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的原因。它会感染包括呼吸道和肠道在内的多个器官。在受感染的成年人中，区域微生物群的动态变化在很大程度上是未知的。在这里，我们通过16 S rRNA基因测序对来自35位COVID-19和19位健康成人对照以及10位非COVID-19其他疾病患者的咽喉和肛门拭子进行了纵向分析。结果显示，根据两个站点的微生物群落类型（I-IV），将患者分为3-4个类别。COVID-19患者的细菌多样性低于健康对照，并且从社区类型I到III / IV逐渐降低。尽管在COVID-19期间微生物组的动态变化很复杂，在6/8例轻度COVID-19成年患者中，观察到了上呼吸道和肠道微生物组从早期营养不良到晚期更多样化状态的同步恢复。这些发现揭示了在COVID-19期间上呼吸道和肠道菌群之间先前未知的相互作用。