Adaptation of the microbiome to changing diets

The human gut houses trillions of microbes from hundreds of species forming an ecosystem called the microbiome. This ecosystem not only aids digestion and gut health, but is wired into diverse physiological processes including immune system regulation, metabolism, and central nervous system function. Unlike our human genome, our microbiome can adapt to changes in its environment on a timescale ranging from days to weeks with diet being one of the most powerful influences on the microbiome. This plasticity enables adaptations to dietary changes, such as those associated with seasons or migrating into new environments; however, it also represents a vulnerability. Extreme or prolonged dietary change can drive microbial extinctions in the gut microbiome, as well as changes in composition and function that are deleterious to human health. Recent evidence has revealed that humans living an industrialized lifestyle harbor a gut microbiome that is radically different from that of our paleolithic ancestors. Adaptation of the gut microbiome to industrial, highly processed foods has resulted in a deteriorated ecosystem that may be causing and contributing to many chronic metabolic and inflammatory diseases.