What is the microbiome?
The human gut microbiome is the community of bacteria, archaea, fungi and viruses that inhabit the gastrointestinal tract — primarily the large intestine. Bacterial species number in the hundreds; the total microbial gene count is estimated at over 3 million, dwarfing the roughly 20,000 genes in the human genome.
The Human Microbiome Project (NIH, 2008–2016) catalogued the microbial communities at several body sites. Its successor, the integrative HMP (iHMP), linked microbiome changes to disease states including inflammatory bowel disease and type 2 diabetes.
For background on the difference between prokaryotic (bacterial) and eukaryotic (human) cells, see our cells and organelles guide.
What does it do?
The microbiome performs functions that the human genome alone cannot:
- Fermentation of dietary fibre — bacteria in the colon ferment soluble fibre into short-chain fatty acids (SCFAs) including butyrate, which fuels colonocytes (colon cells) and has anti-inflammatory effects.
- Vitamin synthesis — gut bacteria produce vitamin K₂ and several B vitamins including B12, folate and biotin.
- Immune education — the microbiome trains the developing immune system to distinguish self from pathogen and prevents autoimmune overreaction.
- Pathogen resistance — a diverse microbiome occupies niches that would otherwise be colonised by pathogens such as Clostridioides difficile.
The gut–brain axis
The gut and brain communicate via the vagus nerve, immune signalling and microbially produced neurotransmitter precursors. About 90% of the body's serotonin is produced in the gut — though gut serotonin does not cross the blood–brain barrier, it influences gut motility and signals via the enteric nervous system.
Mouse studies show that germ-free animals (raised without any microbiome) display altered stress responses and anxiety-like behaviour that can be partly reversed by microbiome transplantation. Human trials of psychobiotics (probiotics targeting mood) are at an early stage. See the Nature Reviews Microbiology review on the gut–brain axis.
What harms the microbiome?
Several factors reduce microbial diversity — a proxy for microbiome health:
- Antibiotics — broad-spectrum courses can eliminate entire bacterial families; recovery takes weeks to months.
- Ultra-processed foods — low in fibre and high in emulsifiers that disrupt the mucus layer protecting gut bacteria.
- Caesarean delivery — babies born by C-section miss colonisation by vaginal bacteria and have different early microbiomes.
- Formula feeding — breast milk contains oligosaccharides that selectively feed beneficial Bifidobacterium species.
For the broader problem of antibiotic overuse and resistance, see our CRISPR article on future approaches to treating bacterial infections without antibiotics.