How to read the numbers: Fact = a finding from research or biology
In the human body
Current estimates put the number of bacteria in the body at roughly the same as human cells, most of them living in the large intestine. You can support microbiome diversity with a varied, fibre-rich plant diet and fermented foods.
Is in the gut
A large share of immune cells resides in the gut lining, constantly distinguishing between food, beneficial microbes and threats; the quoted share is an estimate. Support a healthy gut with fibre, enough sleep and avoiding unnecessary antibiotics.
Produced in the gut
The vast majority of serotonin is produced in the gut, where it controls bowel movement; the brain, however, makes its own, and gut serotonin does not reach it. The microbiome affects mood rather indirectly, so a fibre-rich diet is a sensible investment for your mind too.
The human microbiota consists of ~38 trillion microorganisms — bacteria, archaea, viruses and fungi — living mainly in the large intestine. Their collective genome (the microbiome) contains 200× more genes than the human genome. They are not passive guests — they are active metabolic partners.
Dysbiosis is an imbalance of the microbiome — reduced diversity, overgrowth of pathogenic bacteria or loss of key strains. It is linked to obesity, depression, autoimmunity, IBS, SIBO, allergies and a higher risk of colorectal cancer.
The microbiome — the basics
Key phyla: Firmicutes and Bacteroidetes make up ~90% of the gut microbiota. The Firmicutes:Bacteroidetes ratio is elevated in obesity. Akkermansia muciniphila protects the gut barrier and correlates with longevity. Lactobacillus and Bifidobacterium produce lactate and SCFAs (short-chain fatty acids — butyrate, propionate, acetate), which are the primary fuel of enterocytes and have anti-inflammatory effects.
The gut–brain axis
The gut communicates with the brain via the vagus nerve, immune signals and neuroactive metabolites. 95% of serotonin is produced in the gut. Gut bacteria produce GABA, dopamine precursors and short-chain fatty acids that influence neuroinflammation. Dysbiosis is associated with depression, anxiety, autism and Parkinson's disease (alpha-synuclein appears in the gut years before it reaches the brain).
What destroys the microbiome
Antibiotics (even a single course alters the microbiome for months or even years). Ultra-processed food — low in fibre, with emulsifiers (polysorbate 80, carboxymethylcellulose) that damage the mucus layer. Chlorinated water (it disinfects gut bacteria too). Chronic stress increases intestinal permeability. NSAIDs, proton pump inhibitors, steroids. Glyphosate (a herbicide) is an antimicrobial agent.
How to restore microbial diversity
Target: 30+ different plants per week (American Gut Project). Fermented foods: yoghurt, kefir, kimchi, kombucha, miso — a source of live cultures and prebiotics. Prebiotic fibre: inulin (onion, garlic, artichoke), FOS, pectin, resistant starch (cooled rice and potatoes). Spermidine and polyphenols — selectively feed beneficial bacteria. After a course of antibiotics: Saccharomyces boulardii (a yeast, not a bacterium — it survives antibiotics) + Lactobacillus rhamnosus GG.
