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Could COVID-19 Infection Harm Your Gut Microbiota?

A study shows that COVID-19 infection can harm your gut microbiota, reducing diversity and beneficial bacteria. Will probiotics help?

Over the past decade, scientists have learned a lot about the importance of the gut microbiota. This is the collection of bacteria, fungi and viruses that hang out mostly in the large intestine. All these microbes form a sort of ecological system. A healthy system is diverse and thriving, and helps keep its host healthy as well. But certain drugs and infections can harm your gut microbiota.

COVID-19 Infection Can Harm Your Gut Microbiota:

New research indicates that COVID-19 infection alters the gut microbiota. A study of elderly French patients hospitalized with COVID-19 examined how the bacteria in their digestive tracts differed from uninfected healthcare workers who served as controls (medRxiv, Feb. 8, 2022).

Researchers analyzed stool samples and recorded clinical outcomes among the patients. Bacterial diversity of the gut microbiome was far lower among the COVID patients.

Unfortunately, some of the types of bacteria that were reduced or went missing are known to be beneficial. They secrete butyrate, which improves the intestinal barrier and calms inflammation. In addition, COVID patients were less likely to have normal levels of Bifidobacteria, which are beneficial bacterial strains.

Will Probiotics Protect Your Gut Microbiome?

Sometimes people take Bifidobacteria as probiotic supplements. When most people think about probiotics, they focus on digestive problems. That’s only natural, since these beneficial bacteria are expected to act by influencing the gut microbiome (Nature Medicine, May 2019). However, a previous analysis suggests that people who take probiotics are less likely to lose work time from flu-like illness (Frontiers in Pharmacology, Aug. 28, 2019). We don’t know if that would also apply to COVID infections.

What Is Flu-Like Illness?

People with a respiratory tract infection causing cough and fever that started 10 days ago or less have a flu-like illness. If they see a health care professional and undergo an antigen test for influenza, that diagnosis could change. The test provides a definitive diagnosis of flu. Most respiratory tract infections that keep people out of work or school are never diagnosed as flu, though. Probably the vast majority are caused by some other non-influenza virus. We don’t know if these infections also harm your gut microbiota as COVID-19 does.

How Do Probiotics Affect Respiratory Tract Infections?

Analysts noted the results of two different meta-analyses. One, conducted by the independent researchers of the Cochrane Collaboration, concluded that: “probiotics may be more beneficial than placebo for preventing acute URTIs” (Cochrane Database of Systematic Reviews, Feb. 3, 2015). The investigators lamented the inadequate quality of the research, however. (In case you were wondering, URTI stands for Upper Respiratory Tract Infection.)

The second meta-analysis considered 20 randomized controlled trials of probiotics on respiratory infections (British Journal of Nutrition, July 14, 2014).

Much like the Cochrane scientists, these investigators concluded:

“This systematic review provides evidence from a number of good-quality RCT that probiotics reduce the duration of illness in otherwise healthy children and adults.”

The Economic Impact of Flu-Like Illness:

The analysts used the results of these meta-analysis to create computer models for how many fewer Americans would see health care providers, get antibiotic prescriptions and miss work due to flu-like illness. Although antibiotics are not effective against viral infections, many people get prescriptions anyway. With the use of probiotics linked to fewer upper respiratory tract infections, fewer doctor visits and a lower use of antibiotics, the authors estimated the savings to the U.S. economy at over $1 billion. They reported that side effects of probiotics were uncommon and minor, except for digestive complaints.

The only problem: we don’t know which probiotic species and strains are most cost-effective. However, we do know that probiotics do not speed recovery from antibiotics. You can learn more about this by listening to our interview with investigator Eran Elinav in Show 1159.

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About the Author
Terry Graedon, PhD, is a medical anthropologist and co-host of The People’s Pharmacy radio show, co-author of The People’s Pharmacy syndicated newspaper columns and numerous books, and co-founder of The People’s Pharmacy website. Terry taught in the Duke University School of Nursing and was an adjunct assistant professor in the Department of Anthropology. She is a Fellow of the Society of Applied Anthropology. Terry is one of the country's leading authorities on the science behind folk remedies..
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  • Cervino ACL et al, "Results from EDIFICE : A French pilot study on COVID-19 and the gut microbiome in a hospital environment." medRxiv, Feb. 8, 2022.
  • Suez J et al, "The pros, cons, and many unknowns of probiotics." Nature Medicine, May 2019. DOI: 10.1038/s41591-019-0439-x
  • Lenoir-Wijnkoop I et al, "Probiotics reduce health care cost and societal impact of flu-like respiratory tract infections in the USA: An economic modeling study." Frontiers in Pharmacology, Aug. 28, 2019. https://doi.org/10.3389/fphar.2019.00980
  • Hao Q et al, "Probiotics for preventing acute upper respiratory tract infections." Cochrane Database of Systematic Reviews, Feb. 3, 2015. DOI: 10.1002/14651858.CD006895.pub3
  • King S et al, "Effectiveness of probiotics on the duration of illness in healthy children and adults who develop common acute respiratory infectious conditions: A systematic review and meta-analysis." British Journal of Nutrition, July 14, 2014. DOI: 10.1017/S0007114514000075
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