Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks

Small mammals harbor a diverse array of potentially zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viruses, with limited attention directed to bacterial and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome-defined as the set of microorganisms infecting the host-across 2408 individual samples, representing lung, spleen, and gut from 858 animals in Guangdong province, China, considering the impact of host species, tissue, season, and geographic location on pathogen diversity. We identified 76 potential pathogen species, comprising 29 RNA viruses, 12 DNA viruses, five bacteria, and 30 eukaryotic pathogens, including 33 that are newly discovered. Distinct tissue tropisms were identified, suggesting varied transmission routes. Individual animals carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Total pathogen richness was largely influenced by geographic region, followed by host species and season, while zoonotic pathogen richness was primarily driven by host species. Collectively, these data provide insights into the structure of the pathogen infectome and the drivers of pathogen diversity and transmission in these key mammalian disease reservoirs.

Authors

Institutions

Publication Details

Journal
Nature Communications
Published
2025-12-12
DOI
https://doi.org/10.1038/s41467-025-66462-9
Primary Topic
Zoonotic diseases and public health
Type
article
Field-Weighted Citation Impact
0.00

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks

Shi-Jia Le, Penghui Jia, Qinyu Gou, Gengyan Luo et al.
Nature Communications
Zoonotic diseases and public health
article

Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks

Shi-Jia Le, Penghui Jia, Qinyu Gou, Gengyan Luo, Z. Y. Ren, Changyun Sun, Siew Hua Gan, Jingdiao Chen, Ziqing Deng, Guopeng Kuang, Daxi Wang, Hailong Zhao, Yuhua Liao, Minwu Peng, Jun Wu, Wenqing Lin, Gen-Yang Xin, Edward Charles Holmes, An Chen, Junhua Li, Dongqing Li, Jiajun Liu, Jing Wang, Jianbin Kong, Peibo Shi, Wei-Chen Wu, Mǎng Shī, Weiqi Zhao, Jinxia Cheng, Zhu Pan, Xin Zhang, Xin Hou, Qingquan Cen
article en

Abstract

Small mammals harbor a diverse array of potentially zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viruses, with limited attention directed to bacterial and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome-defined as the set of microorganisms infecting the host-across 2408 individual samples, representing lung, spleen, and gut from 858 animals in Guangdong province, China, considering the impact of host species, tissue, season, and geographic location on pathogen diversity. We identified 76 potential pathogen species, comprising 29 RNA viruses, 12 DNA viruses, five bacteria, and 30 eukaryotic pathogens, including 33 that are newly discovered. Distinct tissue tropisms were identified, suggesting varied transmission routes. Individual animals carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Total pathogen richness was largely influenced by geographic region, followed by host species and season, while zoonotic pathogen richness was primarily driven by host species. Collectively, these data provide insights into the structure of the pathogen infectome and the drivers of pathogen diversity and transmission in these key mammalian disease reservoirs.

Nature CommunicationsVol. 16(1)
BGI Group (China) (CN), The University of Sydney (AU), National Sun Yat-sen University (TW), Sun Yat-sen University (CN), Guangzhou Center for Disease Control and Prevention (CN), Xinjiang Uygur Autonomous Region Disease Prevention and Control Center (CN), The Seventh Affiliated Hospital of Sun Yat-sen University (CN), Beijing Graphene Institute (CN), Yunnan Center for Disease Control And Prevention (CN), Zhanjiang Experimental Station (CN), Guangdong Provincial Center for Disease Control and Prevention (CN), Yunnan Institute of Endemic Diseases Control and Prevention (CN), University of Chinese Academy of Sciences (CN), BGI Research (CN), Laboratory of Data Discovery for Health (HK)
National Natural Science Foundation of China, Innovation and Technology Commission, Natural Science Foundation of Guangdong Province, National Health and Medical Research Council, National Key Research and Development Program of China
Openalex Percentile: Top 49%
Zoonotic diseases and public health
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.