Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk

Antibiotic resistance genes (ARGs) are novel contaminants that pose a significant threat to public health. Whether mare milk products pose a risk of ARGs transmission is rarely reported. In this study, we used samples of lactic acid bacteria (LAB)-inoculated fermented mare milk, naturally fermented mare milk, raw mare milk, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk by metagenomics. The results showed that pasteurized mare milk had the highest microbial diversity, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), whereas LAB-inoculated fermentation significantly reduced these targets (p<0.05). Bacillota was the dominant microbial group in different samples. LAB inoculation and fermentation altered the microbial community structure of raw mare milk and differentiated it from naturally fermented mare milk, not only reduced and eliminated most of the harmful bacteria, but also decreased the abundance of total ARGs and multiple ARG type in mare milk by reducing the number of host bacteria. The combined effects of microbes and MGEs are the main drivers of ARG transfer and dissemination, with microbes being the key factor. Transposase, Bacteroidota and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation reduced the number of nodes in the network between microbes, ARGs, and MGEs in mare milk and prevented the expansion of most ARGs. This study enhances the understanding of resistance genes in various mare milk products, elucidates the impact of LAB inoculation and fermentation on the distribution and dissemination pathways of ARGs in mare milk, and provides valuable data references and theoretical guidance for safer processing of mare milk products.