Tips on diversifying the gut microbiome: Steps to treat leaky gut

May 8, 2023
Gut dysbiosis and loss of microbial diversity in the stomach can lead to oral diseases such as periodontal disease and halitosis. Here are five easy ways to increase gut microbiome diversity.
Scott Froum, DDS, Editorial Director

A review of the dental literature contains many articles that show a connection between a healthy oral microbiome and oral health. An oral microbiome steeped in aerobic bacteria has been associated with an absence of periodontal disease.1 Over the last decade, the oral-gut microbial axis has also been established as an important factor in determining oral health and emphasizes the importance of gut microbiome diversity in warding off inflammatory diseases. Diseases such as diabetes, cardiovascular disease, inflammatory bowel disorder, mental health, and endocrine diseases have all been directly linked to problems with the gut microbiome.2

The literature suggests that gut dysbiosis and loss of microbial diversity in the stomach can lead to oral diseases such as periodontal disease3 and halitosis. This article describes five easy-to-implement ways to increase gut microbiome diversity.

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Probiotic overuse

The overuse and indiscriminate administration of probiotics have reached epidemic proportions. By the end of 2022, the probiotic consumer market was expected to exceed 64 billion dollars.4 The adage of too much of a good thing is a bad thing holds true with probiotic use. Unfortunately, simply taking a probiotic without direction or knowing which bacteria you are deficient in can cause systemic problems. For example, one type of bacteria commonly found in over-the-counter probiotics, Lactobacillus, was associated with an increase in D-lactic acid and caused SIBO (small intestinal bowel overgrowth) in certain patients.

Other studies have shown that overreliance on probiotics can cause brain fog, poor concentration, short-term memory problems, and metabolic acidosis.5 The authors of this study concluded that probiotics should contain strains of bacteria that are patient-specific and should be treated as a medication, not a supplement.

5 at-home methods to increase gut microbiome diversity

Exposure to sunlight

10-15 minutes of sunlight (even daylight), especially first thing in the morning, act as a circadian signal to the gut to restore microbial balance and increase intestinal mucosa, which assists with microbial protection.

Eating fermented foods

Low-sugar wild-fermented foods with live bacterial cultures are an excellent way to promote microbial diversity. Most people think yogurt is a good probiotic source. Unfortunately, most yogurts are high in sugar and not a wild-fermented food source. A wild ferment lets nature do the fermentation, not humans deciding which microbes are chosen. Foods such as low-sugar kombucha, sauerkraut (not canned), and especially sauerkraut brine, kimchi, and natto are all good sources of ferment.

Avoiding artificial blue light at bedtime

Smartphones, computers, TV, and other screened electronics emit blue light that can disrupt the body’s circadian rhythm, telling your gut it’s daytime when it’s night. This can disrupt the mucosal flow and the microbiome.

Buying food from different stores

If you are not shopping at a farm, then buy food from different stores or different geographical regions. Varying food origins varies the microbes that come with that food. Buying from different land regions means different soil, which means different microbes.

Eliminating chemicals and favoring natural home cleaners

Air fresheners, Febreze, cleaning products, lawn sprays and weed killers, perfume, cologne, makeup, and many other man-made chemical products can be problematic. Anything you breathe in or lay against your skin can negatively affect the diversity in your microbiome.

Editor’s note: This article originally appeared in Perio-Implant Advisory, a chairside resource for dentists and hygienists that focuses on periodontal- and implant-related issues. Read more articles and subscribe to the newsletter.


  1. Di Stefano M, Polizzi A, Santonocito S, Romano A, Lombardi T, Isola G. Impact of oral microbiome in periodontal health and periodontitis: a critical review on prevention and treatment. Int J Mol Sci. 2022;23(9):5142. doi:10.3390/ijms23095142
  2. Vijay A, Valdes AM. Role of the gut microbiome in chronic diseases: a narrative review. Eur J Clin 2022;76(4):489-501. doi:10.1038/s41430-021-00991-6
  3. Lourenςo TGB, Spencer SJ, Alm EJ, Colombo APV. Defining the gut microbiota in individuals with periodontal diseases: an exploratory study. J Oral Microbiol. 2018;10(1):1487741. doi:10.1080/20002297.2018.1487741
  4. Bergland C. In a brain fog? Probiotics could be the culprit. Psychology Today. August 8, 2018.
  5. Rao SSC, Rehman A, Yu S, de Andino NM. Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clin Transl Gastroenterol. 2018;9(6):162. doi:10.1038/s41424-018-0030-7
Scott Froum, DDS, a graduate of the State University of New York, Stony Brook School of Dental Medicine, is a periodontist in private practice at 1110 2nd Avenue, Suite 305, New York City, New York. He is the editorial director of Perio-Implant Advisory and serves on the editorial advisory board of Dental Economics. Dr. Froum, a diplomate of the American Board of Periodontology, is a volunteer professor in the postgraduate periodontal program at SUNY Stony Brook School of Dental Medicine. Contact him through his website at or (212) 751-8530.