Gut microbiota could play big role in COVID-19, French researchers find

SARS CoV-2 viral protein is detected in fecal samples of up to 50% of people diagnosed with COVID-19, even when the nasopharyngeal swab test proves negative. However, the role of intestinal infection in COVID-19 disease progression remains to be clarified. 

An exploratory study by a team of French microbiologists and medical researchers examines a possible link between alterations in the gut microbiota and levels of the COVID-19 virus in SARS CoV-2 in the gastrointestinal tract. Their results suggest that the viral load in the GI tract “could be more important than the presence of SARS CoV-2 in the respiratory tract.”

The study appears in the online journal Environmental Microbiology, April 22.

Altered molecular functions in the gut microbiota could influence mechanisms such as inflammation-induced damage to the intestinal wall, increased intestinal permeability (gut leakage), and activation of the immune response, the authors state. 

Understanding the role of COVID infection in the gut could lead to “alternative therapeutic strategies to favor the clearance of the virus and potentially mitigate the effect of the SARS CoV-2 infection,” they argue. 

Biomarkers identified

Using mass spectrometry techniques, the researchers profiled the gut microbiota looking at changes in the populations of bacteria, yeast, fungus, and archaea during COVID-19 infection. Using these studies, known as metaproteomic, they identify 42 biomarkers that are significantly altered during infection. 

These altered microbiota compositions were independent of the presence of SARS CoV-2 virus in the respiratory tract, as well as independent of disease severity and GI symptoms, but they correlated with levels of the virus in the GI tract.

The authors believe these biomarkers could be used to monitor infection and could become useful in the search for alternative therapies that may mitigate the severity of COVID-19. 

“Although hampered by the limited number of patients analysed, the metaproteomics profiles obtained in this exploratory study support the hypothesis that the composition of the gut microbiota may be influenced by the abundance of SARS-CoV-2 RNA in the intestine more than by its presence in the respiratory tract,” the authors note.

On closer examination, they found that a relatively high viral load was associated with significantly higher abundance of specific phyla of archaea and fungi––the Euryarchaeota and Ascomycota––as well as several genera of Actinobacteria. 

In summary, the authors note: 

“Until now, the impact of SARS-CoV-2 infection on the gut microbiota has been scarcely studied. Here, we assessed on a cohort of 39 patients the gastrointestinal SARS-CoV-2 viral load and correlated it with their full-range microbiota, including Bacteria, Archaea, Fungi and Moulds, accessible through metaproteomics.”

They describe three key results “that could be of major importance in the battle against COVID-19: (i) fecal SARS-CoV-2 viral load is not correlated to symptoms, (ii) an important change in the microbial structure is observed for patients with high fecal SARS-CoV-2 viral load and (iii) a list of microbiome and human markers can be drawn from this study as possible candidates for diagnostics.”

“These results should be an incentive for an extensive multi-centric metaproteomics analysis of the gut microbiota of COVID-19 patients,” they conclude.

Lucia Grenga et al. Taxonomical and functional changes in COVID-19 faecal microbiome could be related to SARS-CoV-2 faecal load. Environ Microbiol. (2022) DOI: https://doi.org/10.1111/1462-2920.16028