Coronavirus and the Microbiome: Diversity, Prevotella, Reducing bacterial translocation to reduce severity of COVID-19.
This is an overview of Part 1 of Dr. Code and Kristina Mitts’ Facebook Live series on Coronavirus and the microbiome.
Studies originating in China have revealed characteristic imbalances occurring within the gut and lung microbiomes of COVID-19 patients making them more susceptible to fatality. These differences happen to correlate with the higher risk groups; Diabetes, CVD, Cancer and Elderly. Evidently, this is one aspect of our health that, if imbalanced, will promote disease progression of the Coronavirus.
Paneth Cells: These cells are similar to white blood cells; providing immune defense in the small intestine.
GALT: Gut associated lymph tissue (includes Peyers patches, appendix and cells within gut lining) that works to protect you against gut driven infections.
Atopobiosis: The appearance of microbes in places besides their normal location ie. P. gingivalis in carotid artery plaque.
Bacterial Translocation: the passage of viable bacteria from the GI tract to other sites including the lungs, kidneys and bloodstream (Leaky Gut).
Some of the irregularities found within the microbiomes of deceased or more severely impacted COVID-19 patients:
- Deficiencies in commensal microbes such as Bifidobacterium, Lactobacillus and Eubacterium.
- Increases in pathogenic microbes such as Prevotella, Corynebacterium and Ruthenibacterium. [Lilei Yu et al]
- And perhaps most notable, sequencing data has found Corona Virus integration in Prevotella bacteria strain A2879, indicating that the virus has used this microbe to aid in it’s spread
- The lungs of 8 of Wuhan’s COVID patients were found to be dominated by pathogens – for 2 patients elevated levels of oral and upper respiratory commensal microbes were included in this. [Shen et al]
- Control groups have been characterized by greater diversity and less pathogens than patients
What can we do to support our microbiome?
- Balance our microbial populations; reducing pathogens and increasing both diversity and protective species, such as Bifidobacteria, will support hospitable terrain/environment.
- Reduce bacterial translocation between the oral, lung and gut microbiomes.
- Strengthen the epithelial linings that protect each of these organs.
Diversity is our best shield against Pathogenicity
In Part 1 of our video series we focused largely on Prevotella to provide analogies for reducing pathogens and cultivating a healthy microbial environment. We wanted to drive home the fact that, in most cases, a microbe will only behave as a disease-promoting pathogen if it’s environment or terrain encourages it to do so. The major environmental influencers that are within our control include:
- Competition/diversity: both within a single genus of microbes as well as between the microbe in question and non-related genus.
- Substrate: what foods are available to feed the microbes? is one species out-competing the others for food? Is substrate lacking in diversity or lacking entirely, driving microbes to feed on your own gut lining?
- Temperature: microbes, including viruses, respond to temperature. This is why frequent hand washing with warm-hot water is encouraged to prevent the spreading of coronavirus.
- pH: each biome within the body has it’s own preferred pH, which supports subsets of microbes. In the case of Prevotella, it is flexible enough to withstand the pH and conditions within the oral, lung, intestinal and vaginal microbiomes.
More on Prevotella
Prevotella is a Genus of microbe that contains many species and subspecies underneath this heading. The analogy we used to help you understand this concept better was that of family. Take the Code family for example. The Code family will share certain characteristics, but they won’t necessarily behave the same or produce the same things. Bill has a talent for integrative medicine, while Denise has a flair for business.
The second analogy we used was that of C-difficile. Most will have heard of this microbe by this point as it is the sole cause of C-difficile infection, a severe and often fatal intestinal infection for which Microbiota Transplant is the most effective cure. C-difficile is however, just one species among many in the Clostridia family. 98% of Clostridia species provide us with B-Vitamins, carbohydrate metabolism and provide short-chain fatty acids, which feed the cells of our intestines, modulate immunity and encourage a healthy terrain.
What do we know about Prevotella, besides that the species A2879 was integrated by coronavirus?
a.) Prevotella thrives on a diet rich in starch, particularly those starches from whole grains. If we review the study comparing the microbiome of children living in Burkina Faso vs. those in Italy, we find that the Burkina Faso children microbiome is dominated by Prevotella. Their diet consisted of 50% or greater millet and sorghum, some legumes and limited variety of vegetables. Even those on plant-based diets can experience detriments due to it’s overgrowth, and so, dietary imbalances must be addressed. [Di Paola et al][Leach]
b.) Bacterial Species Matters: some species seem to have more capacity for providing benefit, while others have more capacity for virulence. For example, some species are supportive of carbohydrate metabolism and promote insulin sensitivity; some are immunomodulatory, providing protective benefits; others are unfortunately associated with periododontal disease, arthritis, elevated serum TMAO (a marker for cardiovascular disease risk) and more. [Datchary et al][Scher et al][Fehlner-Peach et al][Vuillermin et al]
c.) We don’t want to be rid of Prevotella entirely. What we want is diversity within the genus and between Prevotella and other Genus. In RA patients, for example, there tends to be a single Prevotella species that has overgrown, while other Prevotella species are missing. [Scher et al][Wells et al]
Supporting our Microbiome
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.
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] The number one way to increase your microbial diversity is through having a diverse diet. Aim to eat at least 50 different foods per week including a range of different coloured fruits and vegetables. We can monitor this progress with microbiome testing, and do sometimes find that if clients are more severely depleted, that certain microbes may not grow back (for example, if someone has a history of excessive antibiotic use). In this case, Microbiota Transplant may be necessary to replenish the diversity.
In reference to Prevotella, if you eat grains we recommend limiting servings to 1-2 per day and rotating different types through your diet. Try eating black rice one day, quinoa the next, sorghum the next day and so on.
2. Protective Microbes. A meta-analysis of multiple countries found that Italy and the US typically have low counts of bifidobacteria and lactobacillus while having high alistipes and more detectable levels of pathogens such as desulfovibrio. Japan, who has maintained a contextually low fatality to infection ratio of coronavirus, has been found to score highest for bifidobacteria (approx. 20% more than the US according to one study), clostridia, flavonifractor and ruminococcus while scoring low for common pathogens.
Boost your bifidobacteria count by providing them with their preferred food sources:
- Nopal (Cactus origin)
- Natto (fermented soy)
3. Bacterial Translocation should be prevented
- Restore and maintain epithelial membranes by correcting microbial balance and using supplements such as colostrum, immunoglobulins, camel’s milk, zinc, Vitamins A,C,D, l-glutamine, butyrate and turmeric.
- Avoid using PPI’s and antacids and these reduce stomach acid – our first line of defense against microbes coming in from the mouth, food and water. If you are having trouble getting off of PPI’s or antacids we recommend investigating underlying causes such as SIBO.
- Take care of the oral (mouth) microbiome so that translocation of pathogenic microbes is lessened. In the same way that our gut microbiome requires balance, so too does our oral microbiome. It needs:
- regular brushing and flossing (with unwaxed floss)
- visits to the dentist
- avoiding low quality/overly antimicrobial mouthwashes and toothpastes (they alter the oral pH and leave the mouth susceptible to pathogens)
- Remove cavitations, mercury amalgams and infected root canals
4. Support your microbiome with Probiotics
Studies have found the following probiotics to promote bifidobacteria:
- Biogaia Protectis
- Usana BB12
- Sacch. Boulardii in Florastor
- Life Extension GI Balance
- Naural Factors Travelbiotic
The following probiotics may 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 Balance
- 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 promote immunity
Refer to this list, but nothing pays off like individualized recommendations from an expert. Our therapists can be reached at email@example.com.
For best results, use our recommendations in combination with those of your medical provider as well as those of the American Nutrition Association
Ahn, Jiyoung, Sinha, Pei, Christine, Wu, … Liying. (2013, December 6). Human Gut Microbiome and Risk for Colorectal Cancer. Retrieved from https://academic.oup.com/jnci/article/105/24/1907/2517573
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
Biagi, E., Franceschi, C., Rampelli, S., Severgnini, M., Ostan, R., Turroni, S., … Candela, M. (2016, June 6). Gut Microbiota and Extreme Longevity. Retrieved from
Bultman, & J., S. (2013, December 3). Emerging roles of the microbiome in cancer. Retrieved from https://academic.oup.com/carcin/article/35/2/249/2463060
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)
Di Paola M et al (2017) Diet, Environments, and Gut Microbiota. A preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy. Frontiers of Microbiology. (8) doi: 10.3389
Elkjær, B. (2020, March 24). Forskere har sporet 40 mutationer af coronavirus – alene på Island. Retrieved from https://www.information.dk/indland/2020/03/forskere-sporet-40-mutationer-coronavirus-alene-paa-island
Francescone, R., Hou, V., & Grivennikov, S. I. (2014, May). Microbiome, inflammation, and cancer. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112188/
Fehlner-Peach et al (2019) Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates. BioRxIV.
Jackson, M. A., Jeffery, I. B., Beaumont, M., Bell, J. T., Clark, A. G., Ley, R. E., … Steves, C. J. (2016, January 29). Signatures of early frailty in the gut microbiota. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/26822992?dopt=Abstract
Jie, Z., Xia, H., Zhong, S.-L., Feng, Q., Li, S., Liang, S., … Kristiansen, K. (2017, October 10). The gut microbiome in atherosclerotic cardiovascular disease. Retrieved from https://www.nature.com/articles/s41467-017-00900-1
Jeff Leach (2013) From meat to microbes to mainstreet: is it time to trade in your george foreman grill? http://humanfoodproject.com/from-meat-to-microbes-to-main-street-is-it-time-to-trade-in-your-george-foreman-grill/
Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., … Wang, J. (2014, July 6). An integrated catalog of reference genes in the human gut microbiome. Retrieved from https://www.nature.com/articles/nbt.2942
Maji, Sharma, Saxena, Gomez, Amato, Sharma, & K, V. (2019, January 30). unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. Retrieved from https://academic.oup.com/gigascience/article/8/3/giz004/5304367
Mancabelli, L., Milani, C., Lugli, G. A., Turroni, F., Ferrario, C., Sinderen, D. van, & Ventura, M. (2017, February 28). Meta‐analysis of the human gut microbiome from urbanized and pre‐agricultural populations. Retrieved from https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1462-2920.13692
Morris, A., Beck, J. M., Schloss, P. D., Campbell, T. B., Crothers, K., Curtis, J. L., … Winestock , G. M. (2012, October 24). Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers. Retrieved February 22, 2013, from https://www.atsjournals.org/doi/full/10.1164/rccm.201210-1913OC
Nextstrain. (n.d.). Retrieved from https://nextstrain.org/
Odamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J.-Z., … Osawa, R. (2016, May 25). Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/27220822?dopt=Abstract
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., … Wang, J. (2012, October 4). A metagenome-wide association study of gut microbiota in type 2 diabetes. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/23023125?dopt=Abstract
Salami, O., Marsland, B.J. Has the airway microbiome been overlooked in respiratory disease?. Genome Med 7, 62 (2015). https://doi.org/10.1186/s13073-015-0184-9
Santoro, A., Ostan, R., Candela, M., Biagi, E., Brigidi, P., Capri, M., & Franceschi, C. (2018, January). Gut microbiota changes in the extreme decades of human life: a focus on centenarians. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/29032502/
Tang, Xiaolu, Wu, Li, Xiang, Yuhe, … Jian. (2020, March 3). On the origin and continuing evolution of SARS-CoV-2. Retrieved from https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463
Tang, Y., Chen, Y., Jiang, H., Robbins, G. T., & Nie, D. (2011, February 15). G-protein-coupled receptor for short-chain fatty acids suppresses colon cancer. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/20979106?dopt=Abstract
The Novel Coronavirus Pneumonia Emergency Response Epidemiology Team. (2020, February 1). The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19) – China, 2020. Retrieved from http://weekly.chinacdc.cn/en/article/id/e53946e2-c6c4-41e9-9a9b-fea8db1a8f51
Woods, A. (2020, March 25). Iceland scientists found 40 mutations of the coronavirus, report says. Retrieved from https://nypost.com/2020/03/24/iceland-scientists-found-40-mutations-of-the-coronavirus-report-says/
Young-Do Nam, M.-J. J., & Seong Woon Roh, M.-S. K. (2011, July 29). Comparative Analysis of Korean Human Gut Microbiota by Barcoded Pyrosequencing. Retrieved from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022109
Zhao, L., Zhang, F., Ding, X., Wu, G., Lam, Y. Y., Wang, X., … Zhang, C. (2018, March 9). Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Retrieved from https://science.sciencemag.org/content/359/6380/1151.abstract
Zijie, Xiao, Yan, Kang, Lu, Ma, … Mingkun. (2020, March 9). Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients. Retrieved from https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa203/5780800
Ley, R. E. Prevotella in the gut: choose carefully.
Nat. Rev. Gastroenterol. Hepatol. 13, 69–70 (2016).
Kovatcheva-Datchary, P. et al. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 22, 971–982 (2015).
Scher, J. U. et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2, e01202 (2013).
Wells et al  A polygenic risk score for RA sheds light on the Prevotella association. MedRxIV
Full text: https://www.medrxiv.org/conte…/10.1101/2019.12.09.19014183v1
Vuillermin et al (2020) Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring. Nature Communications.(11)
GB Huffnagle et al (2016) The respiratory tract microbiome and lung inflammation: a two-way street. Mucosal Immunology. 10(2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765541/