Zheng Ning, Yu Hai-Long, Zhang Bing-Jie, Wang Dan, Ji Ya-Liang, Dai Lu-Lu, Li Wen, Li Sheng-Hui, Hu Zhi-Liang, Zheng Yi-Shan
Department of Critical Care Medicine, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.
Puensum Genetech Institute, Wuhan, China.
Front Cell Infect Microbiol. 2025 Jul 22;15:1562965. doi: 10.3389/fcimb.2025.1562965. eCollection 2025.
Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.
A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.
Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with and as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as , , and as key bacterial hosts.
This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.
宏基因组下一代测序（mNGS）能够对临床样本中的病毒群落进行全面分析。然而，跨解剖部位和疾病状态的病毒组比较分析仍然有限。本研究旨在使用mNGS对患有各种临床疾病的患者的支气管肺泡灌洗液（BALF）和外周血样本中的病毒组进行特征分析。
总共338份临床样本——包括240份用于DNA测序的BALF样本和69份血液样本，以及18份用于RNA测序的BALF样本和11份血液样本——进行了鸟枪法宏基因组测序。去除宿主来源的 reads 后，将高质量的非人类序列与病毒参考数据库进行比对。通过α和β多样性指标评估病毒组组成。主坐标分析用于评估与疾病相关的变异，并通过Spearman相关性研究BALF中的病毒-细菌关联。
测序每个样本平均产生5100万个原始 reads，宿主过滤后产生约800万个非人类 reads。在BALF和血液样本之间观察到不同的病毒组谱。噬菌体在所有组中占主导地位， 和 是最丰富的科，尽管只有13.6%的病毒丰度可归为已知科。多样性分析显示BALF和外周血之间存在显著差异，DNA测序的BALF样本在肺部感染中显示出疾病特异性的病毒特征。相比之下，肿瘤的存在对BALF或血液中的病毒组组成没有显著影响。网络分析确定了BALF中复杂的病毒-细菌相关性， 、 和 等属为关键细菌宿主。
本研究揭示了呼吸系统和循环系统之间病毒组组成的显著差异，并强调了肺部疾病而非肿瘤对肺部病毒组的特定影响。观察到的病毒-细菌网络为肺部微生物生态学提供了新的见解，并强调了在病毒组研究中整合宿主和疾病背景的重要性。
