Microbial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on one modified-atmosphere-packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and beyond. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive of the sensory quality of the beef: acceptable product (AP), early spoilage (ES), and late spoilage (LS). Both the 16S RNA taxonomic assignments from the total RNA and functional annotations of the active genes showed that these stages were significantly different from each other. However, the functional gene annotations showed more pronounced differences than the taxonomy assignments. Psychrotrophic lactic acid bacteria (LAB) formed the core of the SSO, according to the transcribed reads. Leuconostoc species were the most abundant active LAB throughout the study period, whereas the transcription activity of Streptococcaceae (mainly Lactococcus) increased after the product had spoiled. In the beginning of the experiment, the community managed environmental stress by cold-shock responses, which were followed by expression of the genes involved in managing oxidative stress. Glycolysis, the pentose phosphate pathway, and pyruvate metabolism were active throughout the study at a relatively stable level. However, the proportional transcription activities of the enzymes in these pathways changed over time.

中文翻译：

---

肉类腐败微生物组的纵向转录组分析可检测到货架期及以后的大量持续发酵和环境胁迫反应。

微生物的食物变质是一种复杂的现象，与特定的变质生物（SSO）随时间的推移有关。我们对一种改良型大气包装（MAP）牛肉产品进行了纵向转录组学研究，以增加对腐败微生物组在保质期及以后的纵向行为的了解。基于对mRNA读数的注释，我们认识到与活性微生物组有关的三个阶段，它们描述了牛肉的感官质量：可接受产品（AP），早期变质（ES）和晚期变质（LS）。来自总RNA的16S RNA分类分配和活性基因的功能注释都表明，这些阶段彼此之间显着不同。然而，功能基因注释显示出比分类法分配更明显的差异。根据转录的读物，精神营养型乳酸菌（LAB）构成了SSO的核心。明串珠物种是在整个研究期间最丰富的活性乳酸菌，而转录活性链球菌（主要是乳酸），增加了产品宠坏了。在实验开始时，社区通过冷休克反应来管理环境压力，然后表达参与管理氧化压力的基因。糖酵解，戊糖磷酸途径和丙酮酸代谢在整个研究中均处于相对稳定的水平。但是，这些途径中酶的比例转录活性随时间变化。