We are not alone in our own bodies
The human body is home to an enormous community of microorganisms, collectively called the microbiota. The term microbiome is used for those microbes together with their genes, and sometimes for their surroundings too. They include bacteria, archaea, fungi, viruses (including those that infect bacteria) and tiny single-celled organisms. They live on the skin, in the mouth and nose, and in the digestive and urogenital tracts, with the largest and most studied community in the large intestine.
For years, a figure often repeated was that microbes outnumber human cells ten to one. More recent estimates suggest the numbers are of the same order of magnitude, roughly comparable, though precise counts are uncertain and vary between people. What is clearer is that the collective gene count of the gut microbes far exceeds the number of human genes.
Different sites, different communities
Each body site has its own mix of microbes, shaped by conditions such as moisture, acidity, oxygen and available food. Skin has communities adapted to dryness and salt, while the mouth hosts a different set. The gut is largely oxygen-free and nutrient-rich, supporting dense populations dominated by a few major groups of bacteria. The mix varies a lot between individuals, and even in the same person over time.
How the community forms
Microbial colonization is thought to begin around birth, influenced by factors such as the way a baby is delivered and fed, though the details and long-term impact are still debated. Over the first few years, the gut community becomes more diverse and settles into something more stable. Later, diet, medications (especially antibiotics), illness, age, geography and the people and animals we live with all influence it. The relationship with antibiotic resistance is one reason why antibiotics are used carefully.
What microbes seem to do for us
Researchers have documented a range of functions, although how much each matters for health varies.
- Digestion and nutrition: Gut bacteria ferment fibers and other substances that human enzymes cannot break down, producing short-chain fatty acids that the cells lining the colon use as fuel. They also help produce some vitamins, such as vitamin K, and take part in processing bile acids.
- Immune training: The immune system develops in constant contact with microbes. Studies in animals raised without any microbes show their immune systems develop abnormally, indicating that microbes help calibrate defenses and tolerance. The same applies to chronic inflammation, which scientists are exploring in relation to microbial imbalance.
- Colonization resistance: A stable resident community can crowd out disease-causing species by competing for food and space, and by producing substances that inhibit them.
- Chemical communication: Microbial products enter the bloodstream and may influence distant organs. The proposed gut-brain connection is an active topic, with signals potentially traveling through nerves, hormones and immune pathways.
Dysbiosis and disease
The word dysbiosis describes a shift in the microbial community away from a typical or healthy pattern. Differences in microbial composition have been observed in people with conditions such as inflammatory bowel disease, obesity, type 2 diabetes and others. The key limitation is that many findings are associations. Disease can change the microbiome, and the microbiome might contribute to disease, or both might be driven by a third factor, so the lesson of correlation and causation applies strongly here.
One of the clearest medical uses is fecal microbiota transplantation for certain recurrent Clostridioides difficile infections, which has performed well in studies of that specific condition. Extending that success to other conditions has been much harder.
Diet, probiotics and everyday questions
Because many gut microbes feed on dietary fiber, eating a variety of plants such as fruits and vegetables and other whole foods is commonly associated with a more diverse microbiota. Whether specific changes translate into better health outcomes is not settled for most conditions.
Probiotics are live microorganisms taken as supplements or foods. Evidence suggests that some strains help in particular situations, but results depend on the strain and the condition, and many products on the market have limited supporting evidence. Prebiotics are substances that feed beneficial microbes. People with weakened immune systems or serious illness are typically advised to check with a clinician before taking probiotics.
Open questions
Scientists are still working out:
- What a “healthy” microbiome looks like, given the enormous variation between healthy people
- Which microbes and which of their products cause effects, as opposed to merely accompanying them
- How stable the community is and how easily it can be changed in a lasting way
- Whether microbiome-based therapies can be made reliable
Sequencing technologies have made it far easier to catalog microbes by their DNA, but cataloging is not the same as understanding what each one does.
This is a general science overview and not medical advice.