Microbiome profiling using shotgun metagenomic sequencing identified unique microorganisms in COVID-19 patients with altered gut microbiota

Background: Infection of SARS-CoV-2 is mainly associated to respiratory distress syndrome, but recent reports noted gastrointestinal (GI) symptoms and liver damage. Imbalances of gut microbiota composition has been linked to respiratory virus infection. In the present study, we examined the gut microbiota of 47 patients with COVID-19 and 19 healthy individuals.Results: We performed shotgun metagenomic sequencing analyses of fecal samples from two patient cohorts with COVID-19 of various severity (37 from Beijing and 10 from Changsha). Distinct levels of bacterial richness and diversity were found between patients and healthy controls. A total of 4 microbes was unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans and Prevotella bivia. A MaAsLin analysis revealed that the abundances of Bacteroides stercoris, Bacteroides vulgatus, Bacteroides massiliensis, Bifidobacterium longum, Streptococus thermophilus, Lachnospiraceae bacterium 5163FAA, Prevotella bivia, Erysipelotrichaceae bacterium 6145 and Erysipelotrichaceae bacterium 2244A were enriched in COVID-19 patients, whereas the abundances of Clostridium nexile, Streptococus salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes and Adlercreutzia equolifaciens were decreased (p<0.05). The relative abundance of butyrate-producing Roseburia inulinivorans is evidently depleted in COVID-19 patients, while the relative abundances of Paraprevotella sp. and the probiotic Streptococcus thermophilus were increased. We identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules in disease patients. Notably, 15 optimal microbial markers were identified using the random forest model. The correlation matrix based on Spearman's correlation distance revealed that 9 species were associated with 8 clinical indices. Moreover, the gut microbiota compositions across clinical types revealed increased abundance of Bacteroidetes and decreased abundance of Firmicutes.