Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
Microbiome. 2023 Mar 9;11(1):46. doi: 10.1186/s40168-023-01472-7.
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.
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.
Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.
SARS-CoV-2 感染对胃肠道及其常驻微生物群有明显影响。据报道，严重感染病例与健康个体之间存在明显差异，包括共生分类群的丧失。我们旨在了解微生物组的改变，包括功能转变，是否仅存在于严重病例中，还是 COVID-19 的常见影响。我们使用高分辨率系统多组学分析，对无症状至中度 COVID-19 个体与对照组的肠道微生物组进行了分析。
我们发现 COVID-19 中，毒力因子和抗生素耐药基因的总体丰度和表达都显著增加。重要的是，这些基因是由 Acidaminococcaceae 和 Erysipelatoclostridiaceae 等家族的共生分类群编码和表达的，我们发现这些分类群在 COVID-19 阳性个体中富集。与健康对照组相比，我们还发现 COVID-19 阳性个体中 beta 疱疹病毒和轮状病毒 C 基因的表达增加。
我们的分析确定了 COVID-19 患者肠道微生物组改变和增加的感染能力。
