摘要
      由于所谓的健康益处，发酵食品的消费量在全球范围内有所增长。因此，了解主要影响这些食品质量和安全的发酵食品微生物组至关重要。这项研究确定了中东、非洲和亚洲次大陆地区常见的腌制蔬菜中的细菌群落，包括益生菌和抗微生物基因（ARG）的功能特征。从沙特阿拉伯当地市场采集了六种泡菜的18个样本，并使用霰弹枪宏基因组测序进行了分析。统计分析显示，不同泡菜类型之间的细菌群落存在显著的距离和单独的聚类。在大多数样品中，发现了纳穆尔左乳杆菌、布氏慢杆菌、副arraginis慢乳杆菌、五聚乳酸杆菌、胡萝卜乳杆菌、肉毒明串珠菌和Weissella混淆菌的种类在一系列优势中。Binning揭示了33个高质量的宏基因组组装基因组（MAG），其中4个MAG代表了乳酸杆菌、Alcanivorax和二氏杆菌的假定新物种。此外，285个ARG和变体对20类抗生素产生耐药性，主要来自肠杆菌科重叠群。宏基因组含有相对高丰度的碳水化合物发酵酶，以及氨基酸代谢、辅因子和维生素生物合成的代谢途径。总的来说，通过全面概述泡菜中的细菌群落和益生菌，研究结果表明需要更卫生的加工，以避免肠杆菌科污染和ARG传播。
Abstract
Consumption of fermented foods has grown worldwide due to the purported health benefits. It is thus critical to understand fermented foods microbiome that mainly influences the quality and safety of these foods. This study identified bacterial communities, including functional profiles of probiotics and antimicrobial resistance genes (ARGs), in pickled vegetables commonly consumed in the Middle Eastern, African, and Asian sub-continent regions. Eighteen samples from six pickled vegetables were collected from local markets in Saudi Arabia and analyzed using shotgun metagenomic sequencing. Statistical analyses revealed significant distance and separate clustering of bacterial communities among the different pickle types. Species of Levilactobacillus namurensis, Lentilactobacillus buchneri, Lentilactobacillus parafarraginis, Lactiplantibacillus pentosus, Pectobacterium carotovorum, Leuconostoc carnosum, Weissella confuse were found in a range of dominance in most of the samples. Binning revealed 33 high-quality, metagenome-assembled genomes (MAGs), including 4 MAGs representing putatively novel species of Lactobacillus, Alcanivorax, and Dichelobacter. Moreover, 285 ARGs and variants produce resistance against 20 classes of antibiotics were retrieved, mostly from Enterobacteriaceae contigs. The metagenomes harbored relatively high abundances of carbohydrate fermentation enzymes, as well as metabolic pathways for amino acid metabolism, cofactors and vitamins biosynthesis. Overall, by providing a comprehensive overview of bacterial communities and probiotic bacteria in pickled vegetables, the results suggest the need for more hygienic processing to avoid Enterobacteriaceae contamination and ARG spread.

https://www.sciencedirect.com/science/article/abs/pii/S0963996922002472