Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients

• Published in: Frontiers in cellular and infection microbiology 2024-03, Vol.14, p.1352202-1352202
• Main Authors: Rizzello, Fernando, Viciani, Elisa, Gionchetti, Paolo, Filippone, Eleonora, Imbesi, Veronica, Melotti, Laura, Dussias, Nikolas Konstantine, Salice, Marco, Santacroce, Barbara, Padella, Antonella, Velichevskaya, Alena, Marcante, Andrea, Castagnetti, Andrea
• Format: Article
• Language: English
• Subjects: Adult; Aged; Bacteria - genetics; Candida; Cellular and Infection Microbiology; COVID-19; Female; human microbiota; Humans; Male; microbiome; Microbiota; mycobiota; pathogenesis; Patient Acuity; SARS-CoV-2
• ISSN: 2235-2988; 2235-2988
• DOI: 10.3389/fcimb.2024.1352202

COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as , , and . Of note, the genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. COVID-19 was associated with opportunistic bacterial pathogens, and was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.