Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota

• DOI: 10.3389/fmicb.2021.712081
• Publication Date: 2021-10-13T17:05:40Z
• Authors: Sijia Li; Siyuan Yang; Yuzheng Zhou; Cyrollah Disoma; Zijun Dong; Ashuai Du; Yongxing Zhang; Yong Chen; Weiliang Huang; Junru Chen; Deqiang Song; Zongpeng Chen; Pinjia Liu; Shiqin Li; Rong Zheng; Sixu Liu; Aroona Razzaq; Xuan Chen; Siyi Tao; Chengping Yu; Tianxu Feng; Wenyan Liao; Yousong Peng; Taijiao Jiang; Jufang Huang; Wei Wu; Liqiang Hu; Linghang Wang; Shanni Li; Zanxian Xia
• Keywords: Prevotella; Eubacterium; Roseburia; Bacteroides fragilis

COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances gut microbiota have been previously linked to virus infection. Understanding how the gut-lung axis affects progression can provide novel framework for therapies and management. In this study, we examined (n = 47) compared it healthy controls 19). Using shotgun metagenomic sequencing, identified four microorganisms unique in patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, Prevotella bivia. The abundances stercoris, B. vulgatus, massiliensis, Bifidobacterium longum, Lachnospiraceae bacterium 5163FAA, bivia, Erysipelotrichaceae 6145, 2244A were enriched whereas Clostridium nexile, salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes, Adlercreutzia equolifaciens decreased (p < 0.05). relative abundance butyrate-producing Roseburia inulinivorans evidently depleted while Paraprevotella sp. probiotic thermophilus increased. We further 30 KEGG orthology (KO) modules overrepresented, 7 increasing 23 decreasing modules. Notably, 15 optimal microbial markers using random forest model strong diagnostic potential distinguishing COVID-19. Based on Spearman's correlation, eight species clinical indices. Moreover, increased Bacteroidetes Firmicutes also found across types Our findings suggest that alterations may influence disease severity. classifier, which was cross-regionally verified, provides proof concept set distinguish presence