Here's a definition of the microbiome to kick of this brief discussion: A microbiome is "the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space." Joshua Lederberg coined the term, arguing the importance of microorganisms inhabiting the human body in health and disease (see: Microbiome).
This article articulated for me a reasonable explanation for the interaction between our gut bacteria and health/disease. We have a relationship with them and the normal flora seems to have trained the intestinal immune system to leave them alone. However, our gut flora is changing for various reasons such as our modern ideas about hygiene and our extensive use of antibiotics. The huge global food companies like Nestle have been promoting so-called neutraceuticals for years. So "Big Food" seems to have understood this market before "Big Pharma" and the two "Bigs" seem to be getting ready to compete for this new and exciting market (see: Nutraceuticals: Big Pharma or Big Food’s next Big Growth area?). Here's a quote from this article that raises only one of the myriad issues pertaining to neutraceuticals:
Suppose that an oncology drug showed better outcomes when paired with a specially designed nutrition supplement produced by the same company as created the drug. Suppose that the outcomes were well studied to the point of inclusion in the drugs label. If outcomes for this combination treatment were sufficiently different than those of other therapies in the same class, could payers require the combination therapy before competitive monotherapies?