中国鄱阳湖越冬候鸟的多王国微生物组。

The Multi-Kingdom Microbiome of Wintering Migratory Birds in Poyang Lake, China.

机构信息

National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.

School of Public Health, Xiamen University, Xiamen 361005, China.

出版信息

Viruses. 2024 Mar 3;16(3):396. doi: 10.3390/v16030396.

DOI:10.3390/v16030396

PMID:38543762

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10974949/

Abstract

Wild birds are a natural reservoir for zoonotic viruses. To clarify the role of migratory birds in viruses spread in Poyang Lake, we investigated the microbiome of 250 wild bird samples from 19 species in seven orders. The bacterial and viral content abundance and diversity were preliminarily evaluated by Kraken2 and Bracken. After de novo assembly by Megahit and Vamb, viral contigs were identified by CheckV. The reads remapped to viral contigs were quantified using Bowtie2. The bacterial microbiome composition of the samples covers 1526 genera belonging to 175 bacterial orders, while the composition of viruses covers 214 species belonging to 22 viral families. Several taxonomic biomarkers associated with avian carnivory, oral sampling, and raptor migration were identified. Additionally, 17 complete viral genomes belonging to , , , , and were characterized, and their phylogenetic relationships were analyzed. This pioneering metagenomic study of migratory birds in Poyang Lake, China illuminates the diverse microbial landscape within these birds. It identifies potential pathogens, and uncovers taxonomic biomarkers relevant to varied bird habitats, feeding habits, ecological classifications, and sample types, underscoring the public health risks associated with wintering migratory birds.

摘要

野生鸟类是人畜共患病病毒的天然宿主。为了阐明候鸟在鄱阳湖病毒传播中的作用，我们对来自七个目 19 种的 250 只野生鸟类样本的微生物组进行了调查。通过 Kraken2 和 Bracken 初步评估了细菌和病毒的含量丰度和多样性。通过 Megahit 和 Vamb 进行从头组装后，使用 CheckV 鉴定病毒片段。使用 Bowtie2 对映射到病毒片段的读数进行定量。样本的细菌微生物组组成涵盖了 175 个细菌目中的 1526 个属，而病毒的组成涵盖了 22 个病毒科中的 214 个种。确定了与禽肉食性、口腔采样和猛禽迁徙相关的几个分类生物标志物。此外，还对 17 个完整的病毒基因组进行了特征描述，这些病毒属于、、、和，并分析了它们的系统发育关系。这项对中国鄱阳湖候鸟的开创性宏基因组研究揭示了这些鸟类内部多样化的微生物景观。它确定了潜在的病原体，并揭示了与不同鸟类栖息地、摄食习惯、生态分类和样本类型相关的分类生物标志物，突显了与冬季候鸟相关的公共卫生风险。