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

Overview

• This study investigates how inoculating mare milk with lactic acid bacteria (LAB) affects the microbial community and the presence and spread of antibiotic resistance genes (ARGs) in different types of mare milk products.
• By using metagenomic analysis, the research reveals that LAB inoculation reduces harmful bacteria, ARGs, and mobile genetic elements involved in ARG transmission, offering insights for safer equine dairy production.

Background and Importance

• Antibiotic resistance genes (ARGs) are contaminants that pose a significant public health risk because they can promote resistance to antibiotics in bacteria, complicating infection treatment.
• ARGs and pathogenic microbes in food products can facilitate the transmission of antibiotic resistance to humans, raising concerns about food safety.
• Mare milk and its fermented products are significant in some regions, but the role of these products in ARG transmission has been insufficiently studied.
• Lactic acid bacteria (LAB) are commonly used as beneficial inoculants in the fermentation of dairy products due to their ability to suppress harmful microorganisms and improve product safety.

Objectives of the Study

• To analyze and compare microbial communities and ARG distribution in raw, naturally fermented, pasteurized, and LAB-inoculated fermented mare milk.
• To evaluate how LAB inoculation changes microbial community structure and affects the abundance and transmission of ARGs.
• To identify key microbial taxa and mobile genetic elements (MGEs) involved in ARG spread in mare milk.
• To assess the potential of LAB inoculation as a strategy to reduce ARG prevalence and improve the safety of equine dairy products.

Methodology

• Samples analyzed included raw mare milk, naturally fermented mare milk, pasteurized mare milk, and mare milk fermented with added LAB inoculants.
• Shotgun metagenomic sequencing was employed to detect microbial populations, ARGs, and MGEs in these samples.
• Statistical comparisons and network analyses were conducted to identify differences in community composition, ARG abundance, and co-occurrence patterns among microbes, ARGs, and MGEs.

Key Findings

• Microbial Community Structure:
  • Bacillota (a major phylum of bacteria) dominated across all sample types.
  • LAB-inoculated fermentation significantly altered the microbial community compared to naturally fermented and raw milk, reducing certain harmful bacteria.
• ARG Abundance and Diversity:
  • Raw, naturally fermented, and pasteurized mare milk contained higher numbers and relative abundances of ARGs.
  • LAB inoculation significantly reduced total ARG abundance and multiple ARG subtypes including critical resistance types like β-lactam and multidrug resistance genes.
• Mobile Genetic Elements (MGEs):
  • MGEs such as transposons facilitate horizontal gene transfer and play a critical role in spreading ARGs.
  • LAB inoculation reduced the abundance of MGEs, weakening ARG transmission pathways.
• ARG Transmission Dynamics:
  • The co-occurrence network analysis showed that microbes and MGEs jointly drive the transmission of ARGs.
  • Bacteroidota and Pseudomonadota alongside transposons were highlighted as key taxa and MGEs responsible for ARG spread.
  • LAB inoculation disrupted the co-occurrence networks among microbes, ARGs, and MGEs, limiting ARG transmission potential.

Implications

• Inoculating mare milk with LAB during fermentation can serve as an effective strategy to reduce pathogenic bacteria and various ARG types, enhancing food safety.
• The study provides useful metagenomic data characterizing the microbial ecology and ARG profiles of mare milk, an under-researched equine dairy product.
• Understanding microbial dynamics and ARG transmission pathways aids in designing safer dairy processing protocols that minimize antibiotic resistance risks.

Conclusions

• LAB inoculation in mare milk fermentation beneficially modifies microbial communities, suppressing harmful bacteria and ARG carriers.
• This treatment effectively lowers ARG and MGE abundance, thereby potentially reducing the spread of antibiotic resistance via equine dairy products.
• The insights offer theoretical guidance and valuable references for safer production and processing of equine milk products to protect public health.