A growing body of literature indicates that our “second genome”- the genes in our resident microorganisms (microbiome) - affects many aspects of our physiology. From this perspective, we are “supraorganisms” coated and inhabited by a number of microbial cells that are 10 times greater than the sum of all our human somatic and germ cells, carrying150 fold more genetic information than our own human genome. The intestine contains the largest collection of microbes among all of our body “habitats” (sites for microbial colonization). Together, gut microbes form a community, or microbiota, that has a major impact on health through interactions with host cells (including components of the innate and adaptive immune systems), extraction of nutrients and energy from the diet, and complex biotransformations of a variety of ingested compounds, including potential carcinogens. Shifts in microbiome composition occur at different stages in life, from infancy, through puberty and gestation, to old age. Changes in the composition of the gut microbiome (dysbiosis) have also been associated with different disease states such as obesity, inflammatory bowel disease (IBD), diabetes, and metabolic syndrome.It is also becoming widely known that our gut microbiome has important effects on our moods and behavior. Studies have linked gut bacterial composition with risk taking, anxiety, stress, mating and sexual preferences in animals. These are concurrent with alterations found in serotonin levels, levels of brain derived neurotrophic factor (BDNF), and exaggerated corticosterone release in response to stress. Germ free animals also provide an important tool to study the contribution of the microbiota as they have altered serotonergic function in the central nervous system and different behavioral patterns. Taken together, the data indicates the important roles of microbiota in host behavior.