Quick answer: Your gut microbiome is the community of trillions of microbes living in your digestive tract, most densely in the large intestine. These microbes help digest fiber, regulate gut motility, train the immune system, strengthen the gut barrier, process bile acids and make vitamins such as K2 and some B vitamins. Diet shapes this community every day.
Key takeaways
The gut microbiome is mostly bacteria, plus fungi, viruses and other microbes, living from the mouth to the colon.
Gut microbes ferment fiber into short-chain fatty acids, make enzymes and vitamins, and help train the immune system.
A wide variety of plants each week, fermented foods if tolerated and limiting unnecessary antibiotics help keep the microbiome diverse.
What is the gut microbiome?
The gut microbiota is mostly bacteria, plus fungi, viruses and other microbes, living from mouth to colon. For a deeper science overview, see how microbes affect our physiology.
What your gut microbes do
Digest fiber
Microbes ferment fiber into short-chain fatty acids such as butyrate.
Make enzymes
They produce enzymes that help break down carbohydrates, proteins and fats.
Support motility
Microbes influence serotonin made by gut cells, which helps move food along.
Regulate immunity
Microbial metabolites help calm inflammation and train gut immune tissue. See GALT.
Maintain the gut barrier
Short-chain fatty acids support tight junctions, and good microbes crowd out harmful ones.
Process bile acids
Microbes modify bile acids, which affect fat digestion and metabolism.
Make vitamins
Gut bacteria make vitamin K2 and several B vitamins, though diet remains the main source.
The microbiome and healthy aging
The gut microbiome changes with age, and loss of diversity is linked with inflammation and frailty. A diverse, plant-rich diet supports a resilient microbiome. See dysbiosis.
Supporting your microbiome
Aim for a wide variety of plants each week, include fermented foods if tolerated, and limit ultra-processed foods and unnecessary antibiotics. Move daily and sleep well.
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have ongoing bloating, gas, diarrhea or constipation, or food reactions that seem to be multiplying. The same is true if you have fatigue, skin flares or joint aches alongside gut symptoms, or if you want a personalized gut plan instead of guessing.
See a medical provider promptly for blood in your stool, black stools, unexplained weight loss, persistent vomiting, severe abdominal pain, fever, or trouble swallowing.
What the research shows
Diet shapes the microbiome, especially as we age. In a 2012 Nature study by Claesson and colleagues, researchers analyzed stool bacteria from 178 older adults in Ireland living at home or in care. Diet was closely tied to microbiome makeup, people in long-term care had less diverse bacteria, and lower diversity was linked with greater frailty and inflammation. This was an observational study, so it cannot show which came first.
Fermented foods have been tested directly. In a 2021 randomized study by Wastyk and colleagues, 36 healthy adults followed a high-fiber or a high-fermented-food diet for 17 weeks (18 per group). The fermented-food group steadily gained microbiome diversity and had lower inflammatory markers, while the fiber group’s diversity stayed stable. The study was small, and the main immune outcome did not change.
Want help finding the root of your gut symptoms?
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.
Would a stool test help us understand my gut microbiome?
Which of my gut bacteria’s jobs might matter most for my symptoms?
Which foods would best support a healthy microbiome for me?
Would a stool test add useful information for my gut health?
Frequently asked questions
What does the gut microbiome do?
It helps digest food, supports immunity and the gut barrier, and makes some vitamins.
Where is most of the microbiome?
In the large intestine.
How can I improve my microbiome?
Eat a variety of fiber-rich plants and fermented foods.
Do I need a probiotic?
Not always. Food comes first; probiotics can help in specific situations.
Sources
- Claesson MJ, Jeffery IB, Conde S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012. PMID: 22797518. https://pubmed.ncbi.nlm.nih.gov/22797518/
- Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell 2021. PMID: 34256014. https://pubmed.ncbi.nlm.nih.gov/34256014/
- Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 2016. PMID: 27541692. https://pmc.ncbi.nlm.nih.gov/articles/PMC4991899/
- 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/
- 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/
- 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/
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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