Your microbiome is the vast community of microorganisms living in and on your body, along with all the genes they carry. A typical adult hosts roughly 38 trillion bacteria, slightly outnumbering the 30 trillion human cells in the body. That near 1:1 ratio replaced an older claim that microbes outnumbered human cells 10 to 1, which turned out to be a significant overestimate. Despite their tiny size, these microbes collectively weigh about 0.2 kilograms and carry 3.3 million unique genes in the gut alone, roughly 150 times more than the 20,000 or so genes in the human genome.
What Lives in Your Microbiome
Bacteria get most of the attention, but your microbiome also includes fungi, viruses (especially bacteriophages, which are viruses that infect bacteria), and archaea, a lesser-known group of single-celled organisms. Most research has focused on bacteria because they’re the most abundant and easiest to study, though the viral component is increasingly recognized as important. Higher bacteriophage diversity, for example, has been linked to lower bacterial diversity and may play a role in conditions like inflammatory bowel disease.
You’ll sometimes see the words “microbiome” and “microbiota” used interchangeably. Technically, microbiota refers to the actual organisms living on you, while microbiome refers to those organisms plus all their genetic material. In practice, most people use “microbiome” to mean the whole package.
Where These Microbes Live
Different parts of your body host very different microbial communities, each adapted to the conditions of that particular environment.
The gut harbors the largest and most studied community. Its composition varies considerably from person to person, but two major bacterial groups tend to dominate: Bacteroides and Firmicutes. The balance between these shifts depending on diet, genetics, and other factors. Some people carry large populations of Bacteroides, while others have greater diversity among Firmicutes species.
Your mouth is surprisingly complex, with distinct microbial neighborhoods on your tongue, gums, cheeks, teeth, and tonsils. Most oral sites are dominated by Streptococcus bacteria, but the species that follow in abundance differ depending on oxygen levels and surface type. The community living on your teeth above the gumline, for instance, looks quite different from the one just below it.
Skin communities tend to be dominated by one of a few key players: Staphylococcus, Propionibacterium, or Corynebacterium, depending on whether the area is oily, moist, or dry. Staphylococcus epidermidis, a harmless species, is essentially universal on human skin and found in 93% of nasal samples. Its close relative Staphylococcus aureus, the bacterium behind MRSA infections, shows up in about 29% of nasal samples.
The vaginal microbiome is comparatively simple. Lactobacillus species dominate all vaginal sites, creating an acidic environment that helps prevent infections.
How Your Microbiome Develops
Microbial colonization begins at birth, and how you’re born matters. Babies delivered vaginally pick up their mother’s vaginal and gut bacteria during the process, with about two-thirds of these newborns showing detectable microbial communities in their first stool. Babies born by elective cesarean section miss that exposure entirely. Only 17% of C-section newborns showed any microbial presence in their earliest samples, and the bacteria they did carry looked more like skin microbes than gut or vaginal ones. Key beneficial bacteria like Bifidobacterium, which mothers typically pass to infants during vaginal delivery, are notably less common in C-section babies.
Over the first few years of life, the microbiome rapidly diversifies and eventually stabilizes into an adult-like pattern. This early window is considered critical because the microbes that colonize first help shape how the immune system develops.
Training Your Immune System
The microbiome plays a fundamental role in building and calibrating your immune system. This relationship is so deeply intertwined that much of the immune system’s complexity appears to have evolved specifically to manage microbial communities.
Studies in animals raised in completely sterile environments show what happens without a microbiome: key immune structures in the gut remain underdeveloped, and critical immune cell populations are drastically reduced. In a normal body, gut bacteria constantly interact with immune cells, helping to produce regulatory T cells that maintain tolerance to harmless substances like food proteins. When this process goes wrong, the result can be food allergies, autoimmune conditions, or chronic inflammation.
Your microbes also train a class of immune cells called Th17 cells, which help maintain the intestinal lining and defend against infections. Most of the body’s active immune cells reside in tissues that are constantly colonized by bacteria, particularly the gut and skin, reinforcing how central this relationship is to everyday health.
Digestion and Nutrient Production
Gut bacteria break down dietary fiber and resistant starch that your own digestive enzymes can’t touch. The main products of this fermentation are short-chain fatty acids: acetate, propionate, and butyrate. These aren’t waste products. Butyrate is the primary fuel source for the cells lining your colon. Propionate travels to the liver and influences glucose production. Acetate enters the bloodstream and affects metabolism throughout the body.
This is one reason fiber matters so much for gut health. Without it, the bacteria that produce these beneficial fatty acids have nothing to ferment, and their populations shrink.
The Gut-Brain Connection
More than 90% of your body’s serotonin is produced in the gut, not the brain. Several types of bacteria can synthesize serotonin directly, and others produce dopamine and norepinephrine. This has opened up a growing area of research into how the gut microbiome influences mood, stress responses, and neurological function through what’s called the gut-brain axis. Short-chain fatty acids also appear to play a role in this communication, acting as chemical signals between the gut and the nervous system.
What Shapes Your Microbiome Over Time
Diet is the most direct lever you have. A Stanford clinical trial assigned 36 healthy adults to either a fermented food diet or a high-fiber diet for 10 weeks. The fermented food group, eating yogurt, kefir, kimchi, kombucha, and fermented vegetables, saw a clear increase in overall microbial diversity, with larger servings producing stronger effects. They also showed decreases in 19 inflammatory proteins in their blood.
The high-fiber group’s results were more surprising. Despite eating a diet rich in legumes, seeds, whole grains, and vegetables, their gut diversity stayed flat over the 10-week period, and inflammatory markers didn’t improve. Researchers noted that increasing fiber alone over a short period wasn’t enough to shift diversity, possibly because the participants’ microbiomes lacked the bacterial species needed to fully process the extra fiber. The takeaway isn’t that fiber doesn’t matter. It’s that building a diverse microbiome may require both feeding the bacteria you have and introducing new ones through fermented foods.
Beyond diet, antibiotics can dramatically reduce microbial diversity in days. Other factors include physical activity, sleep patterns, stress levels, and environmental exposures. People living in rural areas or with greater contact with soil and animals tend to have more diverse microbiomes than those in highly urbanized settings.