摘要
出身背景
严重急性呼吸系统综合征冠状病毒2型感染对胃肠道及其常驻微生物组有显著影响。据报道，严重感染病例和健康个体之间存在明显差异，包括共生类群的损失。我们的目的是了解包括功能改变在内的微生物群改变是否是新冠肺炎严重病例或常见影响所特有的。我们使用高分辨率系统多组学分析来分析无症状至中度新冠肺炎患者与对照组相比的肠道微生物群。
后果
我们发现新冠肺炎病毒毒力因子和抗菌药物耐药基因的总体丰度和表达显著增加。重要的是，这些基因由来自酸性氨基球菌科和丹毒梭状芽孢杆菌科等家族的共生分类群编码和表达，我们发现这些基因在COVID-19阳性个体中富集。我们还发现，与健康对照组相比，新冠肺炎阳性个体中β-疱疹病毒和轮状病毒C基因的表达增加。
结论
我们的分析发现，新冠肺炎患者肠道微生物组的感染能力发生了改变，并有所增加。
Abstract
Background
Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

Results
We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

Conclusions
Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients.

https://link.springer.com/article/10.1186/s40168-023-01472-7