What is the gut microbiome?
The gut microbiota is the collection of microbes living mostly in the large intestine. It was long claimed that bacteria outnumber human cells 10 to 1, but a 2016 recount put the figure at about 38 trillion—roughly the same as our own cells. The full set of microbial genes is often called the microbiome.
What gut bacteria do
- Digestion and fermentation: they ferment fiber humans can't break down into short-chain fatty acids, which fuel the cells lining the colon.
- Immune regulation: they shape the development and balance of immune cells in the gut lining.
- Defense: by occupying space and competing for nutrients, they make it hard for pathogens to settle in.
- Vitamin production: they make vitamin K and some B vitamins.
Antibiotics and recovery
Antibiotics can sharply reduce gut bacterial diversity, and recovery can take weeks to months. If bugs like Clostridioides difficile take advantage, severe diarrhea can follow. Meta-analyses suggest probiotics reduce antibiotic-associated diarrhea (Hempel et al., 2012), but a 2018 study in Cell reported that multi-strain probiotics after antibiotics may actually delay the return of your native microbes. For recurrent C. difficile infection, fecal microbiota transplantation from a healthy donor is sometimes used.
How should you read gut microbiome research?
Links between gut microbes and obesity, metabolic syndrome, depression and allergies have been reported, but most come from observational or animal studies that can't sort out cause from effect. The finding that a varied, fiber-rich diet is associated with greater microbial diversity is fairly consistent; claims that a specific product cures a specific disease deserve a hard look at the evidence. For how microbes cause disease, see microbial pathogenicity and infection.
This article is general health information and is not a substitute for diagnosis or treatment. If symptoms persist, see a doctor.
FAQ
- Should I take a probiotic after antibiotics?
- It may lower the risk of antibiotic-associated diarrhea, but it isn't necessary for everyone and may slow natural recovery; a fiber-rich diet is a reasonable default—ask your clinician if you're at high risk.
Sources reviewed: 2026-10-25
References
- Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8), e1002533.
- Hempel, S., et al. (2012). Probiotics for the prevention and treatment of antibiotic-associated diarrhea. JAMA, 307(18), 1959–1969.
- Suez, J., et al. (2018). Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell, 174(6), 1406–1423.