Kardaras Filippos S, Siatravani Eirini, Tsilipounidaki Katerina, Petinaki Efthymia, Hatzigeorgiou Artemis G, Miriagou Vivi
DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.
Hellenic Pasteur Institute, Athens, Greece.
Front Microbiol. 2025 Aug 29;16:1631198. doi: 10.3389/fmicb.2025.1631198. eCollection 2025.
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted extensive research into factors influencing the onset and severity of the disease. Among these factors, the role of the nasopharyngeal microbiome, a vital ecosystem critical for respiratory health and immune modulation, remains incompletely understood. This study aimed to elucidate the relationship between the composition of nasopharyngeal microbiota and the clinical presentation of COVID-19 during the initial phase of infection.
A total of 81 nasopharyngeal swab samples were collected from individuals in Central Greece between January and February 2021. Following quality control, 77 samples were selected for microbiome analysis. This selection included SARS-CoV-2-negative controls (NE, = 26) and SARS-CoV-2-positive patients classified as asymptomatic (AS, = 19), mild (MI, = 16), or severe (SE, = 16) based on clinical criteria. All COVID-19-positive samples were collected within 2 days of symptom onset, and participants with recent hospitalization or antibiotic use were excluded. Microbiome profiling was performed using 16S rRNA gene-targeted metagenomic sequencing, followed by comprehensive bioinformatics and statistical analyses.
Significant differences were observed in both alpha and beta diversity measures, with alpha diversity decreasing as the severity of COVID-19 increased. Three of the four individual study groups, namely NE, MI, and SE, exhibited distinct microbial profiles, while the asymptomatic group showed greater heterogeneity. Significant variations in the abundance of specific phyla, families, and genera were identified between the different study groups. When comparing the NE and SE groups, we observed a significant increase in the abundance of the Proteobacteria phylum in the SE group, while the abundance of Fusobacteria was significantly lower in the SE group. In symptomatic COVID-19 patients, we observed a significant reduction in the abundance of key family constituents of the nasopharyngeal microbiota, such as Fusobacteriaceae, Prevotellaceae, and Streptococcaceae, suggesting a disruption in microbial homeostasis during the infection. Conversely, we found an increased prevalence of families associated with pathogenic or opportunistic pathogenic bacteria, including Enterobacteriaceae and Bacillaceae, in the SE group, suggesting a potential role of these taxa in the disease progression of COVID-19.
These findings shed light on specific genera that undergo significant changes during COVID-19 infection and contribute to our understanding of the dynamic nature of the nasopharyngeal microbiome in relation to disease progression and severity.
由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起的2019冠状病毒病（COVID-19）大流行促使人们对影响该疾病发病和严重程度的因素进行了广泛研究。在这些因素中，鼻咽微生物群的作用，这个对呼吸健康和免疫调节至关重要的重要生态系统，仍未被完全理解。本研究旨在阐明感染初期鼻咽微生物群组成与COVID-19临床表现之间的关系。
2021年1月至2月期间，从希腊中部的个体中总共采集了81份鼻咽拭子样本。经过质量控制后，选择了77份样本进行微生物组分析。该选择包括SARS-CoV-2阴性对照（NE，n = 26）和根据临床标准分类为无症状（AS，n = 19）、轻症（MI，n = 16）或重症（SE，n = 16）的SARS-CoV-2阳性患者。所有COVID-19阳性样本均在症状出现后2天内采集，排除近期住院或使用过抗生素的参与者。使用靶向16S rRNA基因的宏基因组测序进行微生物组分析，随后进行全面的生物信息学和统计分析。
在α和β多样性测量中均观察到显著差异，随着COVID-19严重程度的增加，α多样性降低。四个单独研究组中的三个，即NE、MI和SE，表现出不同的微生物谱，而无症状组显示出更大的异质性。在不同研究组之间鉴定出特定门、科和属的丰度存在显著差异。比较NE组和SE组时，我们观察到SE组中变形菌门的丰度显著增加，而SE组中梭杆菌属的丰度显著降低。在有症状的COVID-19患者中，我们观察到鼻咽微生物群的关键科成分，如梭杆菌科、普雷沃氏菌科和链球菌科的丰度显著降低，这表明感染期间微生物稳态受到破坏。相反，我们发现SE组中与致病或机会致病菌相关的科的患病率增加，包括肠杆菌科和芽孢杆菌科，这表明这些分类群在COVID-19疾病进展中可能起作用。
这些发现揭示了在COVID-19感染期间发生显著变化的特定属，并有助于我们理解鼻咽微生物群与疾病进展和严重程度相关的动态性质。
