Alterations in Gut Microbiota Composition in Patients with COVID-19: A Pilot Study of Whole Hypervariable 16S rRNA Gene Sequencing

Abstract

It is crucial to consider the importance of the microbiome and the gut–lung axis in the context of SARS-CoV-2 infection. This pilot study examined the fecal microbial composition of patients with COVID-19 following a 3-month recovery. Using for the first time metagenomic analysis based on all hypervariable regions (V1-V9) of the 16S rRNA gene, we have identified 561 microbial species; however, 17 were specific only for the COVID-19 group (n = 8). The patients’ cohorts revealed significantly greater alpha diversity of the gut microbiota compared to healthy controls (n = 14). This finding has been demonstrated by operational taxonomic units (OTUs) richness (p < 0.001) and Chao1 index (p < 0.01). The abundance of the phylum Verrucomicrobia was 30 times higher in COVID-19 patients compared to healthy subjects. Accordingly, this disproportion was also noted at other taxonomic levels: in the class Verrucomicrobiae, the family Verrucomicrobiaceae, and the genus Akkermansia. Elevated pathobionts such as Escherichia coli, Bilophila wadsworthia, and Parabacteroides distasonis were found in COVID-19 patients. Considering the gut microbiota’s ability to disturb the immune response, our findings suggest the importance of the enteric microbiota in the course of SARS-CoV-2 infection. This pilot study shows that the composition of the microbial community may not be fully restored in individuals with SARS-CoV-2 following a 3-month recovery.

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms

“…Thus, although no significant differences in α and β-diversity were observed in the gut microbiota of post-COVID and control subjects, functional changes were observed in both patients and mice. Of note, enrichment of the Lachnospiraceae family in post-COVID mice is corroborated by previous findings where subjects with COVID-19 had a higher prevalence of this group of bacteria (Al Bataineh et al, 2021;Mańkowska-Wierzbicka et al, 2023).…”

The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

“…However, in mild ill patients, different genera from Clostridia class ( Clostridia , Coprococcus , Dorea , Lachnospiraceae , Roseburia and Ruminococcus ), Barnesiella and Muribaculaceae were identified as highly abundant. While the class Clostridia was associated with a reduced production of proinflammatory cytokines in COVID-19 patients and in those who recovered from the infection [66, 67], Barnesiella prevents colonisation by antibiotic-resistant bacteria such as Enterococcus , which is involved in bloodstream infection in critically ill COVID-19 patients [68, 69]. Furthermore, studies performed in mice have shown that Muribaculaceae abundance is reduced in mice coinfected with different respiratory viruses, suggesting that it may play a protective role under viral infection [70].…”

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms

“…Notably, enrichment of the Lachnospiraceae family in post-COVID mice is corroborated by previous findings, where subjects with COVID-19 had a higher prevalence of this group of bacteria. 62 , 63 …”