Alterations of the Human Oral and Gut Microbiome and Lipid Metabonomics in COVID-19. organismal metagenomes

COVID-19 has emerged as a global pandemic, resulting in over twenty million of infections and over half a million of death. However, the oral and gut microbiota, and lipid molecules characteristic in COVID-19 have not been studied clearly. Here, we collected and sequenced 392 tongue coating samples, 172 fecal samples, and 155 serum samples from different regions, times, and people. Compared with healthy controls (HC, stool, n=48; tongue coating, n=100), Haemophilus and Enterobacteriaceae_unclassifiedwere decreased, while Granulicatella increased in confirmed patients (CP, stool, n=24; tongue coat, n=48) at oral cavity and gut. The classifiers based on 8 optimal oral microbial markers (7 markers in gut microbiome) achieved good diagnostic efficiency and the area under the curve (AUC) reached 98.06% (99.74%) in discovery cohort and 95.75% (99.31%) in validation cohort. Importantly, the AUC reached 89.22% in extra diagnosis cohort from Hangzhou. Moreover, the classifiers successfully diagnosed suspected patients (SP) with IgG-antibody positivity as CP, and the AUC reached 92.11% (98.01%) and we have demonstrated the feasibility of this method from the perspective of microbial characteristic. Besides, with the recovery of COVID-19, among CP, CP recovery (CPR), and HC group,peptostreptococcaceae_incertae_sedis was gradually increased at oral cavity, but decreased at gut. Compared with CP, 47 lipid molecules including SM(d40:4), SM(d38:5), and MG(33:5) were depleted in the CPR group, 122 lipid molecules including PC(36:4p), PE(16:0p/20:5), and DG(20:1/18:2) were enriched in the CPR group. Fifty-two operational taxonomy units (OTU) in oral cavity (37 OTUs in gut) were correlated with 10 lipid molecules, and 68 OTUs in oral cavity (97 OTUs in gut) were correlated with 8 clinical indicators of COVID-19. In conclusion, we characterize the oral and gut microbiota and lipid in COVID-19, demonstrate the potential of microbial markers as non-invasive diagnostic tools for COVID-19 in different regions of China, make up the deficiency of nucleic acid testing, and search the specific therapeutic targets.

新型冠状病毒肺炎（COVID-19）已演变为全球大流行病，累计造成超2000万例感染与超50万例死亡。然而，新冠患者的口腔、肠道菌群特征以及脂质分子特征尚未得到清晰阐释。本研究收集并测序了来自不同地区、不同时段、不同人群的392份舌苔样本、172份粪便样本及155份血清样本。与健康对照组（HC，粪便样本n=48；舌苔样本n=100）相比，确诊患者（CP，粪便样本n=24；舌苔样本n=48）的口腔与肠道菌群中，嗜血杆菌属（Haemophilus）和未分类肠杆菌科（Enterobacteriaceae_unclassified）丰度显著降低，而颗粒链菌属（Granulicatella）丰度显著升高。基于8个最优口腔微生物标志物（肠道菌群含7个标志物）构建的分类器展现出优异的诊断效能：在发现队列中，曲线下面积（area under the curve, AUC）分别达98.06%（肠道菌群对应AUC为99.74%）；在验证队列中，AUC分别达95.75%（肠道菌群对应AUC为99.31%）。值得注意的是，在杭州来源的额外诊断队列中，该分类器的AUC仍达89.22%。此外，该分类器可成功将IgG抗体阳性的疑似患者（SP）诊断为确诊患者，AUC达92.11%（肠道菌群对应AUC为98.01%），本研究从菌群特征层面验证了该诊断方法的可行性。随着新冠患者病情康复，在确诊患者（CP）、康复期确诊患者（CPR）与健康对照组（HC）三组中，暂未分类消化链球菌科（peptostreptococcaceae_incertae_sedis）在口腔中的丰度逐渐升高，而在肠道中的丰度逐渐降低。与确诊患者（CP）相比，康复期确诊患者（CPR）体内共有47种脂质分子（包括SM(d40:4)、SM(d38:5)与MG(33:5)）出现丰度耗竭，另有122种脂质分子（包括PC(36:4p)、PE(16:0p/20:5)与DG(20:1/18:2)）呈现丰度富集。口腔菌群中共52个操作分类单元（OTU，肠道菌群含37个OTU）与10种脂质分子存在显著关联；口腔菌群中共68个OTU（肠道菌群含97个OTU）与新冠的8项临床指标存在显著关联。综上，本研究刻画了新冠患者的口腔与肠道菌群及脂质组特征，验证了菌群标志物作为无创诊断工具的潜力，可应用于中国不同地区的新冠诊断，弥补核酸检测的不足，并为探索特异性治疗靶点提供了科学依据。