Recently Merogenomics embarked on very interesting studies of how the SARS-CoV-2 virus is infecting bacteria in the gut. This discovery has two important implications: the host bacteria can form a reservoir of the SARS-CoV-2 virus in our body that could persist for a long time after the infection in the upper respiratory tract is cleared, and as a consequence of such bacterial infection, the virus could be altering the microbial composition of our gut microbiome.

Below you can see the first video discussing the evidence of bacteria infection by SARS-CoV-2, comprising a nice review of how to study and prove virus infection of cells.

Another important implication of this discovery is a potential new method of how COVID-19 could be considered to be treated. This is because if the severity of COVID-19 is at least partially explained by how the gut microbiome is disturbed by the virus, this raises the unusual possibility of treating virus infection with… antibiotics! In this case, the antibiotics would be used to either prevent the build-up of opportunistic pathogenic bacterial species in our gut or to remove the source of bacteria that could act as hosts for the virus. This has recently been demonstrated that antibiotic treatment early in the viral infection could significantly reduce the duration of COVID-19, summarized in a video below.

This brings us to the most interesting aspect of studying this topic, where I had an opportunity to participate in the production of a scientific review with some of the authors behind the work summarized in the above videos. In this manuscript, currently under editorial review, explored how the disruption of the gut microbiome (gut dysbiosis) by SARS-CoV-2 could be implicated in the inflammatory problems observed in some affected individuals. And my favourite part of that work was the segment dedicated to the potential use of probiotics in order to restore proper gut microbiome function. This has resulted in my further research of what natural food sources of probiotics individuals could consider in their bid of developing a healthy gut microbiome.

Why is this important?

This is because a healthy balanced gut microbiome is essential for controlling the integrity of the intestinal barrier, disruption of which is involved in numerous inflammatory and immunological disorders. The intestinal barrier is made of surface mucus, the epithelial layer underneath, and immunological defenses. The epithelial cells of your gut in turn are kept in close proximity to one another by various cellular junctions. However, dysbiosis, or an imbalance in the gut flora, can lead to increased intestinal permeability, also known as "leaky gut syndrome”. As a consequence, gut microbiome dysbiosis has been linked to chronic diseases prevalent in the elderly, such as diabetes, and other systemic side effects like oxidative stress and increased inflammation.

In dysbiosis, characterized by a decrease in beneficial commensals and/or a proliferation of opportunistic pathogens, certain bacteria, such as Escherichia coli and Salmonella, can increase intestinal permeability, which basically means that now molecular elements from the lumen of the gut (the empty space of our gut) can enter the blood supplied by the vessels underneath the epithelial cells.

In turn, probiotics, meaning “for life” in Greek, comprising a collection of beneficial microorganisms like Bifidobacterium and Lactobacillus, offer health benefits beyond basic nutrition, promoting health in humans by improving the gut barrier function. Probiotics have been shown to reduce intestinal permeability and epithelial barrier dysfunction in gastrointestinal disorders. These include diarrhea, gastroenteritis, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD) like Crohn's disease and ulcerative colitis, cancer, and depressed immune function. They are also beneficial for issues such as inadequate lactase digestion, infant allergies, failure-to-thrive, hyperlipidemia, hepatic diseases, Helicobacter pylori infections, and rheumatoid arthritis. Even in COVID-19, probiotics have shown promise in reducing viral load, hospitalization duration, and inflammatory markers, suggesting their potential as a treatment strategy.

So how do we get these probiotics?

Obviously, you can purchase supplements, but in this article, we want to explore natural food sources.

It appears that fermented foods are going to be your richest source of probiotic live microbial cultures, especially fermented dairy products, but let us break it all down, as non-dairy vegan options are also available, such as juices and plant-based drinks.

Probiotic Foods:

Dairy-Based Products:

• Yogurt: a well-known probiotics source, produced through the bacterial fermentation of milk. In addition to cow’s milk, other types of milk such as those from water buffalo, goat, sheep, horse, camel, and yak are used worldwide to make yogurt. It prevents osteoporosis, reduces high blood pressure risk, and alleviates gastrointestinal issues.
• Soft cheese: also serve as a source of probiotics, often labeled with terms like “probiotics,” “active culture,” or “live culture.” Varieties such as blue cheese and aged cheeses are particularly rich in probiotics.
• Kefir: originating from the Caucasus and Turkey and consumed in Eastern Europe and Southwest Asia, is a fermented milk drink containing various beneficial bacteria and yeasts.
• Whey: the by-product of cheese-making, and buttermilk, the liquid remaining after butter extraction, also contain probiotics.
• Koumiss: a unique fermented mare’s milk drink popular in the Middle East, is fermented with a mix of lactic bacteria and yeasts, providing health benefits like reducing intestinal and pancreatic lipase activity and lowering cholesterol levels.

Non-Dairy Beverages:

• Kombucha: a fermented tea made with yeast, sugar, and black tea, offers health benefits such as antidiabetic activity and anti-inflammatory effects.
• Boza: a Turkish cereal-based fermented drink made from grains like maize and wheat, offering both lactic acid and alcoholic fermentation benefits.
• Kvass: a non-alcoholic fermented cereal beverage from Eastern Europe made from malt, rye flour, and bread.
• Bors: a liquid produced by the natural fermentation of an aqueous suspension of wheat bran (known as "tărațe" in Romanian), rye, and corn flour.
• Hardaliye: a Turkish fermented beverage made from a blend of red grapes, crushed mustard seeds, and dried sour cherry leaves.
• Munkoyo: a spontaneously fermented cereal-based beverage produced in Zambia and the Democratic Republic of Congo.

Alcoholic Beverages:

• European Barley Beer: a cereal-based fermented beverage with probiotic properties.
• Red Wine: contains probiotic strains beneficial for gut health.
• Pulque: a traditional Mexican alcoholic beverage made from the fermentation of agave sap, containing probiotic yeasts.
• Makgeolli: a traditional Korean alcoholic beverage.
• Palm Wine: a beverage made from the sap of various palm trees, consumed in regions like Borneo, India, and Africa.
• African Traditional Beers: such as pito and burukutu, made from malted grains.
• Tchoukoutou Beers: produced in Africa and Asia by malting red sorghum, are traditional, opaque, and often less carbonated with a sour taste.

Fermented Foods:

• Sauerkraut: fermented cabbage rich in lactic acid bacteria, promoting gut health and offering cardioprotective and anti-inflammatory benefits.
• Kimchi: Korean fermented cabbage with similar benefits to sauerkraut.
• Tempeh: Indonesian fermented soybeans bound into a cake.
• Miso: another traditional Japanese food rich in probiotics, a thick paste made from fermenting soybeans with salt and koji.
• Soy Sauce: a fermented condiment made from soybeans as well, also contains lactic acid bacteria and offers numerous health benefits, including lowering cholesterol and anti-diabetic effects.
• Sourdough Bread: fermented dough containing beneficial bacteria.
• Sour Pickles: fermented cucumbers preserved in a saltwater solution.
• Sour Red Soup: from southwest China made from fermented tomatoes and red cayenne.
• Brem: an Indonesian fermented rice snack.
• Ogi-baba: In , a fermented sorghum gruel called is produced. This a traditional dish of West Africa made by fermenting sorghum grains, resulting in a thick, nutritious porridge, commonly consumed for breakfast.
• Natto: a traditional Japanese food made from fermented soybeans using B. subtilis, rich in nutrients, providing various health benefits. Natto is also currently receiving attention as a potential source of spike protein degradation, a topic Merogenomics has covered previously (see videos below).

However, keep in mind that some fermented foods, like sourdough bread and most commercial pickles, undergo processing after fermentation and do not retain live cultures when consumed. The live microorganisms in many fermented foods, including yogurt, generally survive well throughout the product's shelf life. However, many of the microbes often do not survive the acidic environment of the stomach or the enzymatic activity in the small intestine, meaning they may not reach the distal gut. However, specific probiotic strains in yogurt and other foods do withstand this intestinal transit, providing the desired benefits.

Also, while generally safe, probiotic supplementation should be approached with caution by individuals with compromised immune systems or certain medical conditions, including those on anti-rejection medication post-transplant, on immunosuppressive drugs, chemotherapy, or corticosteroids, those with autoimmune diseases, structural heart disease, or a history of infective endocarditis, and those with acute abdominal conditions, active intestinal diseases like colitis, neutropenia, or intestinal perforation.

No story of probiotics would be complete without mentioning prebiotics, non-digestible food ingredients that foster beneficial intestinal bacteria. The microorganisms in probiotics thrive on prebiotics, which stimulate the growth and activity of these healthy bacteria in the gut.

Prebiotic Foods:

• Asparagus, Leeks, Onions, Garlic: rich in inulin and other prebiotic fibers.
• Jerusalem Artichokes and Chicory: contain high levels of prebiotic fibers.
• Soybeans: used in various fermented products and as a prebiotic source.
• Tomato and Banana: common fruits rich in prebiotic fibers.
• Nectarine, Watermelon and Pear: high in oligosaccharides, beneficial for gut health
• Honey and Sugarcane: natural sources of prebiotics.
• Wheat, Oats, Barley, Rye: cereals containing β-glucans and other prebiotics.

Merogenomics has previously made a video on the benefits of β-glucans in stimulating innate immune cells as a potential option for mRNA-vaccinated individuals to enhance their innate immune system. You can see that content below.

In conclusion, these foods have been associated with numerous health benefits, such as improving digestive health, reducing the risk of cardiovascular diseases, and enhancing nutrient bioavailability. By including these probiotic and prebiotic-rich foods and beverages in the diet, one can naturally enhance gut health and overall well-being.

Bon Appetit!

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