Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota
| Autor: | Siyi Tao, Yong Chen, Xuan Chen, Jufang Huang, Cyrollah Disoma, Shiqin Li, Wenyan Liao, Shanni Li, Siyuan Yang, Deqiang Song, Taijiao Jiang, Zijun Dong, Yongxing Zhang, Sixu Liu, Junru Chen, Weiliang Huang, Zanxian Xia, Aroona Razzaq, Linghang Wang, Chengping Yu, Tianxu Feng, Zongpeng Chen, Wei Wu, Yuzheng Zhou, Liqiang Hu, Pinjia Liu, Ashuai Du, Yousong Peng, Sijia Li, Rong Zheng |
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| Rok vydání: | 2021 |
| Předmět: |
Microbiology (medical)
Streptococcus thermophilus Bifidobacterium longum gut microbiota biology SARS-CoV-2 ved/biology Firmicutes ved/biology.organism_classification_rank.species COVID-19 microbiome Gut flora biology.organism_classification Microbiology Prevotella bivia QR1-502 Streptococcus salivarius gastrointestinal symptoms Roseburia inulinivorans Microbiome Original Research |
| Zdroj: | Frontiers in Microbiology, Vol 12 (2021) Frontiers in Microbiology |
| ISSN: | 1664-302X |
| DOI: | 10.3389/fmicb.2021.712081 |
| Popis: | COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances of gut microbiota have been previously linked to respiratory virus infection. Understanding how the gut–lung axis affects the progression of COVID-19 can provide a novel framework for therapies and management. In this study, we examined the gut microbiota of patients with COVID-19 (n = 47) and compared it to healthy controls (n = 19). Using shotgun metagenomic sequencing, we have identified four microorganisms unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, and Prevotella bivia. The abundances of Bacteroides stercoris, B. vulgatus, B. massiliensis, Bifidobacterium longum, Streptococcus 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, Streptococcus 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 further identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules. Notably, 15 optimal microbial markers were identified using the random forest model to have strong diagnostic potential in distinguishing COVID-19. Based on Spearman’s correlation, eight species were associated with eight clinical indices. Moreover, the increased abundance of Bacteroidetes and decreased abundance of Firmicutes were also found across clinical types of COVID-19. Our findings suggest that the alterations of gut microbiota in patients with COVID-19 may influence disease severity. Our COVID-19 classifier, which was cross-regionally verified, provides a proof of concept that a set of microbial species markers can distinguish the presence of COVID-19. |
| Databáze: | OpenAIRE |
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