The gut flora consists of the microorganisms that normally live in the digestive tract of animals. The gut flora includes much of the human flora. The term "gut flora" is interchangeable with intestinal microflora and intestinal microbiota.

The average human body, consisting of about 1013 (10,000,000,000,000 or about ten trillion) cells, has about ten times that number of microorganisms in the intestines. The metabolic activity performed by these bacteria is equal to that of a virtual organ causing some to describe the gut bacteria as a "forgotten" organ.

Bacteria make up most of the flora in the colon and 60% of the dry mass of feces. Somewhere between 300 and 1000 different species live in the gut, with most estimates at about 500. However, it is probable that 99% of the bacteria come from about 30 or 40 species. Fungi and protozoa also make up a part of the gut flora, but little is known about their activities.

Research suggests that the relationship between gut flora and humans is not merely commensal (a non-harmful coexistence), but rather is a mutualistic, symbiotic relationship. Though people can survive with no gut flora, the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system, preventing growth of harmful species, regulating the development of the gut, producing vitamins for the host (such as biotin and vitamin K), and producing hormones to direct the host to store fats. However, in certain conditions, some species are thought to be capable of causing disease by producing infection or increasing cancer risk for the host.

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