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The gut microbiota is the collection of microorganisms (mainly bacteria, but also archaea, fungi, and viruses) that inhabit the human gastrointestinal tract; the adult gut harbors approximately 100 trillion microorganisms belonging to more than 1,000 distinct species, a biological community that the last two decades of research have transformed from "passive commensals" into an "active metabolic organ" with essential functions for human physiology: production of vitamins (K, B12, biotin), metabolism of dietary fibers into short-chain fatty acids, education and modulation of the immune system, maintenance of intestinal barrier integrity, regulation of the gut-brain axis, and modulation of the metabolism of drugs and xenobiotics.
What most distinguishes a healthy microbiota from an altered one (dysbiosis) is not the presence or absence of specific species, but overall diversity: microbiotas with many distinct species in balanced proportions are consistently associated with better cardiometabolic, immune, cognitive, and emotional health; microbiotas with low diversity and dominance of a few species (common in modern Western societies) are associated with obesity, insulin resistance, inflammatory bowel diseases, anxiety, depression, and susceptibility to infections.
Several factors characteristic of modern life impoverish the microbiota:
Plant diversity in the diet: the American Gut Project documented that people who eat more than 30 different types of plants per week have significantly more diverse microbiotas than those who eat fewer than 10. Diversifying plant sources (legumes, vegetables, fruits, nuts, seeds, spices, whole grains) is probably the most cost-effective dietary intervention.
Prebiotic fiber: selectively feeds beneficial bacteria. Natural sources: artichoke, chicory, onion, garlic, leek, asparagus, green banana, oats, legumes. Supplements: inulin, FOS, GOS (introduce gradually to avoid flatulence).
Fermented foods: yogurt, kefir, sauerkraut, kimchi, miso, tempeh, kombucha; they provide live microorganisms and bioactive metabolites. The Wastyk study (Stanford 2021) showed that increasing fermented food consumption for 10 weeks increased microbial diversity and reduced inflammatory markers.
Specific probiotics: by strain and by clinical indication. - Saccharomyces boulardii: with the best evidence for preventing antibiotic-associated diarrhea. - Lactobacillus rhamnosus GG: acute diarrhea in children. - Lactobacillus reuteri DSM 17938: infant colic. - Bifidobacterium infantis 35624: irritable bowel syndrome.
Reduction of ultra-processed foods, emulsifiers, and non-nutritive sweeteners: growing data suggest that these components alter the microbiota unfavorably.
Bacteria in the colon ferment dietary fibers, producing short-chain fatty acids (SCFAs): acetate, propionate, and especially butyrate. Butyrate is the main energy fuel of colonocytes (the cells of the colon), maintains intestinal barrier integrity, has local and systemic anti-inflammatory activity, and regulates gene expression via histone deacetylase inhibition. Low-fiber diets produce poor fermentation, butyrate deficiency, and functional atrophy of the barrier, one of the mechanistic pathways linking the Western diet to chronic inflammation.
The gut microbiota communicates with the central nervous system through multiple pathways: the vagus nerve, circulating cytokines, short-chain fatty acids that cross the blood-brain barrier, bacterial metabolites (tryptophan, GABA, dopamine, serotonin), and modulation of the immune system. This bidirectional communication (the "microbiota-gut-brain axis") explains the documented correlations between dysbiosis and psychiatric disorders (depression, anxiety, autism spectrum disorders) and opens active lines of research on "psychobiotics" as complements in mental health.
Despite the enthusiasm, it is wise to keep expectations realistic: the microbiome field is young, and many popular claims (test kits with personalized recommendations, microbiota "transplants" for various conditions) are still poorly supported; individual heterogeneity is enormous, and there are still no "personalized" recommendations with a robust scientific basis for most people; the most solid intervention remains the generic one: a diet rich in plant diversity and fiber, regular fermented foods, avoiding ultra-processed foods, exercise, sleep, and stress management.
Information, not medical advice.