Microbiome
We host roughly 38 trillion microorganisms in our gut — a number comparable to our own cell count (Sender et al., 2016). Estimates vary by individual and by calculation method. This microbiome communicates constantly with our brain, our immune system, and our metabolism. Science is beginning to measure this conversation with precision.
Gut microbiome: what science is discovering about the gut-brain axis
The gut microbiome may act as a biological infrastructure influencing immunity, inflammation, and certain neurological signals — via the gut-brain axis and the production of bioactive metabolites.
5 key takeaways
- The gut microbiome hosts roughly 38 trillion microorganisms — an estimate comparable to the number of human cells (Sender et al., 2016), though this figure varies by individual and calculation method
- The gut-brain axis relies primarily on the vagus nerve as a bidirectional communication pathway
- About 90 to 95% of the body's serotonin is produced in the gut, partly under microbial influence
- Short-chain fatty acids (SCFAs) produced by bacterial fermentation play a documented anti-inflammatory role
- Microbial diversity is a marker of health — populations eating more than 30 plants/week show a more diverse microbiome
For a long time, the gut was seen as a simple digestive tube. Microbiology research since the 2000s has profoundly changed this view. The gut hosts a complex ecosystem whose interactions with the brain, the immune system, and metabolism are the subject of a growing number of studies.
1. The microbiome — an ecosystem within us
The term "microbiome" refers to the collection of microorganisms (bacteria, viruses, fungi, archaea) that colonize our body, and their collective genes. The gut microbiome is by far the most studied and the densest — roughly 38 trillion microorganisms across 1,500 to 2,000 different species in a healthy individual.
The collective microbial genome (the "metagenome") contains roughly 150 times more genes than the human genome. This genetic richness allows the microbiome to perform metabolic functions that our own cells cannot — notably fermenting dietary fiber into bioactive metabolites. Microbial diversity, measured by the alpha-diversity index, is associated in several epidemiological studies with better overall health.
Thursby E. & Juge N., Biochemical Journal, 2017 · PubMed PMID: 28512250If the human genome is the organism's source code, the microbial metagenome is a plugin library — functional extensions we couldn't write ourselves. Microbial diversity is the equivalent of an operating system rich in drivers: the more compatible drivers exist, the more efficiently the environment can adapt.
2. The gut-brain axis — the vagus nerve as fiber optic cable
The gut contains roughly 500 million neurons — more than in the spinal cord. This neuronal network, called the enteric nervous system (ENS), communicates with the brain via several pathways, the main one being the vagus nerve.
The vagus nerve is a bidirectional pathway: roughly 80 to 90% of its fibers carry information from the gut to the brain (afferent pathway), and only 10 to 20% in the opposite direction. The microbiome can influence this communication through the production of neurotransmitters and precursors. About 90 to 95% of the body's serotonin is synthesized in the gut by enterochromaffin cells, partly under the influence of certain gut bacteria. GABA (gamma-aminobutyric acid), the brain's main inhibitory neurotransmitter, is also produced by certain bacteria such as Lactobacillus and Bifidobacterium — mainly in in vitro and animal models; evidence of direct transfer in humans remains preliminary.
Cryan J.F. et al., Physiological Reviews, 2019 · PubMed PMID: 31460832The vagus nerve is a bidirectional fiber optic cable — but an asymmetric one. The 80/20 ratio favoring upward signals means the brain listens to the gut far more than it dictates to it. What the microbiome "tells" the brain through this fiber can influence mood, anxiety levels, and stress responses. This is a communication architecture whose protocols we are only beginning to understand.
The correlation between microbial composition and psychological states is documented in several studies, but the mechanisms of direct causality in humans remain incomplete. Studies on "psychobiotics" (probiotics with potential cognitive effects) are promising but still rely on small trials. The gut-brain axis is real and documented — its direct therapeutic applications, notably regarding "psychobiotics", are the subject of clinical trials still limited in size and duration.
3. Microbiome and immunity — the GALT
Gut-Associated Lymphoid Tissue (GALT) represents the body's largest concentration of immune cells — roughly 70% of the body's immune cells reside in and around the gut.
The microbiome plays a role in "educating" the immune system. Studies on germ-free animals show underdeveloped immune systems with dysregulated responses. In humans, early microbial diversity (in the first years of life) is associated in several longitudinal studies with a reduced risk of allergies and autoimmune diseases. Gut bacteria notably interact with dendritic cells and regulate the ratio of regulatory T cells to Th17 cells, a balance important for immune tolerance.
Belkaid Y. & Hand T., Cell, 2014 · PubMed PMID: 24679531Dietary diversity is the best-documented lever for maintaining microbial diversity. The American Gut Project study (McDonald et al., mSystems, 2018 · PubMed PMID: 30228273), involving over 10,000 participants, showed that individuals eating more than 30 different types of plants per week had a significantly more diverse microbiome than those eating only 10 (alpha-diversity measure). Diversity matters more than the quantity of any single food.
4. SCFAs — the anti-inflammatory metabolites
Gut bacteria ferment dietary fiber (prebiotics) to produce short-chain fatty acids (SCFAs) — mainly butyrate, propionate, and acetate. These metabolites are today at the heart of much research in immunology and neurology.
Butyrate is the main energy source for colonocytes (colon cells). In vitro and animal-model studies show it can strengthen the tight junctions of the intestinal wall (reducing intestinal permeability), inhibit certain pro-inflammatory pathways via NFκB, and cross the blood-brain barrier to influence neurological processes. Preliminary human data suggest an association between butyrate production and reduced systemic inflammation, but large-scale clinical trials remain few.
Canani R.B. et al., Journal of Nutritional Biochemistry, 2011 · PubMed PMID: 21420827SCFAs function like distributed "software patches". Bacteria take unusable input — undigested plant fibers our own cells can't process — and convert them into anti-inflammatory signals usable by the gut, the immune system, and the brain. The higher the bacterial diversity, the wider the range of "patches" available.
The main dietary sources of fermentable prebiotics (substrates for butyrate production): garlic, onion, leek, asparagus, slightly green banana, oats, barley, chicory, Jerusalem artichoke, legumes. Resistant starch (found in cooled potatoes, cooked-and-cooled rice) is also a documented substrate. Regularity and variety appear more relevant than quantity: daily exposure to diverse fiber sources is better supported by the evidence than sporadic large intakes.
5. Dysbiosis — when the balance breaks
Dysbiosis refers to an imbalance in the composition, diversity, or function of the microbiome. It is not a disease in itself but a state associated in many studies with inflammatory, metabolic, and neurological conditions.
Several modern factors are associated with reduced microbial diversity in epidemiological studies: ultra-processed diets (reduced diversity within weeks in some trials), antibiotic use (major documented impact, partial recovery over several months), chronic stress (cortisol alters microbial composition and intestinal permeability), and a sedentary lifestyle. A study by Sonnenburg et al. (Nature, 2016) showed that generations of a low-fiber diet led to an irreversible reduction of certain microbial species in mice — raising questions about multigenerational effects.
Sonnenburg J.L. et al., Nature, 2016 · PubMed PMID: 27064901The concept of "leaky gut" is real but often used loosely in non-scientific literature to attribute many conditions to intestinal permeability. Solid clinical evidence exists for certain conditions (celiac disease, IBD), but causal links with other conditions are still debated. Intestinal permeability is a measurable parameter — not a universal explanation.
Plant diversity: Aim for 30 different plants per week — vegetables, fruits, legumes, whole grains, nuts, seeds, herbs, and spices all count. Fermented foods: Kefir, live yogurt, miso, tempeh, kimchi introduced regularly. A study by Wastyk et al. (Cell, 2021) showed that a diet rich in fermented foods increases microbial diversity and reduces inflammation markers. Daily prebiotic fiber: Garlic, onion, legumes, oats. Limiting emulsifiers: Carrageenan, polysorbate 80 — associated in some animal studies with disruption of the mucus layer.
Frequently asked questions
Scientific references
- • Cryan J.F. et al. — Physiological Reviews, 2019 · PubMed PMID: 31460832
- • Thursby E. & Juge N. — Biochemical Journal, 2017 · PubMed PMID: 28512250
- • Belkaid Y. & Hand T. — Cell, 2014 · PubMed PMID: 24679531
- • Sonnenburg J.L. et al. — Nature, 2016 · PubMed PMID: 27064901
- • Canani R.B. et al. — Journal of Nutritional Biochemistry, 2011 · PubMed PMID: 21420827
- • Sender R. et al. — Cell, 2016 · PubMed PMID: 27584518 (38 trillion estimate)
- • Wastyk H.C. et al. — Cell, 2021 · PubMed PMID: 34256014
- • McDonald D. et al. — mSystems, 2018 · PubMed PMID: 30228273 · American Gut Project
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