Gut Microbiota

The gut microbiota is the community of microorganisms that inhabits the gastrointestinal tract. It includes bacteria and archaea as well as microbial eukaryotes such as fungi. These organisms are not distributed uniformly along the digestive tract. Different regions provide distinct environments, and the large intestine contains particularly dense microbial communities .^1,2

Members of the gut microbiota interact with one another and with the human host. Among their activities, intestinal microorganisms metabolize substances that human digestive enzymes do not fully break down, including some dietary fibers and resistant starch. This microbial metabolism can produce compounds such as short-chain fatty acids. Gut microorganisms also interact with the intestinal lining and immune system and participate in metabolic processes involving nutrients and other compounds present in the gut .²

The composition of the gut microbiota varies considerably between individuals and can also change within the same person over time. Factors associated with this variation include age, diet, medications, host physiology, and local conditions within different regions of the gastrointestinal tract. There is therefore no single microbial species composition that defines the gut microbiota of every healthy person .²

Gut microbiota and gut microbiome are related but not strictly identical terms. Microbiota refers specifically to the community of microorganisms, whereas microbiome is a broader concept that can include the microorganisms together with their genetic material, metabolites, structural elements, and surrounding ecological environment. Viruses and bacteriophages may also be included within broader definitions of the gut microbiome, although terminology varies between fields .¹