Metagenomic Evidence for Horizontal Gene Transfer and Functional Convergence in the Oral Microbiome of Cohabiting Dogs and Owners

Abstract The intimate cohabitation between humans and their pets facilitates bidirectional microbial exchange, yet the extent and functional consequences of this transfer within the oral niche remain underexplored. Here, we employed metagenomic sequencing to characterize the oral microbiome of dogs and their owners across distinct geographic regions in China, integrating taxonomic, gene-centric, and functional analyses using public databases (BacMet, CARD, eggNOG, KEGG) to assess microbe–host associations. We found that dog–owner pairs exhibited significantly higher gene-level similarity compared to unrelated individuals, indicating a strong cohabitation-driven microbial linkage. While no major taxonomic shifts were observed in the human oral microbiome associated with pet ownership, we identified a marked enrichment of antibiotic resistance genes (ARGs)—particularly those conferring resistance to peptides, fluoroquinolones, antiseptics, diaminopyrimidines, cephalosporins, and carbapenems—in cohabiting pairs. This enrichment, together with the identification of exclusively shared ARGs (e.g., mdtF, macB, RanA), suggests the potential for horizontal gene transfer (HGT) between pet- and human-associated microbiomes. Functional profiling further revealed greater similarity in microbial metabolic pathways between cohabiting pairs than between unrelated individuals, reinforcing the likelihood of HGT as a mechanism underlying functional convergence. Collectively, these findings reveal that cohabitation with dogs reshapes the human oral microbiome at the genetic and functional levels, with potential implications for antimicrobial resistance transmission. This study provides a foundational framework for assessing the health risks associated with pet–human microbial exchange in shared living environments. Competing Interest Statement The authors have declared no competing interest.