What Is the Gut Microbiome? What Scientists Know So Far
Your gut carries tens of trillions of bacteria. Here is what scientists have measured, what has only been shown in mice, and why the supplement aisle is ahead of the science.
The gut microbiome is the community of bacteria, fungi, viruses and other microbes that live in the human intestine, mostly in the large intestine. A 2016 estimate in PLOS Biology put the number of bacteria in a typical adult body at about 38 trillion, roughly the same as the number of human cells. These microbes help break down fiber and help train the immune system.
Much of the rest is still being worked out. Many headline findings come from mice or from studies that show a link but not a cause.
How many microbes live in the human gut?
About 38 trillion bacteria live in and on a “reference” adult man weighing 70 kg (154 lb), according to a 2016 analysis in PLOS Biology by researchers at the Weizmann Institute of Science in Israel. Most of them are in the colon. The same paper estimated about 30 trillion human cells, so the ratio is close to one to one.
That figure replaced an old claim, repeated for decades, that bacteria outnumber human cells ten to one. The authors also put the total mass of those bacteria at about 0.2 kg, or roughly half a pound. Picture a small handful, spread through several meters of intestine.
Bacteria are not the only residents. The gut also holds archaea, fungi and huge numbers of viruses that infect bacteria. Counts for those groups are much less certain.
What does the gut microbiome actually do?
Gut microbes break down parts of food that human enzymes cannot, especially some types of dietary fiber. As they ferment fiber in the colon, they release small molecules called short-chain fatty acids, which the gut lining can absorb and use. Some microbes also make vitamins.
The microbiome also takes up space. A crowded, diverse community leaves less room for harmful bacteria to settle in. The clearest real-world example is Clostridioides difficile, a bacterium that causes severe diarrhea. The CDC explains that antibiotics can kill helpful gut bacteria along with harmful ones, and that people are up to 10 times more likely to get a C. diff infection while taking an antibiotic. The CDC adds that the effects of antibiotics on the gut microbiome can last for several months.
Microbes and the immune system also shape each other. Immune cells in the gut wall constantly sample what is living nearby, and learn which microbes to tolerate. Much of the detailed evidence for this comes from animal studies. For the bigger picture, see how the immune system works.
How does a baby get its microbiome?
A newborn picks up its first microbes during and right after birth, from the mother and the surroundings. A small but widely cited study, published in PNAS in 2010, sampled 10 newborns and their mothers: four born vaginally and six by C-section. The vaginally born babies carried bacterial communities resembling their own mother’s vaginal microbes, while the C-section babies carried communities more like those found on skin.
Ten babies is a very small sample, and the study looked only at the first minutes and hours after birth. It set a baseline for later research rather than settling what delivery mode means for long-term health. The infant microbiome changes a great deal over the first years of life as diet changes.
What has been shown in mice but not in people?
Many headline microbiome results come from germ-free mice, animals raised in sterile conditions with no microbes at all, which researchers can then colonize with chosen bacteria. In a 2013 study in Science, a team transplanted gut microbes from pairs of human twins, one obese and one lean, into germ-free mice. Mice given the obese twin’s microbes gained more fat mass than mice given the lean twin’s microbes. Housing the two groups together prevented that extra gain, and the protection depended on the diet the mice ate.
Results like this show that microbes can influence body composition in a mouse under lab conditions. They do not show that the same transfer works the same way in people, or that changing your microbes will change your weight. Mice differ from humans in diet, anatomy and immune system, and germ-free animals are an extreme situation that no person lives in.
| Finding | Type of evidence | How solid |
|---|---|---|
| About 38 trillion bacteria in an adult body | Calculation from published measurements | Best current estimate, with uncertainty |
| Antibiotics raise the risk of C. diff infection | Clinical data in people (CDC) | Well established |
| Delivery mode shapes a newborn’s first microbes | Small human study (10 babies) | Early finding, later studies built on it |
| Gut microbes can change body fat | Germ-free mice | Shown in animals, not proven in people |
Do probiotics and microbiome diets work?
For most claims, the evidence is limited or mixed. The National Center for Complementary and Integrative Health at NIH says a great deal of research has been done on probiotics but much remains to be learned, and that scientists still do not know which probiotics are helpful and which are not. NCCIH also notes that different strains can have different effects, so a result for one product does not carry over to another.
Regulation matters here too. NCCIH explains that many probiotics are sold as dietary supplements, which do not need FDA approval before they go on sale. A product sold as a drug to treat a disease has to be shown safe and effective in clinical trials.
There is one area where a microbiome treatment has passed that bar. In November 2022 the FDA approved the first fecal microbiota product, made from screened donor stool, to prevent recurrent C. diff infection in adults. That approval covers one specific use. It is not evidence for gut “resets” sold for other purposes.
This is an explainer of the science, not medical advice. Questions about your own digestion, antibiotics or supplements are best taken to a doctor or other clinician.
How do scientists study the microbiome?
Mostly by reading DNA. Researchers sequence genetic material from stool or other samples and match it to known microbes, which lets them count which groups are present without growing each one in a dish. Many gut bacteria are hard to culture, so this approach opened up the field.
The NIH Human Microbiome Project, which NCCIH says ran from 2007 to 2016, used these methods to map the microbes of healthy people at several body sites. Its main lesson was variety: healthy people carry quite different mixes of species. Studies since then look at how the microbiome changes with diet, medicines, age and disease. Many of those studies find associations, and it is often unclear whether a microbial change causes an illness, results from it, or both.
Partnerships between animals and microbes are everywhere in nature. Some sea creatures, for example, glow because of bacteria they host, as we explain in our guide to bioluminescent animals. And microbes make up a huge share of life’s diversity that is still uncounted, a theme in how many species exist on Earth.
Bottom line
An adult carries about 38 trillion bacteria, mostly in the colon, roughly matching the number of human cells. Gut microbes digest fiber, crowd out some harmful bacteria and interact with the immune system. Many bolder claims rest on mouse experiments or small studies, and the first FDA-approved microbiome treatment covers one narrow use: preventing recurrent C. diff.
FAQ
Do bacteria really outnumber human cells ten to one?
No. A 2016 estimate in PLOS Biology found the numbers are roughly equal, about 38 trillion bacteria and 30 trillion human cells in a reference adult. The old ten-to-one figure came from a rough calculation decades ago.
Is everyone’s gut microbiome the same?
No. The NIH Human Microbiome Project found that healthy people carry very different mixes of microbes. Diet, age, medicines and where people live all play a part.
Do antibiotics harm the gut microbiome?
Antibiotics can kill helpful gut bacteria as well as harmful ones, according to the CDC, and the effects can last for several months. That disruption is why people taking antibiotics have a higher risk of C. diff infection. Decisions about antibiotics belong with a clinician.
Can I test my own microbiome?
Consumer stool tests can list which microbes are present, but scientists do not yet have an agreed definition of a “healthy” microbiome to compare results against. Ask a clinician before acting on any result.
