Transcriptional Regulation and Adaptation to a High-Fiber Environment in <i>Bacillus subtilis</i> HH2 Isolated from Feces of the Giant Panda

In the giant panda, adaptation to a high-fiber environment is a first step for the adequate functioning of intestinal bacteria, as the high cellulose content of the gut due to the panda's vegetarian appetite results in a harsh environment. As an excellent producer of several enzymes and vitamins, Bacillus subtilis imparts various advantages to animals. In our previous study, we determined that several strains of B. subtilis isolated from pandas exhibited good cellulose decomposition ability, and we hypothesized that this bacterial species can survive in and adapt well to a high-fiber environment. To evaluate this hypothesis, we employed RNA-Seq technology to analyze the differentially expressed genes of the selected strain B. subtilis HH2, which demonstrates significant cellulose hydrolysis of different carbon sources (cellulose and glucose). In addition, we used bioinformatics software and resources to analyze the functions and pathways of differentially expressed genes. Interestingly, comparison of the cellulose and glucose groups revealed that the up-regulated genes were involved in amino acid and lipid metabolism or transmembrane transport, both of which are involved in cellulose utilization. Conversely, the down-regulated genes were involved in non-essential functions for bacterial life, such as toxin and bacteriocin secretion, possibly to conserve energy for environmental adaptation. The results indicate that B. subtilis HH2 triggered a series of adaptive mechanisms at the transcriptional level, which suggests that this bacterium could act as a probiotic for pandas fed a high-fiber diet, despite the fact that cellulose is not a very suitable carbon source for this bacterial species. In this study, we present a model to understand the dynamic organization of and interactions between various functional and regulatory networks for unicellular organisms in a high-fiber environment.大熊猫的肠道因植食性习性而富含纤维素，形成了严苛的生存环境，因此肠道菌群适应高纤维环境是其正常发挥功能的首要前提。作为多种酶类与维生素的优质生产者，枯草芽孢杆菌（Bacillus subtilis）可赋予宿主诸多有益特性。本团队前期研究显示，从大熊猫体内分离得到的多株枯草芽孢杆菌具备优异的纤维素分解能力，据此我们提出假说：该菌种可在高纤维环境中存活并良好适应。为验证该假说，本研究采用RNA-Seq技术，对筛选出的菌株枯草芽孢杆菌HH2（B. subtilis HH2）在纤维素与葡萄糖两种不同碳源条件下的差异表达基因（differentially expressed genes）进行分析，该菌株在两类碳源环境中均展现出显著的纤维素水解活性。此外，本研究借助生物信息学软件与数据库资源，对差异表达基因的功能及参与通路进行解析。有趣的是，通过对比纤维素组与葡萄糖组的基因表达谱发现，上调基因主要参与氨基酸代谢、脂质代谢以及跨膜运输过程，上述通路均与纤维素利用密切相关。与之相反，下调基因则多参与细菌生命活动中非必需的功能，例如毒素与细菌素分泌，此举或为节省能量以适应高纤维环境。研究结果表明，枯草芽孢杆菌HH2可在转录层面启动一系列适应性机制，这提示尽管纤维素并非该菌种的最优碳源，但其仍可作为高纤维日粮饲喂大熊猫的益生制剂。本研究构建了一套研究模型，可用于解析高纤维环境下单细胞生物各类功能与调控网络的动态构建及相互作用关系。