The microbiome is a complex and dynamic ecosystem, changing with every aspect of our lifestyle. Diet and food choices are capable of creating profound changes in the microbes that constitute a major component of this organ/organ system. Every characteristic of a food is influential on the populations of bacteria that maintain the mucosal layer and its turnover, is responsible for nutrient absorption, the production of various neurotransmitters, and numerous other critical, physiological processes. Different fiber qualities, carbohydrate densities, and types of sugar have distinct effects on the microbiota. Fat and oil qualities can produce measurable changes in the populations of bacteria families, as well as the presence on specific agrochemicals such as glyphosate and food preservatives such as emulsifiers.