Quick answer: Your gut microbiome is the community of trillions of bacteria, fungi and viruses living in your digestive tract. Its main jobs include fermenting fiber into short-chain fatty acids, producing vitamins such as K2 and some B vitamins, modifying bile acids, regulating gut motility, training the immune system and influencing mood through the gut-brain axis.
Key takeaways
The gut microbiome is a community of trillions of bacteria, fungi and viruses living in the digestive tract.
Its jobs include fermenting fiber, making vitamins such as K2, modifying bile acids and regulating gut movement.
Gut microbes also help train the immune system and influence mood through the gut-brain axis.
1. Fermenting fiber
Gut bacteria break down fibers you cannot digest and turn them into short-chain fatty acids such as butyrate, propionate and acetate. Butyrate fuels the cells lining your colon (see short-chain fatty acids).
2. Making enzymes and vitamins
Microbes produce enzymes that help digest complex carbohydrates, and they make vitamin K2 and several B vitamins, including biotin, folate and B12 (though most B12 still has to come from food).
3. Modifying bile acids
Bacteria convert primary bile acids from the liver into secondary bile acids, which affect fat digestion, blood sugar and cholesterol signaling.
4. Regulating gut motility
Microbial signals help set the rhythm of the gut muscles, which is why imbalances can show up as constipation or diarrhea.
5. Training the immune system
Gut microbes help train the immune system by crowding out harmful bacteria (competitive exclusion) and supporting the intestinal barrier. They also play a role in shaping how immune cells such as T cells respond, and in helping the immune system mature in early life.
6. Influencing mood
Most of the body’s serotonin is made in the gut, and microbes influence that production. This is one way the gut talks to the brain (see the gut-brain connection).
How to support a healthy microbiome
Eat a wide variety of plants, include fermented foods if you tolerate them, and limit ultra-processed foods and unnecessary antibiotics. You can read more in how to build a diverse gut microbiome.
The microbiome and healthy aging
Microbial diversity tends to decline with age. That kind of imbalance (dysbiosis) is linked with more chronic inflammation and weaker communication between the gut, immune system and brain. A diverse, well-fed microbiome is one of the foundations of healthy aging.
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have ongoing bloating, gas or irregular bowels, or gut symptoms after antibiotics. The same is true if you have mood, skin or immune issues along with gut symptoms, or if you want a personalized plan for gut health.
See a medical provider promptly for blood in the stool, unexplained weight loss, fever with abdominal pain, or persistent vomiting.
What the research shows
Gut bacteria help explain why people respond differently to the same food. In a 2015 Cell study by Zeevi and colleagues, 800 adults wore glucose monitors for a week while researchers recorded responses to nearly 47,000 meals. Blood sugar responses to identical meals varied widely, and an algorithm that included gut microbiome data predicted them well, which was confirmed in another 100 people. A small blinded diet trial based on these predictions lowered after-meal blood sugar. Most participants were in Israel, so results may differ elsewhere.
Lifestyle shapes the microbiome more than genes. In a 2018 Nature study by Rothschild and colleagues, 1,046 healthy adults of several ancestries in Israel had their genes and gut bacteria analyzed. Genetic ancestry had little link to microbiome makeup, while unrelated people sharing a household had similar microbiomes, and more than 20% of the differences between people were linked to diet, medicines and body measurements. This is observational, but it supports the idea that daily habits can change your gut bacteria.
Want to understand what your gut is telling you?
A free 15-minute consultation with Dr. Kneessi. No cost, no obligation. In-office in Odenton, MD or by telehealth.
Questions to bring to your clinician
These questions can help you get the most out of your next visit.
Which of these microbiome jobs might be connected to my digestive or mood symptoms?
Which of my symptoms might relate to my gut bacteria?
Which foods would best feed a healthy mix of gut bacteria for me?
Would a stool test add useful information in my case?
Frequently asked questions
What is the gut microbiome?
It is the community of microbes that live in your digestive tract, mostly in the colon.
Do gut bacteria make vitamins?
Yes. They make vitamin K2 and several B vitamins, although food remains the main source.
Can gut bacteria affect mood?
Research shows the gut and brain communicate through nerves, immune signals and microbial products.
How can I improve my microbiome?
Eat a variety of fiber-rich plants, include fermented foods, manage stress and avoid unnecessary antibiotics.
Sources
- Zeevi D, Korem T, Zmora N, et al. Personalized Nutrition by Prediction of Glycemic Responses. Cell 2015. PMID: 26590418. https://pubmed.ncbi.nlm.nih.gov/26590418/
- Rothschild D, Weissbrod O, Barkan E, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 2018. PMID: 29489753. https://pubmed.ncbi.nlm.nih.gov/29489753/
- Koh A, et al. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell 2016. PMID: 27259147. https://pubmed.ncbi.nlm.nih.gov/27259147/
- LeBlanc JG, et al. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 2013. PMID: 22940212. https://pubmed.ncbi.nlm.nih.gov/22940212/
- Ridlon JM, Kang DJ, Hylemon PB. Bile salt biotransformations by human intestinal bacteria. J Lipid Res 2006. PMID: 16299351. https://pubmed.ncbi.nlm.nih.gov/16299351/
- Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell 2014. PMID: 24679531. https://pmc.ncbi.nlm.nih.gov/articles/PMC4056765/
- Yano JM, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 2015. PMID: 25860609. https://pmc.ncbi.nlm.nih.gov/articles/PMC4393509/
This article is for educational purposes only and is not medical advice. It does not replace an individual evaluation. Talk with your healthcare provider before starting supplements or changing medications, especially if you are pregnant, nursing, or managing a health condition.
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