Gut microbiota-derived metabolites offer protection against SARS-CoV-2


A new study published in the journal Intestinal microbes highlighted the importance of intestinal bacteria fermenting fibers that release short-chain fatty acids (SCFAs), which limit viral entry and hypercoagulation and induce an immune-mediated antiviral response.

Study: Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection. Image Credit: ART-ur/Shutterstock


The gut microbiome includes billions of bacterial cells that inhabit the digestive tract. These microbial communities significantly influence the physiology of health and disease. The gut microbiota plays a crucial role in performing basic body functions; through these, they impact most pathophysiological processes.

Researchers uncovered the multi-faceted functions of the gut microbiome, for example its role in coagulation processes. Gut microbiomes are of particular importance in viral respiratory infections, such as influenza and COVID-19, as well as in chronic lung diseases such as asthma and COPD. A supportive and healthy gut microbiota can improve the outcome of viral infections.

Recent survey results show that patients with COVID-19 have a variant gut microbiota. Angiotensin-converting enzyme 2 (ACE2) promotes entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and precipitates coronavirus disease 2019 (COVID-19) by facilitating the production of angiotensin converting enzyme.

Many cells in the human body express ACE2, including epithelial cells lining the gastrointestinal (GI) tract and those of the respiratory tract. Up to fifty percent of patients with COVID-19 experience gastrointestinal symptoms as early signs of SARS-CoV-2 infection.

In convalescent or asymptomatic COVID-19 patients, persistent intestinal reservoirs of SARS-CoV-2 may contribute to the evolution of B-cell memory responses. Another feature that exacerbates the mortality and morbidity associated with COVID-19 is the dysfunction of the coagulation response. However, the relevance of gut microbiota in susceptibility to SARS-CoV-2 and COVID-19 remains unknown.

The study

The aim of this study was to investigate the mechanisms by which the gut microbiome confers immunity to mammalian hosts against intranasal SARS-CoV-2 infection by generating short-chain fatty acids (SCFAs).

QPCR analysis was performed on a group of C57BL/6 mice reared under germ-free conditions – wild-type or K18-hACE2 mice, to compare the expression of ACE2 which was specific pathogen-free (SPF ) and germ-free (GF). ACE2 protein expression in GF mouse kidney cells was assessed by flow cytometry, Western blot, and immunofluorescence imaging. SPF mice were given gentamicin or vancomycin in drinking water for two weeks to identify gut bacteria that modulate ACE2 expression.

Nine-week-old male Syrian hamsters were fed SCFA water for two weeks prior to intranasal infection with a replication-incompetent vesicular stomatitis virus (VSV) pseudovirus, with the spike protein SARS-CoV-2 and nanoluciferase.

Additionally, mice were given pectin and other dietary fibers to determine the effect of fiber fermentation commensals. Mice infected with the SARS-CoV-2 Gamma variant were exposed to SCFA water for two weeks prior to infection, and lung tissue was collected 2.5 days post-infection when lung viral titers increased. reached a peak.

SCFA water was administered to hACE2 mice (mice expressing both mouse and human ACE2) for two weeks prior to intranasal infection with rVSV/Spike-nLuc (a chimeric VSV virus competent for replication with SARS-CoV-2 spike and nanoluciferase) – able to interact with human ACE2, but not mouse ACE2. Luciferase activity was assessed in the nasal epithelium, lungs and small intestine of SCFA-treated mice, compared to control mice.

The memory response of hACE2 mice was assessed by administering a primary dose of 6×104 PFU of rVSV/Spike-GFP (SCFA-treated GF mice infected with replication-competent chimeric VSV virus with GFP and SARS-CoV-2 beta-variant spike protein) intranasally, followed by a secondary dose of 3×105 PFU after four weeks. Blood immune cells were analyzed by flow cytometry two weeks after the first infection.

Ribonucleic acid (RNA) sequencing was performed on the lungs of male GF mice fed control water or SCFA for two weeks to examine the effect of additional pathways caused by COVID-19 infection.

The results

In the gut and lungs, Clostridia and SCFA inhibit ACE2 expression.

The main producers of SCFAs such as acetate, butyrate and propionate are Clostridia. By producing SCFAs, commensal species of Clostridia inhibit the expression of ACE2. SCFA treatments inhibited ACE2 expression, decreased viral loads, and enhanced adaptive immunity against VSV/SARS-CoV-2 chimeras.

SCFAs protect mice against intranasal infections.

Reduced luciferase activity was observed in lung epithelium and nasal epithelium of SCFA-treated hamsters compared to control hamsters, indicating a reduced incidence of infection.

In response to intranasal infection with a spike protein-producing VSV pseudovirus, SCFAs enhance T-cell antiviral responses, antibody neutralization, and spike-specific B and T cells. Of note, these phenotypes were observed both in hACE2 mice, whose expression of human ACE2 did not wane upon SCFA treatment, and in wild-type mice inoculated with inactivated virus. by heat. These results suggest that the observed enhancement of immune responses is independent of the effect of SCFAs on ACE2-mediated viral entry.

SCFAs enhance adaptive immunity against VSV/SARS-CoV-2 chimeric viruses via GPR41/GPR43.

In mice treated with SCFA, there was a trend for reduced weight loss, as well as reduced viral titers and viral RNA in the lungs. In the presence of SARS-CoV-2 or VSV-SARS chimeric viruses, AGCCs decrease the viral load.

Based on flow cytometry analysis, CD4+ and CD8+ T cells were found to express higher levels of interferon (IFN); regulatory T cell (Treg) formation was enhanced and granzyme B production was elevated in CD8+ T cells. Dendritic cells were more abundant in the lungs of mice treated with SCFA, but macrophages or polymorphonuclear cells (PMNs) were not. SCFAs have also been shown to stimulate antiviral immune responses in the lungs during acute infection.

SCFAs regulate the coagulation response via the Sh2b3-Mpl axis to optimize platelet turnover.

An important negative regulator of megakaryopoiesis and thrombopoiesis, the Sh2b3 gene (also known as the lymphocyte adapter protein – LNK), plays a fundamental role in the regulation of the coagulation response through its involvement in various transduction pathways of the signal. SCFAs have been shown to promote better SARS-CoV-2 infection outcomes by impeding the coagulation response via the Sh2b3-Mpl axis, according to a possible third axis.

Of note, in the present study, SCFAs influenced ACE2 expression and antibody neutralization in male mice, but not the coagulation response. SCFA-mediated overexpression of Sh2b3 has been found to inhibit Mpl (myeloproliferative leukemia protein) signaling in megakaryocytes, resulting in decreased megakaryocyte proliferation and platelet production as well as restriction of turnover platelet.


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