What is the gut microbiome, and what does it do?

The gut microbiome is the community of trillions of microorganisms living in the intestines, including over a thousand bacterial species along with viruses, fungi and parasites. It helps with digestion, trains the immune system and produces some nutrients. Links to many diseases are well documented, but most of the evidence is observational. Causation has been shown mainly in a small number of conditions, notably recurrent Clostridioides difficile infection. [1] [2]

A biome is an ecosystem defined by its environment and inhabitants, and the gut works as a miniature one. Cleveland Clinic notes that each person's microbiome is unique. Infants acquire their first microbes during vaginal delivery or breastfeeding, and diet and other exposures add new microbes later, while some exposures can reduce them. Most gut microbes live in a symbiotic relationship with the host: the body supplies food and shelter, and the microbes provide services and help keep harmful species in check. [1]

Gut bacteria break down complex carbohydrates and fibers that people cannot digest alone, producing short-chain fatty acids that feed the cells of the gut lining. They supply enzymes needed to make certain vitamins, including B1, B9, B12 and K, and they help recycle bile acids so the body can digest fats. [1]

The gut holds up to 80% of the body's immune cells, according to Cleveland Clinic. Beneficial microbes help the immune system distinguish helpful microbes from pathogens, compete with harmful species for space and nutrients, and, through short-chain fatty acids, help maintain the gut barrier and dampen inflammation. Memorial Sloan Kettering similarly describes the microbiome and immune system as training and balancing each other. A review in PubMed Central adds that the microbiome also influences endocrine, neural and metabolic pathways. [1] [3] [4]

Shifts in the microbiome, called dysbiosis, have been linked to hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, cancer and irritable bowel syndrome. One review states that most of this evidence is observational and does not establish direct causation. An umbrella review of 195 meta-analyses found the microbiome related to many outcomes, from gastrointestinal and metabolic to neurological and psychiatric ones. It judged interventions such as probiotics and fecal microbiota transplant generally safe and often beneficial, but rated the quality of evidence as not high. [4] [5]

A narrative review in BMJ's eGastroenterology describes a past controversy over whether the microbiome truly causes disease. It lists limits of observational studies: large normal variation by location, diet, age and medications, poorly justified control groups, and the difficulty of excluding reverse causality, where illness changes the microbiome rather than the reverse. Randomised trials have since helped. In a 2013 trial in recurrent C. difficile infection, fecal microbiota transplant after vancomycin gave cure without relapse in 93.8% of patients versus 30.8% with vancomycin alone, and the trial was stopped early. The review describes this as definitive for that infection, and calls smaller trials in ulcerative colitis and cancer immunotherapy suggestive of probable benefit. It reports no such benefit in obesity. [2]