Please see this in depth article, derived from published research in China, regarding bacteria in your Microbiome and how you can optimize your chances with COVID-19. Written by my mentee Kristina Mitts.

The Microbiome-COVID Connection 

The microbiome-coronavirus connection and the need to incorporate microbiome considerate treatment approaches was formally established this week (March 20, 2020) when the Zhejiang University School of Medicine released the “Handbook of COVID-19 Prevention and Treatment.” The handbook was compiled by a panel of medical experts at the hospital, according to their clinical experience in fighting the pandemic.  

Handbook Recommendations: 

  • Microbiome analysis to assess the microbial terrain 
  • Monitoring patients for secondary infections such as Candida
  • Nutrition and supplemental support to balance the microbiome and reduce bacterial translocation 

Studies are beginning to reveal potential characteristic imbalances occurring within the gut microbiomes of COVID-19 patients. The Wuhan University released a retrospective study on three critically ill COVID-19 patients wherein sequencing revealed deficiencies in commensal microbes Bifidobacterium, Lactobacillus and Eubacterium. There was also an increase in pathogenic microbes such as Corynebacterium and Ruthenibacterium[Lilei Yu et al]  

Sequencing data has found Coronavirus integration in Prevotella bacteria strain A2879. These findings may have ramifications for those who acquire the virus. A meta-analysis concluded that anti-virals should be supplemented alongside anti-bacterial agents to treat this disease. While confirmation via cross-cultural sequencing on COVID-19 patients would help to confirm this, it could be beneficial to act now. Those experiencing GI symptoms due to the virus, or desiring to get ahead of it, may benefit from nutritional and/or herbal support with anti-bacterial qualities specific to Prevotella. [Chakraborty 2020]  

My suspicions are further piqued by the fact that the countries most heavily impacted by the virus have diets heavy in the foods that promote Prevotella spp. See more on this below. 

Managing Prevotella spp. 

Prevotella is a genus of Gram-negative bacteria belonging to the Bacteroidetes phylaYou can think of phyla as a family and the Prevotella species as one of the children in the family. The family at large may share some similar characteristics, but each individual within the family may not necessarily behave in the same manner. So, while we can extrapolate some information about Bacteroidetes and apply it to Prevotella, it would be better to view Prevotella from a species level. Prevotella species are typical members of the oral and vaginal flora, often recovered from anaerobic infections of the respiratory tract. These infections include aspiration pneumonia, lung abscess, and chronic sinusitis. They have been isolated from abscesses and burns in the vicinity of the mouth, bites, paronychia, urinary tract infection, brain abscesses, osteomyelitis, and bacteremia associated with upper respiratory tract infections. Prevotella species predominate in periodontal disease and periodontal abscesses.  

Our clinical experience (along with many studies) indicate that diet is strongly associated with the gut microbiome composition. For example, a diet high in protein and fat will result in Bacteroidetes dominating the gut microbiome. The Bacteroidetes phyla is relatively tolerant to bile, so when it is released by the gallbladder in response to fat consumption it will decrease the bile intolerant microbes while promoting growth of bile tolerant ones, such as Bacteroidetes.  

Not much is known of the A2879 strain of Prevotellabesides the association with Coronavirus, but if we look to research at the species level there is additional information on Prevotella. Some research claims that Prevotella species are increased with a diet high in fibre, however, a detailed review reveals that the increase is related specifically to grains, not necessarily fibre in general. Dr. Jeff Leech goes to the trouble of analyzing a number of studies and sharing the results in an article on his website “The Human Food Project.” A few of the studies are cross-cultural, comparing the diet and microbiome of nonwesternized peoples to those of the westernized; while others compare diets, specific food items and microbiomes of animals. The conclusion being of course that in order to reduce Prevotella, one would want to reduce whole grain intake and include more legumes, starches, vegetables and fruit. 

My own investigations reveal that reduction of Prevotella species may be accomplished by consuming the following: 

  • Green tea catechins [Peter Taylor et al] 
  • Lauric Acid from coconut oil [Cinta Sol et al] *also anti-viral 
  • One study found that Prevotella was decreased when subjects followed a gluten free diet [Mohan et al] 
  • Luteolin found in celery, thyme, green peppers and chamomile [Soon Choi et al] 
  • Triphala [Shivaprasad et al] 
  • Rosemary [Cobellis et al] 
  • Turmeric [Liang Shen et al] 
  • DGL or licorice root powder for Prevotella in oral microbiome  [Tanabe et al] 
  • Bacteriostatic effects of chicory on Prevotella in oral microbiome [Signoretto et al] 
  • Berberine decreased Prevotella [Hui Shu et al] 
  • Chicory reduced Prevotella in pig gut microbiome [Ivarsson et al] 
  • An omnivorous diet, rather than vegetarian or vegan, will help to reduce Prevotella [Dhakan et al] 

 Items/conditions that increased Prevotella included: 

Diversity is always worth a mention. A study done on monkeys discovered reduced microbial diversity was associated with greater presence of Prevotella species [Mohan et al]. This is typical of a Westernized Gut Microbiome and something we often counsel our clients on. Regardless of whether the Prevotella – COVID connection is valid country to country, the above recommendations would be considered helpful for establishing a healthy microbiome. A more precise approach would be to use PCR based microbiome testing to assess the microbial landscape before making modifications.  

The Gut-Lung Connection 

The gut microbiome–lung connection is becoming apparent as COVID-19 is impacting respiration and lung function. While this most recent study is yet to be peer-reviewed, the researchers conclude that the vicious cycle between immune disorders and gut microbiota imbalance may be a high risk of fatal pneumonia. Given the cases we have witnessed at the Taymount Canada Clinic, I am inclined to agree. We must view weakened gut barrier homeostasis as promotive of immune dysregulation, bacterial translocation and secondary problems (in COVID) such as acute respiratory distress syndrome. [Lilei Yu et al] 

Gut translocation of bacteria is defined as the passage of gastrointestinal microbes across the intestinal mucosa to local lymph nodes and from there to external sites. [O’boyle et al] To reduce bacterial translocation we want to consider upstream causes as well as nutritional and supplemental support.  

What To Do 

Our microbiome reflects all that we touch, taste, breathe and encounter throughout our everyday lives. The domestication of the microbiome, along with our human selves, is a detriment to our health and ability to fend off viruses such as COVID-19. While the following recommendations will be helpful, I encourage you to think and experiment beyond this list, as COVID-19 will likely not be the last virus to send humanity into quarantine. 

  • Remove processed foods and food additives from your diet. If you can’t name the ingredient it’s not a food! 
  • Balance your microbiome; identify deficiencies or excesses of key players and remediate. 
  • Restore diversity to your microbiome; eat 40-50 different foods per week, diversity on the plate equals diversity in the gut. 
  • Toxins impair gut barrier function; rule out mold, chemical or metal toxicity. You can assess the state of your detox pathways with a Hair Tissue Mineral Analysis. 
  • High intensity and endurance exercise without adequate recovery will increase gut barrier permeability, while low-moderate exercise will improve gut barrier homeostasis. Focus on the latter until we are on the other side of this pandemic. 
  • Identify food sensitivities and reduce your intake of them.  
  • Reduce histamine, salicylate or oxalate overload if these are an issue for you 
  • Circulation of endotoxins is shown to increase bacterial translocation.

Use the following to reduce endotoxemia:

~Support nutrient breakdown via promotion of HCL, bile or enzyme production if required. Supplementation is            generally quite safe, but if you are unsure please work with a practitioner, as trickier cases may not tolerate. 

~Bacillus Subtilis HU58 found in Megaspore Probiotic can reduce post meal endotoxaemia [use code meetyourmicrobiome to purchase via their website]. 

~Consider mucosal strengtheners such as Zinc Carnotine, Slippery Elm, Marshmallow root, Colostrum, MegaIgg2000 [also ~see], Camel’s milk, Collagen and L-Glutamine. 

~Intermittent fasting or short fasts can also reduce endotoxaemia and help to restore gut homeostasis. However, avoid overdoing it during this time. 

 ~ Probiotics improve the microbiome, establish gut barrier homeostasis and support immunity: 

~L. Rhamnosus GG has been shown to reduce Intestinal Permeability. You can find this product in Super Smart or Inner Health Eczema Shield. 

~B. Longum BB536 can increase beneficial microbes such as bifido and lactobacilli. It can be found in Bioclinic Naturals or Life Extension Bifido GI Balan.

~L. Reuteri DSM 17938 has been shown to protect against upper respiratory and GI symptoms. Biogaia Infant Drops found here. 

~B. animalis subsp lactic BB-12 decreased respiratory infections in infancy, found in Usana BB12. 

~Jarro-dophilus by Jarrow Formulas contains strains found to improve immunity and restore gastric barrier function.

~L. Casei Shirota in Yakult has been found to modulate immunity. 

~Turmeric and L-glutamine have both been shown to reduce bacterial translocation. 

~Phenols, flavonoids, quinones, tannins and terpenoids can reduce pathogenic microbes while boosting friendly ones. These items tend to be prolific in colorful fruits and vegetables, herbs, tea and cacao. Particularly rich items include green tea, saffron, garlic, moringa, pomegranate, berries, flowers, cinnamon, apple. 

~Hyperbaric Oxygen can be extremely helpful for reducing inflammation, restoring gut barrier integrity and reducing pathogenic overload [Memar et al]. 


Kristina Mitts, RHN, GFT Therapist, Colon Hydrotherapist, SIBO Practitioner, is the lead Practitioner at the Taymount Canada Clinic which specializes in gut health and microbiome restoration. To learn more, email the clinic at or visit Kristina’s website 


  1. Wu F, Zhao S, Yu B, Chen Y, Wang W, et al. (2020) Complete genome characterization of a novel coronavirus associated with severe human respiratory disease in Wuhan. China bioRxiv 24.  
  2. Chen L, Liu W, Zhang Q, Xu K, Ye G, et al. (2020) RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerging Microbes & Infections 9: 313–319.  
  3. Chan JFW, Yuan S, Kok KH, To KKW, Chu H, et al. (2020) A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. The Lancet. 
  4. Chakraborty S (2020). The 2019 Wuhan outbreak could be caused by the bacteria prevotella, which is aided by the coronavirus, possibly to adhere to epithelial cells – prevotella is present in huge amounts in patients from both China and Hong Kong. doi:10.31219/ URL
  5. Chakraborty S (2020). The Wuhan coronavirus has integrated in Prevotella, which possibly causes the observed extreme virulence – as sequencing data from 2 different studies in China and Hong-Kong shows unequivocally. doi:10.31219/ URL 
  6. Memar et al (2019) Hyperbaric Oxygen Therapy: Antimicrobial Mechanisms and clinical application for infections. Biomedicine and Pharmacotherapy (109) 




1 Comment

  • Doug Darlington Posted April 3, 2020 9:31 am

    Thanks Bill. That’s a lot to absorb, but we are working on it. Your neighbor and fan, Doug Darlington

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