Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella enterica serovar Cubana-contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina MiSeq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A “core” SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter. The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, totals of 541, 723, and 424 S. Cubana genes, respectively, were transcribed at either higher or lower levels than at 0 h in SSIW during sprouting. An array of S. Cubana genes (107) were induced at all three time points, including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome.

中文翻译：

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苜蓿种子对沙门氏菌污染的响应中萌芽灌溉水微生物组的分类和功能变化

尽管沙门氏菌-芽苗菜研究的最新进展，但对沙门氏菌与发芽过程中芽孢微生物组之间的关系知之甚少。发芽的废灌溉水（SSIW）提供了这种主要水生作物的总微生物组的丰富信息。这项研究旨在表征肠炎沙门氏菌中SSIW中最活跃转录的基因的功能和分类。整个发芽过程中，被古巴人污染的血清型苜蓿种子。定期收集来自SSIW的基因组DNA和总RNA，并使用Illumina MiSeq和NextSeq平台进行测序。使用四个不同的管道对核酸数据进行注释。宏基因组学和元转录组学分析均显示了多种多样且高度动态的SSIW微生物组。“核心” SSIW微生物包括克雷白杆菌，肠杆菌属，成团泛菌和坂。但是沙门氏菌的影响苜蓿种子的污染不仅在结构上而且在功能上都影响了SSIW微生物群落的动态。与新陈代谢，遗传信息处理，环境信息处理和细胞过程相关的基因变化十分丰富，且具有时间依赖性。在24小时，48小时，和96小时，541，723，和424的总计时间点小号。在萌芽过程中，分别在SSIW中以比0h更高或更低的水平转录Cubana基因。S的数组。在所有三个时间点都诱导了Cubana基因（107），包括与生物膜形成和调控，应激反应以及对抗生素的毒力和耐受性有关的基因。综上所述，这些发现扩大了我们对沙门氏菌效果的理解 种子污染对发芽作物的微生物组和代谢组。