The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.
The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.
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DOI：
10.1007/s00248-022-02148-9
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发表时间：
2023-08
影响因子：
3.6
通讯作者：
Ma, Zhanshan (Sam)
中科院分区：
文献类型：
--
作者：
Li, Wendy;Ma, Zhanshan (Sam)
关键词：
上呼吸道微生物群(URT)对宿主的呼吸健康起着把关作用。然而，关于SARS-CoV-2感染对城市轨道交通微生物群落微生物种类组成和共生关系的影响，特别是SARS-CoV-2与其他微生物之间的关系，目前还知之甚少。在这里，我们基于从新冠肺炎患者收集的1737份鼻咽样本的RNA元基因组测序数据集，描述了URT微生物群。构建了由细菌、古菌和RNA病毒组成的URT微生物群网络，并从核心/外围物种、集群组成、正负相互作用的平衡等方面进行了分析。发现新冠肺炎患者尿路微生物群中富含肠杆菌科细菌，这是一个肠道相关家族，含有多种致病菌。这些病原体形成了一个密集的合作协会，似乎集体抑制了有益的微生物。除细菌和古菌外，在新冠肺炎患者的尿路感染微生物群中还发现了72种真核RNA病毒。在超过10%的样本中，只有五种病毒存在，包括SARS-CoV-2和一种蝙蝠冠状病毒(即蝙蝠冠状病毒BM48-31)，这是常规方法在人类身上没有检测到的。SARS-CoV-2被一个由89个物种组成的合作联盟所抑制，但似乎与BatCoV BM48-31合作，因为它们在统计上具有显著的正相关性。SARS-CoV-2(BatCoV BM48-31)的合作蝙蝠冠状病毒伙伴(BatCoV BM48-31)的存在令人费解，鉴于其明显的影响，值得进一步研究。微生物从肠道到城市轨道交通的可能移位机制也值得进一步研究。网上版载有补充材料，可在10.1007/s00248-022-02148-9查阅。
The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies. The online version contains supplementary material available at 10.1007/s00248-022-02148-9.
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影响因子：
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影响因子：
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