Gut Microbiome Changes even in mild COVID-19 and what to do about it

Mild infections of SARS-CoV-2 can cause long-lasting changes in the gut microbiome, according to a UCSF study.

Trillions of good microbes compose the gut microbiome in the intestinal tract. They affect an individual’s health significantly, so there have been proposals to consider it as another organ system, like the nervous and cardiovascular systems.

The authors of the recently released study are from the University of California in San Francisco. The study is still a preprint at BioRxiv.

Humans and mice were the subjects of the research. A mild  SARS-CoV-2 infection disrupted the gut microbiome in fourteen humans until five months after testing positive.

The human studies ruled out the effect of hospitalization and treatment on the gut microbiome of the virus. They continued their research in mice to remove other variables and make their findings more specific.

Mice with human ACE2 receptors (K18-hACE2) were inoculated with SARS-CoV-2 variants; the USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron.

They found that, over time, all the variants could deplete the Akkermansia muciniphila bacteria in the gut.

A. muciniphilia typically resides in the intestines and comprises 1-4% of the fecal microbiome. They improve the immune system by restricting bacterial penetration in the gut to prevent inflammation.[3]

Immune cells are found in the visceral fat lymph nodes inside the abdominal cavity. Their job is to kill any microbes that might go thru the intestines.

If the intestinal barrier is compromised, the immune cells will produce pro-inflammatory cytokines overflowing into the systemic circulation and affecting the blood vessels and other organs.

This results in inflammatory conditions like hypertension, diabetes, and cardiovascular diseases. It is not surprising that low levels of Akkermansia are seen in obesity, diabetes, and inflammatory bowel diseases.[2],[3]

In COVID-19, depletion of Akkermansia may result in uncontrolled inflammation and tissue damage like acute lung injury.

After acute COVID-19, the abnormally low levels of Akkermansia may prolong its symptoms resulting in Post Acute Sequelae of COVID-19 Syndrome, also known as Long COVID syndrome.

Experiments by Everard and colleagues show that restoring the Akkermansia to its normal levels in obese mice increased fat metabolism resulting in lower body weight, decreased inflammation, and prevented high blood sugar. All without any decrease in food intake.[3]

How to increase Akkermansia

Akkermansia can be replaced by using a probiotic. Another way is to increase your prebiotic intake, which is food the gut microbiome needs to multiply.

Examples of prebiotics are inulin (not insulin) and oligofructose. They are not digested in the upper gastrointestinal tract and therefore reach the large intestines and be digested by the microbiome. More food means more good bacteria. 

Humans can not digest inulin and oligofructose. That means they do not increase caloric intake, blood sugar, and insulin secretion.

All are ideal for those who want to lose weight and keep their blood sugars low. Making them ideal for people with diabetes.[4]

They are found in wheat, onions, bananas, garlic, and chicory.[4]

Chickory is used as a coffee substitute. Inulin can also be bought as a powder. 

Amazon reviewers say it should be used in warm beverages like coffee so it dissolves better.

One warned not to use too much because gas can form, resulting in bloating and cramping. The same thing happens with lactose intolerance. 

Take away message

Mild COVID-19, even with the Omicron variant, can produce lasting changes in the gut microbiome and deplete the beneficial bacteria Akkermansia Municiphilia.

The result could be weight gain and higher blood sugar in diabetes. How many people do you know gained weight during the pandemic?

Thus, it is beneficial to eat foods with prebiotics to make the gut microbiome healthy again.

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