What the gut microbiome is
The gut microbiome is the community of trillions of microorganisms — bacteria, viruses, fungi and archaea — that inhabit the human gastrointestinal tract, particularly the large intestine. Far from being passive passengers, these microorganisms play active roles in digestion, immune function, inflammation regulation and the production of metabolites that affect brain function.
What the research shows
Microbiome research has linked gut composition to an extraordinary range of conditions: inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, depression, anxiety and even some cancers. The mechanisms are multiple: gut bacteria ferment dietary fibre to produce short-chain fatty acids (SCFAs) that regulate immune function; they produce neurotransmitters including serotonin (around 90% of the body's serotonin is produced in the gut); they train and regulate the immune system; and they influence metabolic signalling.
What we do not yet know
The microbiome field is young and many findings are associative rather than causal. The direction of causality — does poor microbiome composition cause disease or does disease alter the microbiome? — is often unclear. The composition of a "healthy" microbiome is not well-defined; diversity (more species, more evenly distributed) is a consistent correlate of health but not a target that can be precisely specified.
Practical implications
The most consistently supported intervention for improving microbiome composition is increasing dietary fibre — particularly diverse plant foods (different types of fibre feed different bacterial species). Fermented foods (live yoghurt, kefir, kimchi, sauerkraut) increase microbiome diversity in short-term studies. Probiotic supplements have good evidence for specific conditions (antibiotic-associated diarrhoea, some forms of IBS) but limited evidence for most of the broad claims made for them.