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Microbiome

Table of Contents

What the microbiome actually does
Microbiome diversity and why it matters for longevity
What drives dysbiosis

What the microbiome actually does

Your gut harbors roughly 38 trillion microorganisms, including bacteria, archaea, fungi, and viruses. Together they encode over 3 million genes, about 150 times more than the human genome. This microbial community operates like an organ: it produces vitamins (K2, B12, folate), synthesizes neurotransmitters (about 90% of your body's serotonin is made in the gut), metabolizes bile acids, trains immune cells, and maintains the intestinal barrier that keeps pathogens and toxins out of the bloodstream.

Microbiome diversity and why it matters for longevity

Microbial diversity, the number and balance of species in your gut, is the single best predictor of gut health. Higher diversity correlates with lower rates of obesity, type 2 diabetes, inflammatory bowel disease, and allergies. Diversity declines with age, contributing to "inflammaging," the chronic low-grade inflammation that accelerates biological aging ^[1]. But this decline isn't inevitable. A 2020 systematic review found that centenarians and other long-lived populations maintain higher microbial diversity than typical elderly adults, with elevated levels of Akkermansia muciniphila, Bifidobacterium, and Christensenellaceae ^[2]. These taxa produce butyrate and other short-chain fatty acids that strengthen the gut lining, tamp down inflammation, and support metabolic health.

The gut-brain axis

The gut and brain communicate through the vagus nerve, immune signals, and microbial metabolites. Gut bacteria produce short-chain fatty acids that stimulate serotonin synthesis in intestinal enterochromaffin cells ^[3]. Dysbiosis, an imbalance in microbial composition, can disrupt tryptophan metabolism and reduce serotonin availability, which has been linked to depression, anxiety, and cognitive decline ^[4]. This isn't a one-way street. Chronic psychological stress alters gut permeability and shifts microbial composition, creating a feedback loop between mental and digestive health.

What drives dysbiosis

Dysbiosis typically shows up as reduced diversity, overgrowth of pathogenic species, and loss of beneficial bacteria like Faecalibacterium prausnitzii. Common triggers include antibiotic overuse (even a single course can disrupt the microbiome for months), chronic stress, high-sugar diets, ultra-processed foods, and environmental toxins. Recovery timelines vary: dietary changes can shift microbial composition within 24 to 72 hours, but restoring stable diversity after antibiotics may take one to two months or longer ^[5].

How to build a healthier microbiome

The evidence consistently points to a few strategies. First, eat at least 30 different plant species per week. This includes vegetables, fruits, legumes, nuts, seeds, herbs, and whole grains. Population studies show this threshold produces the highest diversity scores ^[6]. Second, include fermented foods daily: sauerkraut, kimchi, kefir, yogurt, miso, and kombucha introduce live cultures and boost microbial diversity. A 2021 Stanford trial found that a high-fermented-food diet increased microbiota diversity and decreased inflammatory markers over 10 weeks ^[7]. Third, prioritize prebiotic fibers like inulin (garlic, onions, chicory), resistant starch (cooled potatoes, green bananas), and beta-glucans (oats, mushrooms). Aim for 30+ grams of total fiber daily.

A note on microbiome testing

Direct-to-consumer gut microbiome tests have become popular, but a 2024 international consensus statement published in The Lancet Gastroenterology concluded that there is currently no validated benchmark for a "normal" microbiome, and clinical recommendations based on these tests are premature ^[8]. The high inter-individual variability in healthy microbiomes makes meaningful interpretation difficult. For now, stool testing is more useful for research than for guiding personal supplementation decisions.

References

Eat 30 plant species per week

The American Gut Project found that people who eat 30 or more different plant types per week have significantly more diverse gut microbiomes than those who eat fewer than 10. Count vegetables, fruits, legumes, nuts, seeds, herbs, spices, and whole grains.

pubmed.ncbi.nlm.nih.gov

Add fermented foods daily

A 2021 Stanford trial showed that eating 6 or more servings of fermented foods per day for 10 weeks increased microbiome diversity and lowered 19 inflammatory markers. Start with sauerkraut, kimchi, kefir, or plain yogurt.

pubmed.ncbi.nlm.nih.gov

Use resistant starch as a prebiotic

Cooled cooked potatoes, green bananas, and overnight oats contain resistant starch that passes undigested to the colon, where it feeds beneficial bacteria and increases butyrate production. Cooking and then cooling starchy foods increases their resistant starch content.

Rebuild after antibiotics deliberately

A single antibiotic course can reduce microbiome diversity for one to two months. After antibiotics, prioritize high-fiber foods and fermented foods rather than jumping straight to probiotic supplements, which may actually slow natural recovery in some cases.

Manage stress to protect your gut

Chronic stress increases intestinal permeability ("leaky gut") and shifts microbial composition toward inflammatory species. The gut-brain axis is bidirectional: regular breathwork, meditation, or vagus nerve stimulation can measurably improve gut microbial profiles.

Are gut microbiome tests worth it?

Currently, most experts say no for clinical decision-making. A 2024 international consensus statement in The Lancet concluded that there is no validated benchmark for a "normal" microbiome, and the high variability between healthy individuals makes results hard to interpret. These tests are useful for research purposes, but basing supplement or diet decisions on them is premature.

Does the gut microbiome affect mental health?

Yes. About 90% of the body's serotonin is produced in the gut, and gut bacteria directly influence this process through short-chain fatty acid production. The gut-brain axis, a bidirectional communication network involving the vagus nerve, immune signals, and microbial metabolites, links gut health to mood, anxiety, and cognitive function. Dysbiosis has been associated with higher rates of depression and anxiety in clinical studies.

What is the connection between the microbiome and aging?

Microbial diversity naturally declines with age, contributing to "inflammaging," a state of chronic low-grade inflammation linked to age-related diseases. However, studies of centenarians show they maintain unusually high microbial diversity with elevated levels of beneficial bacteria like Akkermansia muciniphila and Bifidobacterium. These bacteria produce butyrate, which strengthens the gut barrier and reduces systemic inflammation.

Should I take probiotics?

It depends on the situation. Specific probiotic strains like Lactobacillus rhamnosus GG and Saccharomyces boulardii have good evidence for targeted conditions such as antibiotic-associated diarrhea and IBS. Generic multi-strain supplements have weaker evidence. For most healthy people, eating a diverse diet rich in fiber and fermented foods is more effective than supplementation for building long-term microbial diversity.

How long does it take to change your gut microbiome?

Your microbiome starts responding to dietary changes within 24 to 72 hours. However, these shifts are temporary unless you maintain the new habits. Sustaining a diverse, high-fiber diet for about six months produces more durable changes. After antibiotic use, full recovery of microbial diversity typically takes one to two months, though some species may take longer to return.