Gut Microbiome
The 39 trillion microorganisms that regulate immunity, metabolism, and brain function
Definition
The gut microbiome is the set of microorganisms (bacteria, fungi, viruses, archaea) inhabiting the human digestive tract. It is composed of approximately 39 trillion cells (3.8×10¹³), comparable to the number of human cells in the body, with more than 1,000 different bacterial species and a genetic content 150 times greater than the human genome. It is essential for digestion, vitamin synthesis (K2, B12, folate, biotin), immune system maturation, regulation of the gut-brain axis, and production of key metabolites such as short-chain fatty acids.
Detailed explanation
Critical microbiome functions:
SCFA production: butyrate (preferred fuel of colonocytes, anti-inflammatory, epigenetic regulator), propionate, and acetate. Produced by bacteria like Faecalibacterium prausnitzii, Roseburia, and Eubacterium rectale. Immune modulation: 70% of the adaptive immune system is located in the intestinal mucosa (GALT). Microbial diversity trains the immune system to discriminate friend from foe. Neurotransmitter synthesis: 95% of serotonin and 50% of dopamine are synthesised in the gut under microbial influence. Xenobiotic metabolism: gut bacteria metabolise medications, polyphenols, and environmental toxins. Colonisation resistance: by occupying ecological niches, commensal bacteria prevent pathogen growth.
Enterotypes (Arumugam, Nature 2011): classification of humans into 3 predominant patterns — Bacteroides (Western diet), Prevotella (plant-based high-fibre diet), and Ruminococcus (mixed). They predict different responses to the same diet.
Factors shaping the microbiome: delivery (vaginal vs caesarean), feeding (breast vs formula), antibiotics in infancy (long-lasting effects), diet (especially plant-fibre diversity), stress, sleep, exercise, age, geography, and, increasingly, environmental pollution.
Scientific sources
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