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 (<i>n</i> = 8). The patients' cohorts revealed significantly greater alpha diversity of the gut microbiota compared to healthy controls (<i>n</i> = 14). This finding has been demonstrated by operational taxonomic units (OTUs) richness (<i>p</i> < 0.001) and Chao1 index (<i>p</i> < 0.01). The abundance of the phylum <i>Verrucomicrobia</i> 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 <i>Verrucomicrobiae</i>, the family <i>Verrucomicrobiaceae,</i> and the genus <i>Akkermansia</i>. Elevated pathobionts such as <i>Escherichia coli</i>, <i>Bilophila wadsworthia,</i> and <i>Parabacteroides distasonis</i> 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.