Gut Microbiome Related to COVID-19 Severity

Yun Kit Yeoh

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic researchers have attempted to classify and characterize other systems in the body, including the gastrointestinal tract.

A team, led by Yun Kit Yeoh, Department of Microbiology, The Chinese University of Hong Kong, investigated whether the guy microbiome is associated with disease severity in patients with COVID-19, as well as whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus.

In the cohort, the investigators obtained blood, stool, and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infections at 2 hospitals.

The team collected stool samples from 27 patients up to 30 days following clearance of SARS-CoV-2 and characterized gut microbiome compositions by shotgun sequencing total DNA extracted from stools.

Finally, they measured concentrations of inflammatory cytokines and blood markers from plasma.

The patients with COVID-19 were also classified into 4 severity groups based on symptoms. Patients were classified as mild if there was no radiographic indications of pneumonia, moderate if pneumonia with fever and respiratory tract symptoms were detected, severe if the respiratory rate was at least 30 breathes per minute, oxygen saturation was less than 93% when breathing ambient air or PaO₂/FO₂ was at least 300 mm Hg, and severe if respiratory failure requiring mechanical ventilation or organ failure requiring intensive care.

Findings in the Gut

Overall, the investigators found gut microbiome composition was significantly altered in patients with COVID-19 when compared to a control group who did not contract the virus. This was found to be true whether or not the COVID-19 patients received medication (P <0.01).

The research team also found several guy commensals with known immunome odulatory potential, including Faecalibacterium prausnitzii, Eubacterium rectale, and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution.

They also found the perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers including C reactive protein, lactate dehydrogenase, asparate aminotransferase, and gamma-glutamyl transferase.

“Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses,” the authors wrote. “Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.”

Implementing the Findings

The findings ultimately suggest the depletion of immunomodulatory gut microorganisms contribute to severe COVID-19 disease and dysbiotic gut microbiota that persists following disease resolution could be a factor in developing persistent symptoms or multisystem inflammation syndromes that occur in some patients after they clear the virus.

However, to overcome this the investigators suggest bolstering beneficial gut species depleted in COVID-19 could be a novel method to mitigate severe disease, underscoring the importance of managing patient’s gut microbiota during and after COVID-19.

The study, “Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,” was published in Gut.