Gut Bacteria and What They Eat

Which foods feed which microbes, and simple ways to care for your gut.

Different microbes like different foods. Open one section at a time.

About 7 min read

Types of Gut Bacteria and What They Eat

There are thousands of species in the gut, and each group has its own favorite foods. Scientists do not think of them as simply “good” or “bad.” Context, strain, and balance matter. Here are some well-studied groups:

Bifidobacterium

Common in the gut and in some probiotic and fermented dairy products. They feed on prebiotic fibers such as inulin and fructo-oligosaccharides, found in onions, garlic, leeks, asparagus, bananas, and oats. They make acetate and lactic acid, which help keep the gut environment healthy.

Lactobacillus and relatives

Found in live-culture yogurt, kefir, sauerkraut, and kimchi. They ferment sugars into lactic acid. Many probiotic strains are thought to pass through the gut rather than settle permanently. The group was reorganized into several genera in 2020.

Faecalibacterium prausnitzii

A leading maker of butyrate, which fuels the cells lining the colon and has anti-inflammatory effects. It feeds on fibers from fruits, vegetables, legumes, and whole grains. Levels are lower in inflammatory bowel disease, and higher levels were linked to better quality of life in a large 2019 study.

Roseburia, Coprococcus, and other butyrate makers

These bacteria also turn fiber and resistant starch (found in whole grains, legumes, and cooled potatoes or rice) into butyrate. Coprococcus was lower in people with depression in the 2019 study mentioned above. This is an association.

Akkermansia muciniphila

Lives in the protective mucus layer of the gut and feeds on mucin. Higher levels are associated with metabolic health and a healthy gut lining. Some research, mostly in animals, suggests that polyphenol-rich foods such as berries, pomegranate, and cranberries and plant fiber may support it. Evidence in people is still limited.

Bacteroides and Prevotella

Two large, common groups. Prevotella has been linked to plant-rich, Mediterranean-style diets and short-chain fatty acid production (De Filippis et al., 2016). Bacteroides has been linked to diets higher in animal protein and fat, although studies looking at finer subgroups show the picture is more complex. Neither is “bad.” They reflect long-term eating patterns.

Microbes that can cause trouble

Some microbes can overgrow when the balance is upset. Clostridioides difficile can overgrow after antibiotics and cause severe diarrhea. Certain Enterobacteriaceae, such as some E. coli strains, tend to rise with gut inflammation. See a doctor for severe or lasting diarrhea.

The takeaway: a varied, mostly plant-based way of eating feeds many different groups at once, which is why diversity is the goal.

How to Care for Your Gut and Your Mood

Eat a variety of plants. In a large citizen-science study (the American Gut Project), people who ate more than 30 different kinds of plants a week had more diverse gut microbes than people who ate 10 or fewer. Counts were self-reported, so this shows an association. Vegetables, fruits, whole grains, beans, lentils, nuts, seeds, herbs, and spices all count.
Get enough fiber. Most adults eat far less than recommended, often around 15 grams a day. A common target is 14 grams per 1,000 calories, which is about 25 grams a day for women and 38 for men (US guidance; targets vary by country and age). Increase slowly and drink water to limit gas and bloating.
Add fermented foods. In a 2021 Stanford trial of 36 healthy adults, 10 weeks of eating more fermented foods (such as yogurt, kefir, kimchi, and kombucha) increased microbe diversity and lowered markers of inflammation. A high-fiber diet did not raise diversity over the same period. It was a small, short study. Choose products with live cultures and start with small servings.
Try a Mediterranean-style pattern. In the SMILES trial, adults with moderate to severe depression who got dietitian support to eat a modified Mediterranean diet for 12 weeks improved more than a comparison group that received social support. It was a small trial, it did not measure gut microbes, and the diet was added to usual care, not used instead of it.
Limit what tends to work against you. Eating patterns high in ultra-processed foods are linked in observational studies with higher odds of depression (Lane et al., 2022). These studies show an association, not proof of cause.
Move, sleep, and calm your stress. Regular physical activity, steady sleep, and stress-reduction practices all affect digestion and gut signaling. See our Tools for breathing and meditation practices.
Use antibiotics wisely. Take them only when a clinician prescribes them, and exactly as directed.

What about probiotics? Probiotics are live microbes sold as supplements. The National Center for Complementary and Integrative Health says strong evidence is lacking for most uses, with some support for conditions such as antibiotic-associated diarrhea. Effects depend on the specific strain, and results of mental-health trials have been inconsistent. They usually cause few side effects, but people with weakened immune systems or serious illness, and premature infants, can face serious risks. Talk with your doctor first. Probiotics are not a substitute for treatment for depression or anxiety.

When to get help: Talk with a doctor if you have lasting changes in bowel habits, blood in your stool, unexplained weight loss, or severe pain, or if digestive symptoms come with mood symptoms. Avoid strict diets or cleanses without guidance, and if thoughts about food feel consuming, reach out to a professional who treats eating concerns. If low mood or anxiety is affecting your life, a licensed therapist can help. See How to Choose a Therapist. If you are in crisis, call or text 988 in the United States. Elsewhere, contact your local emergency number or find a helpline at findahelpline.com.

Sources

Sources for the gut–brain section

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Ataei, P., Kalantari, H., Bodnar, T. S., & Turner, R. J. (2025). The gut–brain connection: microbes’ influence on mental health and psychological disorders. Frontiers in Microbiomes, 4.
Valles-Colomer, M., et al. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology, 4.
Layunta, E., et al. (2021). Crosstalk between intestinal serotonergic system and pattern recognition receptors on the microbiota–gut–brain axis. Frontiers in Endocrinology, 12.
Strandwitz, P. (2018). Neurotransmitter modulation by the gut microbiota. Brain Research, 1693.
De Filippis, F., et al. (2016). High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut, 65(11).
McDonald, D., et al. (2018). American Gut: an open platform for citizen science microbiome research. mSystems, 3(3).
Wastyk, H. C., et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16); Stanford Medicine summary.
Jacka, F. N., et al. (2017). A randomised controlled trial of dietary improvement for adults with major depression (the SMILES trial). BMC Medicine, 15.
Lane, M. M., et al. (2022). Ultra-processed food consumption and mental health: A systematic review and meta-analysis of observational studies. Nutrients, 14(13).
Zamani, M., et al. (2019). Systematic review with meta-analysis: the prevalence of anxiety and depression in patients with irritable bowel syndrome. Alimentary Pharmacology & Therapeutics, 50.
Gwak, M.-G., & Chang, S.-Y. (2021). Gut-brain connection: Microbiome, gut barrier, and environmental sensors. Immune Network, 21(3), e20.
Johns Hopkins Medicine. The Brain-Gut Connection.
Bonaz, B., Bazin, T., & Pellissier, S. (2018). The vagus nerve at the interface of the microbiota-gut-brain axis. Frontiers in Neuroscience, 12, 49.
Fock, E., & Parnova, R. (2023). Mechanisms of blood–brain barrier protection by microbiota-derived short-chain fatty acids. Cells, 12(4), 657.
Erny, D., et al. (2021). Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease. Cell Metabolism, 33(11), 2260–2276.
Kim, S., et al. (2019). Transneuronal propagation of pathologic α-synuclein from the gut to the brain models Parkinson’s disease. Neuron, 103(4).
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National Center for Complementary and Integrative Health. Probiotics: Usefulness and Safety.

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Within Your Light is an educational platform. We do not provide medical advice, diagnosis, or treatment recommendations. This page is for educational purposes only and is not a substitute for professional medical advice. Always consult a healthcare provider before making significant dietary changes or if you have concerns about your mental health.