Genetic diversity of Microviridae phages in the human respiratory tract.

IF 4.8 2区医学 Q2 IMMUNOLOGY

Frontiers in Cellular and Infection Microbiology Pub Date : 2025-09-08 eCollection Date: 2025-01-01 DOI:10.3389/fcimb.2025.1629120

Peiting Yang, Huanyan Zhang, Liang Yin, Jiaheng Chen, Yue Chen, Hongfeng Yang, Qi Liu, Wen Zhang

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Abstract

Recent studies have revealed that Microviridae, a family of ssDNA viruses, are widely distributed in natural environments and play significant roles in various ecosystems. While Microviridae members dominate the human gut microbiome, their genetic diversity in the human respiratory ecosystem remains unclear. The distribution, genetic characteristics, and ecological roles of Microviridae are still poorly understood. This study identified 327 Microviridae-associated contigs from nasopharyngeal swab samples of healthy individuals through metagenomic sequencing and comparative genomics analysis, including 15 near-complete Microviridae-related genomes. These genomes exhibited high sequence divergence from each other, revealing their high genetic diversity. Phylogenetic analysis based on VP1 (major capsid protein; F protein) demonstrated that the 15 genomes could be classified into seven distinct Microviridae groups. CRISPR spacer matching predicted the host of the 15 genomes. The total read counts of Microviridae across all 12 libraries were quantified and compared using the Kruskal-Wallis test. This work significantly expands the understanding of the diversity, genomic architecture, and evolutionary dynamics of Microviridae within the human respiratory tract.

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人类呼吸道微病毒科噬菌体的遗传多样性。

近年来的研究表明，微病毒科是ssDNA病毒的一个科，广泛分布于自然环境中，在各种生态系统中发挥着重要作用。虽然微病毒科成员在人类肠道微生物组中占主导地位，但它们在人类呼吸生态系统中的遗传多样性仍不清楚。微病毒科的分布、遗传特征和生态作用仍然知之甚少。本研究通过宏基因组测序和比较基因组分析，从健康个体鼻咽拭子样本中鉴定出327个微病毒相关基因组，其中包括15个接近完整的微病毒相关基因组。这些基因组之间序列差异较大，具有较高的遗传多样性。基于VP1（主要衣壳蛋白；F蛋白）的系统发育分析表明，15个基因组可分为7个不同的微病毒科。CRISPR间隔序列匹配预测了15个基因组的宿主。使用Kruskal-Wallis检验对所有12个文库中微病毒科的总读取计数进行量化和比较。这项工作极大地扩展了对人类呼吸道微病毒科的多样性、基因组结构和进化动力学的理解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Frontiers in Cellular and Infection Microbiology IMMUNOLOGY-MICROBIOLOGY

CiteScore

7.90

自引率

7.00%

发文量

1817

审稿时长

14 weeks

期刊介绍： Frontiers in Cellular and Infection Microbiology is a leading specialty journal, publishing rigorously peer-reviewed research across all pathogenic microorganisms and their interaction with their hosts. Chief Editor Yousef Abu Kwaik, University of Louisville is supported by an outstanding Editorial Board of international experts. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics, clinicians and the public worldwide. Frontiers in Cellular and Infection Microbiology includes research on bacteria, fungi, parasites, viruses, endosymbionts, prions and all microbial pathogens as well as the microbiota and its effect on health and disease in various hosts. The research approaches include molecular microbiology, cellular microbiology, gene regulation, proteomics, signal transduction, pathogenic evolution, genomics, structural biology, and virulence factors as well as model hosts. Areas of research to counteract infectious agents by the host include the host innate and adaptive immune responses as well as metabolic restrictions to various pathogenic microorganisms, vaccine design and development against various pathogenic microorganisms, and the mechanisms of antibiotic resistance and its countermeasures.