The mammalian intestinal tract is colonized by an indigenous diverse microbial community that remains highly stable throughout the individual’s life. Over 1000 different bacterial species are estimated to be present in the human gastrointestinal tract¹, with a density of 1011 bacterial cells per gram wet weight in the distal large bowel contents, outnumbering eukaryotic cells by an order of magnitude. The “normal” intestinal microflora represents a complex equilibrium of microbial populations and builds the first line of defense against enteric pathogenic infections and toxic or otherwise noxious agents (e.g. from food)². It is becoming increasingly clear that the close symbiotic relationship between hosts and a resilient microbiota is a vital part of the homeostasis of intestinal physiology. The microbial communities are crucially involved in diverse processes such as the production of short chain fatty acids, metabolism of nutrients and organic substrates, the development of intestinal epithelium, protection against foreign pathogens and importantly, the maturation and development of the immune system^3,4 Intestinal infections, such as acute infectious diarrhea, or antibiotic treatment are typical conditions leading to “dysbiosis”, a state characterized by the destruction of the sensitive intestinal microbial balance. Physiologically, the gut microflora shows a tendency to self-regeneration (so-called resilience phenomenon) resulting in a more or less exact reconstitution of the microbial composition observable before the dysbiosis event⁵.
The stable host-microbe association of an individual is established during the first months of life. The transition from a sterile prenatal intestine to the adult gut – harboring region-specific complex microbial communities – is accompanied by a distinct change in host cellular responses and programs. The transition is influenced by both host genetic factors and environmental influences (e.g. vertical and horizontal transmission). We hypothesize that epigenetic marks (i.e. DNA methylation and histone modification) are important biological master switches that contribute to the stability of the physiological host-flora association⁶.