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Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting
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  • Published: 05 February 2026

Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting

  • Yuan Zhou1,
  • Kaiyue Liu2,
  • Ping Gong2,
  • Jian Wu1,
  • Zhuqing Ren1 &
  • …
  • Erguang Jin2 

Scientific Reports , 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

  • Computational biology and bioinformatics
  • Environmental sciences
  • Microbiology

Abstract

Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide–lincosamide–streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.

Data availability

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

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Authors and Affiliations

  1. Huazhong Agricultural University, Wuhan, Hubei, China

    Yuan Zhou, Jian Wu & Zhuqing Ren

  2. Wuhan Academy of Agriculture Sciences, Wuhan, Hubei, China

    Kaiyue Liu, Ping Gong & Erguang Jin

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  1. Yuan Zhou
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  2. Kaiyue Liu
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  3. Ping Gong
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  4. Jian Wu
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  5. Zhuqing Ren
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  6. Erguang Jin
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Contributions

All the authors (Yuan Zhou, Kaiyue Liu, Ping Gong, Jian Wu, Zhuqing Ren*, Erguang Jin) equally contributed to the production of this article.

Corresponding authors

Correspondence to Zhuqing Ren or Erguang Jin.

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Zhou, Y., Liu, K., Gong, P. et al. Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting. Sci Rep (2026). https://doi.org/10.1038/s41598-026-37092-y

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  • Received: 20 October 2025

  • Accepted: 19 January 2026

  • Published: 05 February 2026

  • DOI: https://doi.org/10.1038/s41598-026-37092-y

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Keywords

  • Antibiotic resistance genes (ARGs)
  • Dairy manure composting
  • Horizontal gene transfer
  • Microbial community succession
  • Resistome co-selection
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