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Diet and environmental factors jointly drive the gut microbiome, resistome, and virulome of urban bats
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  • Published: 04 February 2026

Diet and environmental factors jointly drive the gut microbiome, resistome, and virulome of urban bats

  • Long Huang1,
  • Ying-Ting Pu1,
  • Yan-Hui Zhao1,
  • Xiao-Yu Sun1,
  • Yue Zhu1,
  • Ya-Ping Lu1,
  • Hai-Xia Leng1,
  • Jiang Feng1,2,3,
  • Long-Ru Jin1,4 &
  • …
  • Ke-Ping Sun1,2 

npj Biofilms and Microbiomes , Article number:  (2026) Cite this article

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Ecology
  • Microbiology

Abstract

The coexistence and horizontal transfer of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) carried by urban wildlife represent an emerging form of biological pollution, constituting a significant threat to public health. We employed meta-omic approaches to evaluate the effects of host traits (sex, age, etc.), environmental factors (including geographical location and time), and diet (including food composition and antibiotic residues) on the bacterial, ARG, and VFG profiles of Vespertilio sinensis, an urban-dwelling bat. Our results demonstrate that the feces of V. sinensis harbor diverse ARGs and VFGs, but their genomic evidence for horizontal mobility in bacterial communities is limited. Notably, environmental changes over time and across geographical locations are associated with the ARG and VFG profiles, potentially due to the influence of pollutants in specific habitats. Dietary factors are associated with their dynamics through the microbiome, with antibiotic residues exerting selective pressure on ARG profiles. No significant impacts of sex, age, body size, and reproductive status on the gut microbiota, resistome, or virulome were observed. This study provides valuable insights into the ecological drivers of the gut microbiome, resistome, and virulome in bats, thereby contributing to our understanding of the public health risks associated with urban wildlife.

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Data availability

Sequence data that support the findings of this study have been deposited in the NCBI Sequence Read Archive (SRA) database with the primary accession code PRJNA1298781.

Code availability

The underlying code used for ARG-VFG-MGE contigs identification in this study is available in Zenodo and can be accessed via this link [https://doi.org/10.5281/zenodo.17628441].

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (grant nos. 32430066 and 32171525). The funder played no role in study design, data collection, analysis and interpretation of data, or the writing of this manuscript.

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Authors and Affiliations

  1. Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China

    Long Huang, Ying-Ting Pu, Yan-Hui Zhao, Xiao-Yu Sun, Yue Zhu, Ya-Ping Lu, Hai-Xia Leng, Jiang Feng, Long-Ru Jin & Ke-Ping Sun

  2. Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China

    Jiang Feng & Ke-Ping Sun

  3. Jilin Provincial International Cooperation Key Laboratory for Biological Control of Agricultural Pests, Changchun, China

    Jiang Feng

  4. Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics, School of Life Sciences, Northeast Normal University, Changchun, China

    Long-Ru Jin

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Long Huang: Writing—original draft; writing—review and editing; visualization; formal analysis; conceptualization. Ying-Ting Pu: Investigation; writing—review and editing. Yan-Hui Zhao: Investigation; writing—review and editing; visualization. Xiao-Yu Sun: Investigation; visualization. Yue Zhu: Investigation; writing—review and editing. Ya-Ping Lu: Investigation; visualization. Hai-Xia Leng: Investigation; visualization. Jiang Feng: Conceptualization; funding acquisition. Long-Ru Jin: Conceptualization; writing—review and editing; supervision. Ke-Ping Sun: Conceptualization; writing—review and editing; project administration; supervision; funding acquisition. All authors reviewed the manuscript.

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Correspondence to Long-Ru Jin or Ke-Ping Sun.

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Huang, L., Pu, YT., Zhao, YH. et al. Diet and environmental factors jointly drive the gut microbiome, resistome, and virulome of urban bats. npj Biofilms Microbiomes (2026). https://doi.org/10.1038/s41522-026-00930-y

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  • Received: 28 August 2025

  • Accepted: 27 January 2026

  • Published: 04 February 2026

  • DOI: https://doi.org/10.1038/s41522-026-00930-y

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