Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
Food Res Int. 2022 Jul;157:111190. doi: 10.1016/j.foodres.2022.111190. Epub 2022 Mar 26.
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.
由于据称发酵食品具有健康益处，因此其在全球范围内的消费有所增加。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。本研究鉴定了腌制蔬菜中的细菌群落，包括益生菌和抗菌药物耐药基因 (ARGs) 的功能谱，这些蔬菜在中东、非洲和亚洲次大陆地区普遍食用。从沙特阿拉伯当地市场采集了来自 6 种腌制蔬菜的 18 个样本，使用鸟枪法宏基因组测序进行分析。统计分析表明，不同泡菜类型之间的细菌群落存在显著的距离和分离聚类。Levilactobacillus namurensis、Lentilactobacillus buchneri、Lentilactobacillus parafarraginis、Lactiplantibacillus pentosus、Pectobacterium carotovorum、Leuconostoc carnosum 和 Weissella confuse 等物种在大多数样本中具有不同的丰度。分类分析揭示了 33 个高质量的宏基因组组装基因组（MAG），其中 4 个 MAG 代表了乳酸菌、Alcanivorax 和 Dichelobacter 的推定新种。此外，还检索到了 285 个 ARGs 和变体，它们对 20 类抗生素产生抗性，这些抗性主要来自肠杆菌科的 contigs。宏基因组中含有相对丰富的碳水化合物发酵酶，以及氨基酸代谢、辅酶和维生素生物合成的代谢途径。总的来说，通过提供腌制蔬菜中细菌群落和益生菌细菌的综合概述，结果表明需要更卫生的加工方法来避免肠杆菌科的污染和 ARG 的传播。
