Your microbiome is the entire community of microorganisms living in and on your body, along with their collective genetic material. This includes bacteria, fungi, viruses, and other microscopic life forms that inhabit your gut, skin, mouth, and other surfaces. A revised 2016 estimate published in PLoS Biology found that the average human body contains roughly 38 trillion bacterial cells alongside about 30 trillion human cells, putting the ratio at approximately 1:1. That’s a far cry from the old claim that microbes outnumber our cells 10 to 1, but it still means you’re carrying about half a pound of bacteria at any given time.
Microbiome vs. Microbiota
You’ll often see “microbiome” and “microbiota” used interchangeably, but they refer to slightly different things. Microbiota describes the actual organisms themselves: the bacteria, fungi, and other microbes physically present in a given location. Microbiome is a broader term that includes those organisms plus all of their genes and the molecules they produce. When someone says “gut microbiome,” they’re talking about the whole ecosystem, not just a list of species.
Where Microbes Live in Your Body
The gut gets the most attention, but microbes colonize nearly every surface of your body that contacts the outside world.
In the gut, six bacterial groups dominate in most healthy people. The colon, which is largely oxygen-free, favors two of those groups that specialize in breaking down complex carbohydrates. The upper digestive tract has a different mix, with more oxygen-tolerant bacteria taking over. This distribution matters because bacteria in different sections of the intestine perform different jobs.
Your skin hosts its own distinct community. Resident bacteria like Staphylococcus epidermidis produce antimicrobial compounds that control the growth of harmful species, while other common skin microbes convert oils in your pores into fatty acids that maintain an acidic skin surface and discourage invaders. The specific mix varies dramatically between oily areas like your face and dry areas like your forearms.
The mouth has yet another ecosystem. Certain streptococci produce hydrogen peroxide that inhibits cavity-causing bacteria. Oral bacteria also convert dietary nitrate into nitrites, compounds that influence blood pressure and cardiovascular health. When this oral community falls out of balance, conditions like gum disease and tooth decay follow.
What Your Microbiome Does for You
Gut bacteria ferment dietary fiber that your own digestive enzymes can’t break down. The end products of that fermentation are short-chain fatty acids, primarily acetate, propionate, and butyrate. These three compounds account for over 95% of the short-chain fatty acids in your colon, and collectively they supply roughly 10% of your daily calorie needs.
Each one plays a distinct role. Butyrate is the preferred fuel for the cells lining your colon, providing 60 to 70% of their energy. Acetate travels to the liver, where about 70% of it gets used for energy production and as a building block for cholesterol and long-chain fatty acids. Propionate serves as a raw material for the liver to produce glucose.
Beyond energy, these fatty acids help regulate fat metabolism throughout the body. They activate fat burning while slowing down fat production and fat release from storage, which leads to lower levels of free fatty acids circulating in the blood. They also help normalize blood sugar levels by stimulating gut hormones that improve how your body handles glucose, and they’ve been shown to reduce cholesterol concentrations in both animal and human studies.
Training the Immune System
Your microbiome plays a critical role in teaching your immune system what to attack and what to leave alone. Short-chain fatty acids from gut bacteria promote the development of regulatory immune cells that keep inflammation in check and maintain tolerance to harmless substances like food proteins. Compounds released by certain bacteria help mature a branch of the immune system that fights infections, while simultaneously preventing the overactive immune responses involved in allergies.
This training process starts at birth. Babies born vaginally pick up microbes from the birth canal and intestine, including beneficial species like Bifidobacterium that are important for early immune development. Babies born by cesarean section miss this initial transfer, often ending up with fewer of these beneficial microbes and a higher proportion of opportunistic species instead. Breastfeeding further shapes the infant microbiome: exclusively breastfed infants show enhanced microbial richness and diversity compared to formula-fed infants. The combination of vaginal delivery, exclusive breastfeeding, and no early antibiotic exposure is considered the optimal starting point for microbial colonization.
When the Balance Tips: Dysbiosis
Dysbiosis is the term for a disrupted microbiome. It can mean a shift in which species are present, a change in what those species are producing, or a change in where they’re located within the gut. This imbalance has been linked to a range of chronic conditions, including inflammatory bowel disease, obesity, type 1 and type 2 diabetes, colorectal cancer, allergic disorders, and autism.
Antibiotics are one of the most common triggers. A course of antibiotics doesn’t just kill the bacteria causing your infection; it can significantly reduce the diversity of your entire gut community. Research in mice has shown that even after antibiotics are removed, overall diversity may stabilize at a level significantly lower than before treatment. One key bacterial group saw permanent diversity drops of 36% to 70% depending on the antibiotic used. How quickly and completely you recover depends on your diet, which surviving species remain to repopulate, and what environmental sources of bacteria you’re exposed to afterward.
How Diet Shapes Your Microbiome
Dietary fiber is the single most important fuel source for your gut bacteria. Since your own enzymes can’t break down most fiber, it passes intact to the colon, where bacteria ferment it into the short-chain fatty acids that drive so many health benefits. Clinical trials have found that supplementing with specific fiber types, including fructo-oligosaccharides, galacto-oligosaccharides, whole grains, and wheat bran, significantly increases populations of beneficial Bifidobacteria and Lactobacilli. In one trial, consuming 45 grams of whole-grain oats per day led to significant increases in both of those beneficial groups.
The relationship between fiber and microbial diversity appears to be dose-dependent. People consuming higher amounts of insoluble fiber (at least 7 grams per 1,000 calories daily) tend to have greater microbial diversity than those eating less. For someone eating 2,000 calories a day, that translates to about 14 grams of insoluble fiber, the type found in whole grains, vegetables, and the skins of fruits. A varied, fiber-rich diet gives different bacterial species the substrates they need to thrive, which helps maintain the kind of diverse community associated with good health.