The gut factor: associations between the microbiome and Ace2 expression

From the Dey Lab, Clinical Research Division

Gastrointenstinal symptoms are associated with worse COVID-19 outcomes, and live SARS-CoV-2 virus can be recovered from fecal samples, indicating that the gastrointestinal tract may serve as a viral reservoir in this disease. Indeed, Ace2, encoding the surface protein to which the SARS-CoV-2 spike protein binds during the infection of host cells, is expressed within the gut. Thus, factors impacting Ace2 expression in this tissue, as in the lung, could be important disease modifiers for COVID-19. Interestingly, previous studies have linked ACE2-deficiency to amino acid malnutrition, alterations in the microbiome, and intestinal inflammation. Members of the Dey Laboratory, including research technicians Sean Koester and Naisi Li, in the Fred Hutch Clinical Research Division, investigated whether Ace2 expression levels in the gastrointestinal and respiratory tracts might be impacted by the microbiota that inhabit them. Their work, recently published in PLOS ONE, reveals an association between Ace2 expression and microbiome composition.

Schematic depicting the diverse gut microbiome.
Study finds evidence for a link between microbiome composition and expression of the SARS-CoV-2 spike-binding receptor, Ace2, in the digestive and respiratory tracts. "File:202004 Gut microbiota.svg" by DataBase Center for Life Science (DBCLS) is licensed under CC BY 4.0:

The human body is co-inhabited by a diverse collection of micro-organisms, both beneficial and potentially harmful, called the microbiome. Influenced by factors ranging from genetics to diet to birthing method, the makeup, richness, and diversity of individuals’ microbiomes varies widely throughout the human population. There is an increasing appreciation for the role of microbiota in shaping myriad aspects of human health and physiology, including immunity, obesity, cancer, and cardiovascular and respiratory health, to name a few. As a result, prophylactic and therapeutic treatments aimed at manipulating the microbiome have emerged as promising strategies for disease intervention.

Comparing mouse systems with altered microbiota content, the Dey group sought to examine potential associations between microbiota and Ace2 expression in the gastrointestinal and respiratory tracts. They utilized quantitative reverse transcription PCR (RT-qPCR), a sensitive technique for quantifying gene expression, to measure Ace2 expression in the trachea, lungs, small intestine and colons of mice kept either under standard housing conditions, referred to as specific pathogen-free (SPF) conditions, or under germ-free (GF) conditions, lacking all micro-organisms. Strikingly, the GF mice had significantly higher levels of Ace2 throughout the small intestine and colon. Similar trends were observed in the respiratory tract tissues but did not reach statistical significance in this study. To directly test the impact of microbiota on Ace2 expression, the investigators treated SPF mice with antibiotics. Indeed, antibiotic-treated animals exhibited higher intestinal Ace2 expression compared to control animals, albeit to a lesser magnitude than the GF mice. Having established a role for microbiota in Ace2 expression, the group turned to gnotobiotic mice, animals that are colonized defined communities of microbial species, to examine the effects of microbiome composition. Significantly, they observed that colonization of the gut with distinct 6-member communities yielded altered regional patterns of Ace2 receptor expression, compared to SPF and GF mice.

Ace2 functions as an amino acid transporter in the intestine. Given this role, the group hypothesized that differences in microbial proteases and peptidases, enzymes that break proteins down into their amino acid constituents, might explain the observed changes in Ace2 expression. Indeed, they found that mice colonized with bacterial communities whose genomes encoded more proteases and peptidases expressed higher levels of Ace2, indicating a potential mechanism through which different microbial communities could differentially regulate receptor expression. However, this failed to explain the higher levels of Ace2 expression that they observed in GF mice (in the absence of microbial proteases and peptidases). The group hypothesized that other factors might be impacting Ace2 expression in this setting. For example, work by others has shown that patients with inflammatory bowel disease exhibit higher levels of Ace2. Indeed, when they examined GF mice that were engineered to carry a mutation in the cytokine IL-10 which leads to intestinal inflammation in both mice and humans, they observed higher levels of Ace2 expression.

“Our paper links expression of ACE2 — the protein to which SARS-CoV-2 binds — to the gut microbiome, ostensibly via a diet-dependent mechanism involving a pathway that has been previously described in the context of undernutrition,” explained the authors. “Our findings fit within the context of a paradigm that gut microbes may impact physiology not only in the gut but also in other parts of the body.” Importantly, this study raises the possibility that the microbiome could play a role in COVID-19 disease progression. “It remains to be determined how diet and the microbiome can be leveraged to minimize risk of COVID-19 and related infections. Of course, we still strongly encourage everyone to get vaccinated!” the group cautioned. “Despite our findings, we do not believe that kombucha and probiotics are going to cut it,” they joked.

This work was funded by the National Institutes of Health, institutional funds from the Fred Hutchinson Cancer Research Center (Pathogen-Associated Malignancies Integrated Research Center, Microbiome Research Initiative, and donor-sponsored COVID-19 Evergreen pilot study funds), and the Washington Research Foundation.

UW/Fred Hutch Cancer Consortium member Neelendu Dey contributed to this work.

Koester ST, Li N, Lachance DM, Morella NM, Dey N. Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome. PLoS One. 2021 Mar 16;16(3):e0248730. doi: 10.1371/journal.pone.0248730. PMID: 33725024; PMCID: PMC7963026.