Microbiomes in health, diseases and therapeutics

A microbiome is the aggregate of populations of bacteria, viruses and fungi in an organ system, of which the highly dominant numbers are in the gastrointestinal tract. Some of the bacteria, termed microbiota, support viability and functions of host cells directly by generating beneficial short-chain fatty acid components of dietary fibers and other metabolites of host compounds including secondary bile acids and indole derivatives of tryptophan. Short-chain fatty acids also recruit immune protective elements exemplified by IL-22, which has beneficial effects on intestinal epithelium by their IL-22 receptors. Other bacteria have detrimental effects on host cells through lipopolysaccharides and diverse toxins. An increased ratio of detrimental to beneficial microbiomal bacteria, a state termed dysbiosis, is observed in human diseases of many systems. Therapies for dysbiosis involve largely dietary manipulation and more recently fecal microbiota transplantation. Resistant and recurrent Clostridium difficile diarrhea responds dramatically to fecal microbiota transplantation, but this approach requires additional evaluation in other diseases. The potential prognostic value of microbiome characteristics suggests future uses in precision medicine.