In Blog, Diet

Increasingly scientists recognize the importance of our microbiome to health. The microbiome is a unique fingerprint—each individual has a slightly different microbiome that is stable and unique to them and influenced by major events in their early life. By the time we are three years old, our microbiome community has established itself. Unfortunately, I, like many with autoimmune disease, had a sub-optimal start to my microbiome, which faced several challenges that reduced its quality.

I was born vaginally at term, which is a great start for a microbiome. In vaginal births, the baby travels through the mother’s vagina, which inoculates them with all the bacteria that live there. Babies born via C-section are seeded with different bacterial species at birth and have a higher risk than babies born vaginally of developing a variety of chronic health problems, including autoimmune, metabolic, and mental health issues.

As I passed through my mother’s vagina, I was seeded with bifidobacterial species that thrive on the oligosaccharides in breast milk. Unfortunately, I was born in an era when it was not fashionable to breastfeed and the health benefits of breast milk were not as well known. I was formula fed, which meant I missed out on the boost my bifidobacterial species would have gotten breast milk.

As a toddler, I had several episodes of streptococcal infections of the throat and tonsils and was given multiple rounds of penicillin before the age of three. I had my tonsils removed when I was four because of recurrent tonsillitis. Penicillin prevented the development of rheumatic fever and valvular heart disease, which I am grateful for. But each time I took penicillin, the bacteria in my bowels died and the yeast candida albicans grew more dominant. Because all of this happened before the age of three, my microbiome was established with an overgrowth of candida species in my bowels that will stay with me forever.

I have since learned that having an excessive amount of candida in the bowels leads to increased risk of anxiety and other mental health issues as well as autoimmunity.1-3 Candida infections are increased in patients with MS as compared to healthy controls.4,5 In addition, candida can create a biofilm with multiple other bacterial and fungal organisms that is resistant to antibiotic and antifungal treatment.

Signs of candida overgrowth that I look for in my patients are:

  • thickened toenails or fingernails,
  • redness under the breasts, in the groin, around the testicles or anus,
  • and a history of recurrent vaginal yeast infections.

I tell patients whose history suggests they have increased yeasts in the gut due to early or chronic antibiotic use that issues with mood, fatigue, and brain fog may also be associated with candida overgrowth.

Controlling yeasts is a lifelong commitment. Gut microbes will always revert to what the person had at age three. In addition, over the age of 50 the diversity of the gut microbiome tends to decline, more so with each decade. As the diversity declines, the risk of cognitive decline and frailty increases.

My approach for myself and my patients with autoimmune or mental health issues is to assess the first three years of life to better understand how their individual microbiome was established. Was the person born vaginally? Did they receive antibiotics in the first 3 years of life? Did they have a diet high in sugar and processed foods? Did they have multiple rounds of antibiotics? The more questions a patient answers yes to, the more likely they are to have excessive candida and other yeasts in their bowels and not enough bifidobacterial and lactobacillus species.

For these individuals, I recommend a lower carbohydrate diet (to starve the yeast), an ongoing herbal suppression of yeast, and a probiotic that has multiple strains of lactobacillus and bifidobacterial species that have been shown to improve metabolic health and mood. I also explain that this will be a lifelong intervention because the microbiome is mostly set by the age of 3 and that over the age of 60, microbiome diversity tends to decline, increasing the risk of frailty and cognitive decline.

I feel much better following a low carbohydrate diet and taking an herbal candida suppression product and a probiotic. I also rely on herbs and essential oils that have demonstrated effectiveness at controlling candida and restoring a healthier microbial community in the gut, including oregano oil 7, ginger oil 8, olive leaf 9, and turmeric 10.

In addition, I take a probiotic with a blend of over 10 strains of Bidifobacterium lactis and Lactobacillus rhamnosus. These species have demonstrated efficacy for rebalancing the gut immune balance 11,12 and increasing production of butyrate in the bowels.13 These probiotic bacteria blends have also been shown to improve the health of the gut-immune-brain axis.14 Butyrate-producing probiotics have been shown to be beneficial to mood, general health, and disease progression in the setting of multiple sclerosis.15

I now recognize that my microbiome will always drift back towards what it was when I was 3 years old. I will always need to tend the microbial garden living in my bowels. If I eat more carbohydrates or stop the candida suppression herbs or probiotics, I do not feel as well. I also tend my microbial garden by eating sauerkraut and kimchi and plenty of greens.

How do you tend your microbial garden? Given that our microbiome gravitates to what it was when we were 3 and begins to deteriorate further over age 60, it’s important to take care of it. There is a lot you can do to support your microbiome and increase your chances of thriving as you age.

The Wahls Protocol® Supplements carry two helpful items: Candida Clear capsules or the more comprehensive Candida Clear Support Kit... If you suspect you have a candida overgrowth, assess which option is best for you!



  1. Aaron L, Torsten M. Candida albicans in celiac disease: A wolf in sheep’s clothing. Autoimmun Rev. 2020;19(9):102621
  2. Palma-Carlos AG, Palma-Carlos ML. Candida and human disease. Eur Ann Allergy Clin Immunol.2004;36(8):291-296.
  3. Gerard R, Sendid B, Colombel JF, Poulain D, Jouault T. An immunological link between Candida albicans colonization and Crohn’s disease.Crit Rev Microbiol.2015;41(2):135-139.
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  10. Samadi FM, Suhail S, Sonam M, et al. Antifungal efficacy of herbs.J Oral Biol Craniofac Res. 2019;9(1):28-32.
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  13. Srivastav S, Neupane S, Bhurtel S, et al. Probiotics mixture increases butyrate, and subsequently rescues the nigral dopaminergic neurons from MPTP and rotenone-induced neurotoxicity.J Nutr Biochem.2019;69:73-86.
  14. Michels M, Jesus GFA, Abatti MR, et al. Effects of different probiotic strains B. lactis, L. rhamnosus and L. reuteri on brain-intestinal axis immunomodulation in an endotoxin-induced inflammation.Mol Neurobiol.2022;59(8):5168-5178.
  15. Mirashrafi S, Hejazi Taghanaki SZ, Sarlak F, Moravejolahkami AR, Hojjati Kermani MA, Haratian M. Effect of probiotics supplementation on disease progression, depression, general health, and anthropometric measurements in relapsing-remitting multiple sclerosis patients: A systematic review and meta-analysis of clinical trials.>Int J Clin Pract. 2021;75(11):e14724.
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