What Is the Microbiome? The 39 Trillion Organisms Living Inside You
Your microbiome is the vast community of bacteria, viruses, and fungi that live in and on your body. Learn how these organisms influence your digestion, immunity, mood, and even your weight — and why your gut is sometimes called your 'second brain.'
Explain It Simply Editorial Team
Published May 17, 2026
What Lives Inside You
Your microbiome is dominated by bacteria, but it also includes archaea (single-celled organisms distinct from bacteria), viruses (including bacteriophages that infect your bacteria), fungi (including yeasts like Candida), and even some protists. The composition varies dramatically by body site.
Your gut (particularly the large intestine) contains the vast majority of your microbiome — roughly 70% of all microbial cells. The large intestine alone harbors approximately 100 billion bacteria per gram of content. Major gut bacterial phyla include Firmicutes and Bacteroidetes, which together make up about 90% of gut bacteria. The ratio between these two phyla has been linked (controversially) to obesity, with some studies suggesting obese individuals have a higher Firmicutes-to-Bacteroidetes ratio.
Your skin hosts about 1,000 species of bacteria, varying by location. Oily sites (face, back) are dominated by Propionibacterium, dry sites (forearms) by Staphylococcus and Corynebacterium, and moist sites (armpits, groin) by Staphylococcus and Corynebacterium species that produce body odor as metabolic byproducts.
Your mouth contains roughly 700 species — the second most diverse microbial community after the gut. Streptococcus mutans produces acid that causes tooth decay. The oral microbiome is so individually distinctive that it could potentially be used for identification.
Your microbiome is established in the first 2-3 years of life and is shaped by delivery method (vaginal birth provides different initial colonizers than C-section), breastfeeding versus formula, antibiotic exposure, diet, environment, and genetics. By age 3, your microbiome composition roughly resembles an adult pattern.
Different body sites host distinct microbial communities, with the gut harboring the vast majority.
The Gut-Brain Axis: Your Second Brain
The connection between your gut and brain is so extensive that scientists call the gut the 'second brain.' The enteric nervous system — a network of 500 million neurons lining your gastrointestinal tract — can operate independently of your brain and spinal cord.
The gut-brain axis is a bidirectional communication highway using three pathways. The vagus nerve — the longest cranial nerve — directly connects the gut to the brainstem. Gut bacteria stimulate vagus nerve signaling, which influences mood, stress response, and memory. Studies in mice showed that cutting the vagus nerve blocked the anti-anxiety and antidepressant effects of certain probiotic bacteria.
Gut bacteria produce neurotransmitters. Roughly 95% of your body's serotonin (a key mood regulator) is produced in the gut, not the brain. Gut bacteria also produce GABA (an inhibitory neurotransmitter that reduces anxiety), dopamine, and norepinephrine. The mechanism isn't fully understood — these molecules may signal locally through the enteric nervous system rather than crossing the blood-brain barrier directly.
The immune system mediates gut-brain communication. Approximately 70% of your immune cells reside in the gut. Gut bacteria constantly interact with these immune cells, influencing systemic inflammation. Chronic low-grade inflammation (which can be influenced by gut microbiome composition) has been linked to depression, anxiety, and neurodegenerative diseases.
Human clinical evidence is growing but still preliminary. A 2019 study in Nature Microbiology found that people with depression had consistently lower levels of two bacterial genera (Coprococcus and Dialister) compared to non-depressed individuals, even after controlling for antidepressant use. However, correlation doesn't prove causation — depression might change the microbiome rather than vice versa, or both might be influenced by a third factor like diet.
Feeding Your Microbiome: What Actually Works
The microbiome field is plagued by hype, with supplement companies making claims far ahead of the science. Here's what evidence actually supports.
Dietary fiber is the most well-supported intervention. Gut bacteria ferment fiber that humans cannot digest, producing short-chain fatty acids (SCFAs) — particularly butyrate, propionate, and acetate. These SCFAs nourish the cells lining your intestine, reduce inflammation, and influence metabolism. The average American consumes about 15 grams of fiber daily; the recommended amount is 25-35 grams. Increasing fiber intake consistently improves microbiome diversity in clinical studies.
Dietary diversity matters more than any single food. A landmark study by the American Gut Project found that people who ate 30 or more different plant foods per week had significantly more diverse microbiomes than those eating fewer than 10 — regardless of whether they identified as vegetarian, vegan, or omnivore. Diversity of input creates diversity of microbes.
Fermented foods (yogurt, kefir, sauerkraut, kimchi, kombucha) contain live microorganisms. A 2021 Stanford study by Sonnenburg and colleagues found that a diet high in fermented foods increased microbiome diversity and reduced markers of inflammation in healthy adults — one of the strongest dietary interventions yet demonstrated.
Probiotics (supplemental live bacteria) have strong evidence for specific conditions — particularly antibiotic-associated diarrhea and some types of irritable bowel syndrome. However, the general claim that 'probiotics improve gut health' is not well-supported. Most probiotic supplements contain a few generic strains (Lactobacillus, Bifidobacterium) that may not colonize your gut permanently. A 2018 study in Cell found that in many people, probiotic bacteria passed through the gut without establishing residence.
Antibiotics are the most significant disruptors of the microbiome. A single course of broad-spectrum antibiotics can eliminate 30-50% of gut bacterial species. While most recover within weeks to months, some species may not return for years or ever. This doesn't mean antibiotics should be avoided when medically necessary — it means they shouldn't be used for viral infections (where they don't work anyway).
Sources: Sender et al., Cell (2016), Sonnenburg et al., Cell (2021), Valles-Colomer et al., Nature Microbiology (2019), Human Microbiome Project (NIH), McDonald et al., mSystems (2018).
💡 AHA Moment
Here's the insight about the microbiome that fundamentally changes how you think about yourself: you are more bacteria than human.
Your body contains approximately 30 trillion human cells. Your microbiome contains approximately 39 trillion microbial cells. By cell count, you are only about 43% human. The rest is bacteria, archaea, viruses, and fungi — a teeming ecosystem that weighs about 2-3 pounds (roughly the weight of your brain).
But the gene count is even more striking. The human genome contains roughly 20,000 genes. Your microbiome collectively contains 2-20 MILLION unique genes — 100 to 1,000 times more genetic information than your own DNA. These microbial genes encode functions your human genome can't perform — breaking down certain fibers, synthesizing essential vitamins (K, B12, folate), training your immune system, and producing neurotransmitters.
You are not an individual organism. You are an ecosystem — a walking, talking coral reef of interacting species. And the composition of that ecosystem affects everything from your digestion to your mental health to your response to medications. The 'you' that you think of as a single being is actually a democratic republic of 39 trillion organisms that happen to mostly agree on which direction to walk.
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