Quick answer: A diverse gut microbiome is built mostly through daily habits: eating a wide variety of plants each week, plenty of fiber and resistant starch, polyphenol-rich foods, fermented foods if tolerated, good sleep and regular movement. Supplements such as prebiotics, probiotics and postbiotics can help in specific situations, and short, targeted antimicrobial courses are sometimes needed when overgrowth is present.
Key takeaways
A diverse gut microbiome is built mostly through daily habits rather than supplements.
Eating a wide variety of plants each week, plenty of fiber and resistant starch, polyphenol-rich foods and fermented foods if tolerated all help.
Prebiotics, probiotics and postbiotics can be useful in specific situations, and microbiome testing is optional.
Why diversity matters, and how it is measured, is covered in microbiome diversity: how it is measured. This guide is about how to build it.
Daily habits that build diversity
Aim for plant variety: many people aim for around 30 different plant foods a week, counting vegetables, fruits, legumes, whole grains, nuts, seeds, herbs and spices. Fiber and resistant starch come from beans, oats, flax, green bananas and cooked-and-cooled potatoes or rice, and polyphenols come from berries, pomegranate, green tea, olive oil, cocoa and herbs.
Fermented foods such as kefir, yogurt, sauerkraut, kimchi or natto help if you tolerate them. Sleep and daily rhythm matter because irregular sleep and late-night light disrupt microbial rhythms, and movement matters because regular exercise is associated with greater microbial richness.
What lowers diversity
Diversity can drop with repeated antibiotic courses (take them when truly needed, as prescribed) and with low-fiber, ultra-processed diets. Chronic stress and short sleep lower it too, as does frequent use of some medications, such as PPIs, when not needed.
When supplements help
Prebiotic fibers, such as PHGG, GOS, inulin or resistant starch, can help when introduced slowly, and postbiotics such as butyrate can help especially when fiber is poorly tolerated. Probiotics, including spore-based strains, are particularly useful after antibiotics.
Short antimicrobial courses are used only when overgrowth or pathogens are present (see hidden gut pathogens). Gut-lining support may include glutamine and zinc carnosine (see supporting the gut lining).
Amounts should be individualized. If you work with me, products I commonly use are in my microbiome gut support plan on Fullscript.
The microbiome and healthy aging
Dysbiosis, a loss of microbial balance and diversity, is one of the recognized processes behind aging. A diverse microbiome makes butyrate and other compounds that help keep the gut lining sealed, calm inflammation, support mitochondria and help regulate how the body senses and uses nutrients. Some bacteria also help produce compounds such as urolithin A from foods like pomegranate and walnuts, which is being studied for mitochondrial renewal. Learn more in short-chain fatty acids and my longevity protocol.
Is microbiome testing needed?
Most people can start with the habits above. Functional labs are optional. They can be helpful in more complex cases, and in my practice they are available only to patients working 1-on-1 with me.
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have digestive symptoms despite eating “healthy,” or if fiber or fermented foods make you feel worse. The same is true if you have taken many antibiotics and never felt the same, or if you want a microbiome plan tailored to you.
See a medical provider promptly for blood in the stool, unintended weight loss, persistent diarrhea, severe abdominal pain or fever.
Want a gut plan built around your microbiome?
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.
How many different plant foods should I aim for each week, given how my gut tolerates fiber?
Which foods or daily habits would be most worth adjusting first for my gut health?
Could any of my current medications or supplements be relevant to my gut health?
How would we track my progress with my gut health over the next few months?
Practitioner-grade options in my Fullscript catalog: if you and your clinician decide a supplement makes sense, my supplement guide by health goal links to the practitioner-grade products I trust.
Frequently asked questions
How many plants should I eat for gut health?
Many people aim for around 30 different plant foods per week. Herbs, spices, nuts and seeds count.
Are probiotics necessary for a healthy microbiome?
Not for everyone. Diet and lifestyle shape the microbiome most. Probiotics can help in specific situations such as after antibiotics.
Why does fiber make me bloated?
A sensitive gut or bacterial overgrowth can make fiber uncomfortable at first. Increasing slowly or choosing gentler fibers can help.
How fast can the microbiome change?
Diet changes can shift the microbiome within days, but lasting changes in diversity build over weeks to months.
Sources
- McDonald D, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 2018. PMID: 29795809. https://pmc.ncbi.nlm.nih.gov/articles/PMC5954204/
- Wastyk HC, et al. Gut-microbiota-targeted diets modulate human immune status. Cell 2021. PMID: 34256014. https://pmc.ncbi.nlm.nih.gov/articles/PMC9020749/
- Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011. PMID: 20847294. https://pmc.ncbi.nlm.nih.gov/articles/PMC3063582/
- Imhann F, et al. Proton pump inhibitors affect the gut microbiome. Gut 2016. PMID: 26657899. https://pmc.ncbi.nlm.nih.gov/articles/PMC4853569/
- David LA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014. PMID: 24336217. https://pmc.ncbi.nlm.nih.gov/articles/PMC3957428/
- NIH Common Fund: Human Microbiome Project
- NCCIH: Probiotics: Usefulness and Safety
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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