Human physiology is strongly dependent on its interaction with gut microbial composition and function. Some important associations between lifestyle and health are mediated at least in part by the impact of lifestyle decisions on the gut microbiome. The response of the gut microbiome to diet is in part determined by trophic interactions among unrelated members of the microbial community, so the success of dietary interventions may depend on the pre-existing microbial environment. Trimethylamine oxide (TMAO) is the product of gut microbial metabolism of dietary choline to trimethylamine (TMA), followed by hepatic oxidation of TMA to TMAO. D-lactate, a neurotoxin, is one of the products of microbial fermentation of carbohydrates. Minor dietary components may have a greater impact on microbial growth and function than do macronutrients. Exposure to substances that range from alcohol and tobacco to over-the-counter medications and personal hygiene and cleaning products may impact gut microbial taxonomy or function, sometimes in conjunction with a change in intestinal permeability.