*If you prefer not to explore all the science and my thought process feel free to skip right to collecting your printout of our nutrition/lifestyle recommendations. Refer to the following printout of recommendations, but nothing pays off like individualized recommendations from an expert. Our registered holistic nutritionists can be reached at info@taymountcanada.com. For best results, use our recommendations in combination with those of your medical provider as well as those of the American Nutrition Association found here: American Nutrition Association

For those who like a good scientific rhetoric, here is a re-cap before I get to the meat of my next discussion.

The relationship between Coronavirus and the microbiome has been formally established by this point:

1. The Zhejiang University School of Medicine released the “Handbook of COVID-19 Prevention and Treatment.” In the handbook, they recommended:

  • microbiome analysis to assess microbial status
  • monitoring patients for secondary infections such as Candida
  • nutrition and supplemental support to balance the microbiome and reduce bacterial translocation (the passage of viable bacteria from the GI tract or oral biome to other sites: liver, kidney and bloodstream).

2. Studies reveal characteristic imbalances occurring within the gut microbiomes of COVID-19 patients. Such characteristics include 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 Corona Virus integration in Prevotella bacteria strain A2879.

3. A meta-analysis concluded that anti-virals should be supplemented alongside anti-bacterial agents to treat this disease.

The Most Recent Research As It Pertains To COVID-19 And The Microbiome

Most recently, after DNA sequencing of the lungs of 8 of Wuhan’s COVID-19 patients, researchers declared a “missing microbiota signature.” This study found that the lung microbiome of 6 of these patients was dominated by pathogens and for 2 patients elevated levels of oral and upper respiratory commensal microbes. [Shen et al] Meanwhile, the control groups were characterized by greater diversity and less pathogens.

I’d like to draw your attention to the part about oral microbes, as this could easily be glossed over. Care for our oral (mouth) biome is of utmost importance when addressing other aspects of microbiome health and will be covered in our recommendations. Second, in my opinion, we can’t very well blame individual microbes without having a better comparison. So, I’d like to zoom out for a moment.

Geographical-microbial Spread Of COVID-19

The consensus is that our individual microbial diversity differs more by region than it does intra-personally. Thus, we can gain useful information if we look at the geographical spread of this virus and the generalized microbial characteristics per region. Specifically, we want to know geographical, cultural and dietary influences on microbial diversity, pathogenic load and commensal populations, which in turn can help us make inferences about dietary and lifestyle choices that promote immunity against COVID.

As of April 15th, 2020, the countries with the highest reported cases include the USA, Italy, China, Spain, Germany, France, Iran and the UK, in that order. The countries with the worst death to infection rates are Italy 10.8%, Spain 8.1%, and Iran 7.1%. I’d also like to consider countries with unusually low infection rates given their spatial relevance, such as Japan.

1. Microbial diversity. We know that the more diverse the human microbiome is, the better the potential for overall health to be. [Deng et al] (1) [Santoro et al] In multiple meta-analysis, the US and China tied for having the least diversity, while other countries, such as France, scored higher. Surprisingly, Japan did not score much higher than China. [Mancabelli et al] [Jung et al] [Dhakan et al] [Finegold et al] [Junhua et al] [Odamaki et al]

2. Commensal Microbes vs Pathogenic. The same research reveals that Italy and the US have low bifidobacteria and lactobacillus while having high alistipes and more detectable levels of pathogens such as desulfovibrio. Japan has been found to score highest for bifidobacteria (approx. 20% more than the US according to one study), clostridia, flavonifractor and ruminococcus while being low in lactobacillus, and some common pathogens such as Desulfovibrio, Klebsiella, Odoribacter, Methanobacter.

As for phyla, the US and China have both been found to have characteristically high levels of Bacteroidetes (see my last blog post for more on this phyla) and low levels of Actinobacteria, the opposite of Japan.

Based on the information covered thus far, and within the context of the coronavirus situation, we can see that diversity may not be the only factor as France scored high for diversity, while Japan scored lower. Secondly, lactobacillus, as featured in the 8 COVID-19 patient study, may not be that important. I would make the case that a combination of low diversity, high pathogenic load/high bacteroidetes and reduced butyrate producing microbes, such as bifidobacteria and beneficial clostridia are likely the most important features here.

Risk factors for fatality due to COVID-19 and how they relate to the microbiome

As reported by the WHO and CCDC, the greatest risk factors for coronavirus include:

  •     Age: 21% of confirmed deaths are 80+ years old. (also characterized by Leaky Gut)
  •     Cardiovascular Disease: 13.2% of deaths
  •     Diabetes: 9.2%
  •     Respiratory Disease: 8%
  •     Hypertension: 8.4%
  •     Cancer: 7.6%

What do these conditions have in common? According to research, dysbiosis of the microbiome. [Nayfatch et al] [Deng et al] (1) [Santoro et al]  Several studies have characterized the microbiome by age; finding that microbial diversity decreases with age due to poor dietary choices, use of multiple medications as well as lifestyle choices. [Deng et al] (1) Elderly experiencing frailty are more likely to have less butyrate producing microbes, such as Faecalibacterium Prausnitzii and Roseburia, in exchange for more Proteobacteria and pathogens. They have increases in microbes known to be abundant in the periodontal environment and tend to have chronic low grade inflammation. [Jackson et al] [Biagi et al][Round et al] These changes result in increases in systemic inflammation. In a paper that looked at those who experienced longevity through aging (living to 105!) researchers found their gut microbiome to be characterized by lower intestinal permeability, as well as increased Akkermansia, Bifidobacterium, Clostridia  and Christensenellaceae.[Biagi et al] [Kong et al]

The subsequent risk factors for COVID-19 fatality are correlated with similar intestinal and microbial terrains. Type 2 Diabetes is characterized by moderate dysbiosis, decreases in butyrate producers (including but not limited to Clostridia), increases in opportunistic pathogens, increases in the phyla Bacteroidetes and mechanisms negatively influencing levels of oxidative stress and sulphate reduction. [Qin et al] [Larsen et al] There are some (including me) who theorize that Type 2 Diabetes is, at least in part, due to a consequence of deficiency in Short Chain Fatty Acids (SCFA) production from the gut ecosystem. [Zhao et al] Short Chain Fatty Acids are the metabolites produced by the fermentation of prebiotics by your intestinal flora. The one shown to have the most benefit is Butyrate, also called Butyric Acid. You can also increase dietary Butyrate by eating grass-fed organic butter.

A 405 cohort study found COVID-19 patients to have elevated Enterobacteriaceae, such as E-Coli, Klebsiella and Enterobacter, as well as greater quantities of microbes present in the oral cavity. Butyrate producers are also quite low for CVD patients. [Jie et al] In 47 patients with colorectal cancer the tendency was to have elevated levels of the phyla Bacteroidetes, elevated levels of microbes associated with periodontal disease, and have depletion of butyrate producers such as Clostrida.. do I sound like a broken record yet? [Ahn et al] Furthermore, the microbiota influences susceptibility to cancer in general by diverse mechanisms such as modulating inflammation and production of metabolytes. Nutritional therapy is recommended. [Bultman] [Francescone et al] [Tang et al][Chang et al] The effects of the microbiome on respiratory disease and lung health is only just beginning to be elucidated. Interestingly, the status of early-life nasopharynx biome can influence respiratory issues later on in life and there seems to be a distinct connection between the oral microbiome and lung biome. [Salami et al] [Morris et al]

What To Do

You and your microbes are a product of your environment and routine daily practices. As I’ve said before, the westernization/domestication/industrialization 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.

Nonetheless, the following dietary and lifestyle recommendations will be helpful in the context of coronavirus:

  •      Reduce pathogenic microbes
  •      Reduce the phyla Bacteroidetes
  •      Increase Butyrate producing microbes
  •      Support healthy oral microbiome to decrease the spread of oral based pathogens from mouth to other bodily biomes  
  •      Increase microbial diversity
  •      If you already have one of the listed risk factors, we recommend working with an Integrative MD

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Biagi, E., Nylund, L., Candela, M., Ostan, R., Bucci, L., Pini, E., … De Vos, W. (2010, May 17). Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/20498852?dopt=Abstract

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Chang, P. V., Hao, L., Offermanns, S., & Medzhitov, R. (2014, February 11). The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/24390544?dopt=Abstract

Deng, F., Li, Y., & Zhao, J. (2019, January 15). The gut microbiome of healthy long-living people. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366966/  (1)

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1 Comment

  • Pat Harding Posted April 18, 2020 10:35 am

    Thank You Dr Code

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