Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
Commun Biol. 2021 Feb 18;4(1):240. doi: 10.1038/s42003-021-01796-w.
SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed a partitioning of the patients into 3-4 categories based on microbial community types (I-IV) in both sites. The bacterial diversity was lower in COVID-19 patients than healthy controls and decreased gradually from community type I to III/IV. Although the dynamic change of microbiome was complex during COVID-19, a synchronous restoration of both the upper respiratory and gut microbiomes from early dysbiosis towards late more diverse status was observed in 6/8 mild COVID-19 adult patients. These findings reveal previously unknown interactions between upper respiratory and gut microbiomes during COVID-19.
SARS-CoV-2 是 COVID-19 的病原体。它感染包括呼吸道和肠道在内的多个器官。感染成年人中局部微生物组的动态变化在很大程度上尚不清楚。在这里，我们通过 16S rRNA 基因测序，对 35 名 COVID-19 患者和 19 名健康成年人对照组以及 10 名患有其他疾病的非 COVID-19 患者的咽喉和肛门拭子进行了纵向分析。结果表明，基于两个部位的微生物群落类型（I-IV），可以将患者分为 3-4 类。COVID-19 患者的细菌多样性低于健康对照组，并且从群落类型 I 逐渐降低到 III/IV。尽管 COVID-19 期间微生物组的动态变化很复杂，但在 8 名轻度 COVID-19 成年患者中的 6 名中观察到上呼吸道和肠道微生物组从早期的失调向晚期更多样化的同步恢复。这些发现揭示了 COVID-19 期间上呼吸道和肠道微生物组之间以前未知的相互作用。
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