Genome-resolved metagenomics reveals microbiome diversity across 48 tick species

Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host-microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.

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Publication Details

Journal
Nature Microbiology
Published
2025-09-23
DOI
https://doi.org/10.1038/s41564-025-02119-z
Citations
3
Primary Topic
Insect symbiosis and bacterial influences
Type
article
Field-Weighted Citation Impact
5.02
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article

Genome-resolved metagenomics reveals microbiome diversity across 48 tick species

Shi-Jing Shen, Dan Feng, Jin-Guo Zhu, Dai-Yun Zhu et al.
3 citations
Nature Microbiology
Insect symbiosis and bacterial influences
5.02
article

Genome-resolved metagenomics reveals microbiome diversity across 48 tick species

Shi-Jing Shen, Dan Feng, Jin-Guo Zhu, Dai-Yun Zhu, Chongcai Wang, Zhe-Tao Lin, Jinfeng Wang, Run‐Ze Ye, Wu‐Chun Cao, Liangang Deng, Tengcheng Que, Cai Bian, Xiangdong Ruan, Tao Xiong, Na Jia, Yu-Sheng Pan, Bao‐Gui Jiang, Luo‐Yuan Xia, Yi Sun, Chunhong Du, Lin Zhao, Li-Kiang Tan, Qiao‐Cheng Chang, Tian‐Ci Yang, Mingzhu Zhang, Lian‐Feng Li, Li-Feng Du, Wenyu Shi, Fangqing Zhao, Xin Wang, Cheng Li, Yifei Wang, Ning Wang, Qian Wang, Zhihong Liu, Huimin Fan, Juan Wang, Yating Liu, Yiwen Liu, Yan Zhu, Di Tian, Tingting Yuan, Tianhong Wang, Yuyu Li, Jianying Chen, Xiaohu Han, Jia-Fu Jiang, Xiao-Ming Cui, Lin Zhan, Xiaoyu Shi, Xiaoyu Han, Wenqiang Shi, Xiao-Fan Wang, Yan Liu, Wan‐Ying Gao
article en
3 citations

Abstract

Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host-microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.

Nature MicrobiologyVol. 10(10)
Mansfield University (US), Shenyang Agricultural University (CN), Shandong University (CN), Anhui Medical University (CN), Chinese Academy of Sciences (CN), Chinese Academy of Medical Sciences & Peking Union Medical College (CN), Nankai University (CN), Huawei Technologies (China) (CN), Fudan University (CN), Academy of Military Medical Sciences (CN), Chinese PLA General Hospital (CN), Shantou University (CN), China Animal Disease Control Center (CN), Mudanjiang Medical University (CN), Shenzhen International Travel Health Care Center (CN), Tourism College of Zhejiang (CN), Qinghai Institute for Endemic Diease Prevention and Control (CN), Shandong Provincial Hospital (CN), Ningxia Medical University (CN), Chengdu Center for Disease Control and Prevention (CN), State Forestry and Grassland Administration (CN), Taiwan Centers for Disease Control (TW), Yunnan Institute of Endemic Diseases Control and Prevention (CN), Guizhou Provincial People's Hospital (CN), Qilu Hospital of Shandong University (CN), Shandong First Medical University (CN), Wuhan Center for Disease Control and Prevention (CN), University of Chinese Academy of Sciences (CN), Institute of Zoology (CN), Shenyang University (CN), China Agricultural University (CN), City University of Macau (MO)
Openalex Percentile: Top 5%
Insect symbiosis and bacterial influences
5.02
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