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News announcement20 October 2021

COVID-19 and our gut microbiome: evidence of a close relationship

A JRC study shows for the very first time that SARS-CoV-2 may replicate in the bacteria of our guts, opening new scenarios in the understanding of the biology of this virus.

Recent research shows for the first time that Covid-19 replicates in the gut bacteria
Recent research shows for the first time that Covid-19 replicates in the gut bacteria
© picture-waterfall - 2021

JRC research activities highlighted how the microorganisms present in the human gastrointestinal tract could influence COVID-19 severity and show for the first time that the virus replicates in the gut bacteria.

Often called the second brain of the human body, the gut microbiome is a set of bacteria, fungi, viruses and small parasites lodged in our intestines. There is growing evidence of a strong relationship between the gut and the brain. It makes people develop emotional eating or stomach ulcer under stress or “feel” anxiety, happiness or intuition “in their gut”.

Coronaviruses replicate in human and animal cells. A new JRC study shows however, and for the very first time, that SARS-CoV-2 may replicate in the bacteria of our guts, suggesting the hypothesis of a close relationship between our guts and COVID-19. This newly observed viral replication mechanism opens new scenarios in the understanding of the biology of SARS-CoV-2.

The gut microbiome communicates with other organs in the body. It plays a role in the digestion, in the partitioning of the intestine and digestive waste from other organs, in our inflammatory and immune responses to diseases and in the communication between our different organs.

It is therefore easy to understand that, if SARS-CoV-2 mainly affects the respiratory system, an increasing number of studies show that the virus could also interact with our gut microbiome, potentially making the disease more severe.

By reviewing more than 70 scientific papers, this JRC study summarises the interactions hypothesised between the gut microbiome and COVID-19. Many studies assume links between SARS-CoV-2 infection and an imbalance in the gut microbiome, also known as gut dysbiosis. Understanding whether COVID-19 severity is primary cause, secondary cause, concomitant cause or consequence of gut imbalance is still under debate. Several studies also show that SARS-CoV-2 could potentially compromise our intestinal barrier.

This permeability allows bacterial endotoxins to escape from the intestine and to reach the blood circulation. Intestinal bacteria have been found in the lungs of patients suffering from COVID-19. In order words, this permeability can lead to multi-organ complications, affecting patients’ lung, heart, liver, kidney.

How to take care of our gut?

The gut microbiome of each person is unique. Its composition varies according to its age, genes, diet and environmental factors.

In any case, scientists recommend the adoption of a healthy diet, rich in cereals, fruit and vegetables, to help the gut microbiome to fulfil its functions.

Beside a healthy diet, the use of pre- and probiotics to restore the gut microbiome before, during and after SARS-CoV-2 infection, is also highlighted in the scientific literature. By stimulating the growth of specific microbes in the guts, they both can limit the gastrointestinal symptoms due to COVID-19 and, eventually, limit the secondary infections.

However, a healthy diet and the intake of probiotics will never replace the vaccination and official medical treatments, which remain the best way to protect ourselves from severe forms of COVID-19.

Related Content

Technical report (review of 70 scientific papers)

JRC study: SARS-CoV-2 may replicate in the bacteria of our guts

Factsheet version

Short factsheet version


Publication date
20 October 2021