The gut microbiota could play a key role in the course of SARS-CoV-2 infection . This was revealed in a study published in Environmental Microbiology by a team of researchers coordinated by Jean Armengaud of Université Paris-Saclay, France.
SARS-CoV-2 (Severe Acute Respiratory Syndrome – Coronavirus 2), the etiologic agent ofCOVID-19(Coronavirus Disease 19) counts among its symptoms, in addition to cough, fever and dyspnea related to respiratory tract involvement, also diarrhea, vomiting, nausea and abdominal pain of a purely gastrointestinal nature.
Covid and intestines
Various hypotheses have been advanced to explain the involvement of the gastrointestinal system including loss of absorption capacity by enterocytes, microinflammatory processes to the damage of the mucosa of the stomach or intestine, and impairment of angiotensin-converting enzyme (ACE 2) function.
Despite these preliminary observations, the role of gastrointestinal involvement in the pathogenesis of COVID-19 remains to be elucidated.
The excretion of SARS-CoV-2 virions in the feces of infected patients between days 1 and 12 after negativization assessed by nasopharyngeal swab suggests that viral particles are secreted from infected gastrointestinal cells. In particular, it has been noted that SARS-CoV-2 is able to penetrate through the apical surface of enterocytes that make up mature villi because they express three proteins that the virus uses to enter cells: ACE2, TMPRSS2 and TMPRSS4. Moreover, little is known about the changes that SARS-CoV-2 infection brings about at the gastrointestinal level. Experimental evidence suggesting that the gut microbiome influenced the expression of ACE2 receptors has led to speculation that the microbiome also plays a role in COVID-19, but there is very little data on the microbiome of SARS-CoV-2 positive patients.
The analysis of fecal samples
A total of 39 fecal samples were analyzed of which 33 were from patients who tested positive for COVID-19 by nasopharyngeal swab and 6 were negative. RT-qPCR analysis performed on the fecal samples showed 10 positive samples among the 33 previously nasopharyngeal swab positive.
No significant association was shown between the serum presence of C-reactive protein and the fecal content of SARS-CoV-2 as well as between the levels of SARS-CoV-2 mRNA in the feces and the swab positivity and between the content of SARS-CoV-2 and disease severity.
Samples tested positive for the presence of SARS-CoV-2 mRNA were classified into two groups: high level or low level.
Each was then analyzed by mass spectrometry techniques to categorize, through metaproteomics approaches, the content and composition of the proteome. Initial analyses showed higher protein content in the weakly SARS CoV-2 mRNA-positive or negative samples than in those with higher viral messenger content.
In general, the most represented microorganisms were bacteria, followed by fungi and archaea. The most represented bacterial phyla are: Firmicutes, Proteobacteria, Actinobacteria , and Bacteroidetes; among archea, the phylum Euryachaeota; and among eukaryotes, the phylum Streptophyta.
Subsequent analyses identified different gut microbiota profiles for patients with high SARS-CoV-2 RNA levels compared with those with low or negative viral load. In addition, in patients with high viral load, microbial diversity was found to be reduced compared with negative or low-charge patients. Patients who were positive for nasopharyngeal swab and also tested positive for the virus in stool had increased relative abundance of some genera of fungi such as Candida, Fusarium, Penicillium, Aspergillus, and Saccharomyces; for archaea, Methanosphaera and Halobacteriales were more abundant in positive patients while, among bacteria, for example, Streptomyces, Actinomadura, Amycolatopsis, Nocardia, Mycobacterium , and Arthrobacter.
In contrast, the following were found to be relatively less abundant: Ruminococcaceae, Lachnospiraceae , and Firmicutes.
Metaproteomics and potential biomarkers for SARS-CoV-2 infection.
Functional information was subsequently collected on the metaproteome of the groups examined (SARS-CoV-2 positive versus negative) as well as profiles of the microbiota and host-expressed proteins. Thus, 341 pathways were identified whose proteins were found to be differentially expressed in the two groups: for example, metabolic pathways, biosynthetic pathways of secondary metabolites, biochemical pathways of glycolysis and gluconeogenesis, and microbial metabolism.
An increase in metabolites related to citrulline flux was also noted in COVID-19 patients, suggesting an attempted adaptation of the Firmicutes phylum to gain an energetic advantage under stressogenic conditions.
In particular, an increase in peptides belonging to the mcp and yesN biosynthetic pathways as well as those derived from cobalamin production (cobS and cobV) was shown. The same applies to the drug transport pump, NADPH quinone reductase and the NTA protein family for Actinobacteria. Proteins involved in sulfate metabolism for Bacteroidetes as well as those for glutathione metabolism in Actinobacteria were also found to be increased in patients with SARS-CoV-2 detected in feces, reflecting the dynamics of adaptation of these microorganisms to the inflammatory and stressogenic conditions to which the gut is subjected.
The expression of immunoglobulin heavy chain, known to be an index of host response, was also noted to be increased in conjunction with the increase in the relative abundance of Firmicutes and Actinobacteria.
As for fungi, some functional molecules have shown alterations, such as those involved in retinol metabolism (AdhP) or histone modifications (SET2), the latter of which is also known to be a key molecule in the mucosal inflammatory response.
Alterations in the functionality of host molecules were also noted by comparing the two categories analyzed (SARS-CoV-2 positive versus negative). Specifically, the pathways whose protein components were found to be increased in COVID-19-positive patients include the ACE2 receptor signaling system such as peptidyl dipeptidase A, aminopeptidase, glutamyl aminopeptidase, and neprilsin, but also pathways that allow for the limitation of oxidative stress such as SOD1 and SOD2, membrane proteins located on enterocytes that mediate their mutual exchanges.
In addition, samples with the highest SARS-CoV-2 content contain statistically greater amounts of immunomodulators such as Gal-9, glutathione-S-transferases to counteract the action of reactive oxygen species, and enzymes involved in lysosomal degradation pathways.
Conclusions
In the context of SARS-CoV-2 infection, the gastrointestinal system was found to be of critical importance in the development of the disease and its severity.
In particular, it was found that the gut microbiome undergoes changes as to composition and function in relation to the presence or absence of the virus in the enterocytes themselves, which can be identified by searching for viral mRNA in the feces.
Specifically, the changes identified in patients with increased viral presence relate to proinflammatory pathways, activated as a result of enterocyte damage, intestinal permeability, activation of the immune response, and those to contain oxidative stress.