What is the microbiome and what does it actually do?
The microbiome is the community of microorganisms living in and on your body — bacteria overwhelmingly, plus fungi, viruses and archaea. Most live in the large intestine.
The numbers. An often-repeated claim is that microbial cells outnumber human cells ten to one. That figure was an estimate from 1972 and has been revised — a 2016 reassessment put the ratio closer to 1:1, with roughly comparable numbers. The revision does not diminish the importance; it corrects a widely repeated statistic.
What it does, with reasonable evidence:
Digests what we cannot. Humans lack enzymes for most dietary fibre. Gut bacteria ferment it, producing short-chain fatty acids — butyrate, propionate, acetate — which feed the cells lining the colon and have systemic effects. This is the clearest and best-established function.
Synthesises vitamins, including vitamin K and several B vitamins.
Trains and regulates the immune system. A large proportion of immune tissue surrounds the gut, and the microbiome influences how it develops and how it distinguishes threat from harmless.
Provides colonisation resistance — occupying niches and consuming resources so pathogens cannot establish. This is why antibiotic disruption enables C. difficile infection.
Metabolises drugs and compounds, sometimes affecting how well a medication works.
Where the evidence is weaker than the coverage suggests. Associations between microbiome composition and obesity, mood, autism, allergy and numerous other conditions are widely reported. Most are correlational, causal direction is frequently unclear, and much of the striking work is in mice. The gut-brain axis is real; specific claims about particular bacteria changing mood in humans are far less established.
Faecal microbiota transplant is genuinely effective for recurrent C. difficile and remains experimental elsewhere.
Commercial probiotics are far less well supported than marketed. Dietary fibre diversity has better evidence than any supplement.