摘要

发酵红辣椒酱（FRP）已在世界范围内食用多年。含盐量和常驻微生物群落影响FRP酱的质量，在某些情况下可能会给消费者带来健康（如益生菌）或伤害（如抗生素抗性基因）；然而，盐介导的微生物群落和抗生素抗性基因的改变鲜为人知。本研究采用全基因组测序和扩增子分析相结合的方法，研究了红椒发酵过程中不同含盐量对微生物群落和耐药基因的影响。虽然肠杆菌科在高盐（15-25%）样品中占优势，但在10%盐样品中，乳酸杆菌科在24天后迅速取代肠杆菌科成为优势种群。与10%盐样中平均每细胞0.05个耐药基因（ARGs）相比，高盐样中平均有16.6个ARGs，其中宿主菌主要为肠杆菌科，包括肠杆菌属、柠檬酸杆菌属、大肠杆菌属、沙门氏菌属和克雷伯菌属。多药耐药基因是主要的ARG类型。功能分析表明，在高盐样品中，组氨酸激酶的功能要高得多，并且包括几个与渗透压相关的双组分系统，这些系统同时编码ARGs。这些结果首次揭示了盐介导的微生物群落组成的变化，并对食品发酵过程中相关的抗生素抗性基因进行了广泛的研究。

Fermented red pepper (FRP) sauce has been eaten in worldwide for many years. The salt content and resident microbial community influences the quality of the FRP sauce and may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers in some circumstances; however, the salt-mediated alteration of microbial community and antibiotic resistance genes are little known. In this study, a combination of whole genome sequencing and amplicon analysis was used to investigate the changes in microbial community and antimicrobial resistance genes in response to different salt content during red pepper fermentation. While the family Enterobacteriaceae dominated in high-salt (15–25%) samples, Lactobacillaceae quickly became the dominant population in place of Enterobacteriaceae after 24 days in 10% salt samples. Compared to 0.05 antibiotic resistance genes (ARGs) per cell number on average in 10% salt sample, 16.6 ARGs were present in high-salt samples, wherein the bacterial hosts were major assigned to Enterobacteriaceae including genera Enterobacter, Citrobacter, Escherichia, Salmonella and Klebsiella. Multidrug resistance genes were the predominant ARG type. Functional profiling showed that histidine kinase functions were of much higher abundance in high-salt samples and included several osmotic stress-related two-component systems that simultaneously encoded ARGs. These results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.

https://www.sciencedirect.com/science/article/pii/S0740002019302989