Transcriptome signatures for robustness of Lactococcus lactis IL1403

Recently, we demonstrated that fermentation conditions strongly impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied a similar transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11. These strains were employed in an identical fermentation regime as was performed earlier for strain MG1363 which consisted of twelve conditions, varying in the presence of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. Association of transcriptomes and robustness phenotypes identified highly strain-specific transcriptome signatures for robustness, indicating that multiple mechanism exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nanE and genes encoding transport proteins. The transcript levels of these genes can function as indicators of robustness and could aid in selection of fermentation parameters, potentially resulting in more optimal robustness during spray drying. two connected loops, both containing samples derived on a single day (sample 1-6, sample 7-13)

近期，本团队已证实发酵条件会显著影响乳酸乳球菌（Lactococcus lactis）MG1363菌株在热胁迫与氧化胁迫下的后续存活能力，而这两类胁迫均为喷雾干燥（spray drying）过程中的核心影响参数。此外，通过转录组（transcriptome）-表型（phenotype）匹配分析方法，本团队还鉴定出了与热/氧化胁迫抗逆性（robustness）相关的基因簇。
为探究其他乳酸乳球菌菌株是否具备相似或独特的抗逆转录组特征，本研究针对乳酸乳球菌IL1403、KF147及SK11菌株采用了类似的转录组-抗逆表型匹配分析方法。上述菌株的发酵方案与此前针对MG1363菌株所采用的完全一致，共包含12种培养条件，其变量涵盖盐与氧气的存在状态、发酵温度及pH值。在菌株生长的指数生长期（exponential phase），收集菌体用于转录组分析以及热胁迫与氧化胁迫存活表型的检测。
发酵条件的差异可导致菌株热胁迫与氧化胁迫存活能力产生最高达5个对数级的变化。尽管发酵条件对不同菌株的生长特性总体影响相似，但其对乳酸乳球菌菌株胁迫存活能力的影响通常呈现菌株特异性。通过关联转录组与抗逆表型数据，本研究鉴定出了高度菌株特异性的抗逆转录组特征，这表明提升抗逆性的机制存在多样性，因此各菌株的抗逆性均需进行个性化优化。
不过，本研究也发现不同菌株的转录组响应存在少量共通区域，这类通用转录组特征包含此前已被证实与胁迫相关的基因（ctsR与lplL）以及包括nanE和编码转运蛋白（transport protein）基因在内的新型功能基因。上述基因的转录水平可作为抗逆性的指示指标，有助于筛选最优发酵参数，进而有望在喷雾干燥过程中提升菌株的抗逆性能。
本研究的样本包含两个相连的实验循环，每个循环的样本均采集自单日（样本1-6、样本7-13）。