The intestinal microbiota refers to the vast community of microorganisms inhabiting the human digestive tract. This complex ecosystem, often compared to a hidden organ, includes trillions of microbes such as bacteria, archaea, fungi, and viruses. They reside predominantly in the large intestine. The collective genetic material of these microbes is sometimes referred to as the gut microbiome.
Composition of the Intestinal Microbiota
The intestinal microbiota is a diverse collection of microorganisms, with bacteria being the most numerous and studied component. While bacteria dominate, this microbial community also includes fungi (mycobiome), viruses (virome), and archaea (archaeome). In humans, the gut microbiota can contain approximately 1,000 species of bacteria, 66 genera of fungi, and at least 5 genera of archaea.
The bacterial population in the gut is primarily composed of two dominant phyla: Firmicutes and Bacteroidetes. Other bacterial phyla, such as Proteobacteria, Actinobacteria, and Verrucomicrobia, are also present, though typically in lower abundances. A balanced proportion between these main bacterial groups is considered important for maintaining overall health. The specific composition of an individual’s microbiota is unique, much like a fingerprint, and is established early in life, becoming relatively stable by around two to three years of age.
Key Roles in Human Health
The intestinal microbiota performs several key functions beneficial to human health. One primary function involves the metabolism of nutrients, particularly the breakdown of dietary fiber. Humans cannot fully digest dietary fiber, but gut bacteria ferment these compounds in the large intestine. This fermentation process produces short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which serve as an energy source for colon cells and maintain the gut barrier. SCFAs are also involved in regulating glucose and lipid metabolism throughout the body.
The microbiota also plays a role in supporting the immune system. From birth, gut microbes train the host’s immune defenses, promoting the development of immune cells like regulatory T cells that maintain immune balance. The bacteria strengthen the gut lining, forming a physical barrier that prevents harmful substances and pathogens from entering the bloodstream. Microbial metabolites, including SCFAs, also modulate inflammation and regulate immune responses.
A third function is the synthesis of essential vitamins the human body cannot produce. Gut bacteria synthesize:
B12 (cobalamin)
B1 (thiamine)
B2 (riboflavin)
B3 (niacin)
B5 (pantothenic acid)
B6 (pyridoxine)
B7 (biotin)
B9 (folate)
Vitamin K, which is involved in blood clotting processes.
The Gut-Brain Connection
The gut-brain axis is a continuous communication network linking the gastrointestinal tract and the central nervous system. This bidirectional connection allows the gut to influence brain function and vice versa. One primary pathway for this communication is the vagus nerve, a major nerve transmitting signals between the gut and the brain.
Gut microbes contribute to the production of neurotransmitters, such as serotonin, which influences mood, sleep, and appetite. Approximately 90% of the body’s serotonin is synthesized by enterochromaffin cells in the gut, with microbial metabolites like SCFAs influencing this production. These neurotransmitters can activate vagal nerve fibers, sending signals to brain regions involved in emotional processing and stress responses.
Communication also occurs through the immune system, as gut microbes influence immune cell activity and cytokine release. These immune signals can travel to the brain, affecting mood, stress response, and cognitive functions. Microbial metabolites, including SCFAs, can also directly influence brain physiology and behavior.
Factors Influencing Microbiota Balance
Several external factors shape the composition and balance of the intestinal microbiota. Diet is a primary modulator, with high-fiber foods positively impacting gut health by feeding beneficial bacteria. Dietary fiber acts as prebiotics, promoting the growth of beneficial bacterial strains. Fermented foods, such as kimchi, sauerkraut, and kefir, contain beneficial bacteria (probiotics) and their metabolites. Polyphenols, found in fruits, vegetables, coffee, tea, and wine, also influence the gut microbiota by being metabolized by microbes.
Antibiotics have a strong effect on the gut microbial community, often leading to a rapid reduction in bacterial diversity. These drugs can eliminate beneficial microbes alongside harmful ones, altering the balance of species. While the gut microbiota can show some resilience and recover after antibiotic treatment, these effects can sometimes be long-lasting or permanent. Other lifestyle factors, including chronic stress and sleep quality, also affect the diversity and composition of the intestinal microbiota.
Understanding Dysbiosis
Dysbiosis refers to a disruption in the balance of the intestinal microbiota, characterized by changes in composition, functional activities, or distribution. It involves an overgrowth of potentially harmful microbes, a reduction in beneficial organisms, and a loss of overall microbial diversity. These aspects often occur concurrently.
When dysbiosis occurs, the protective functions of the microbiota can be compromised. This imbalance can lead to a less stable microbial community and is associated with increased susceptibility to various health issues. Issues may include chronic inflammation, as the disrupted microbiota affects immune responses, and digestive problems due to altered metabolic activities.