Center for Biofilm Engineering and Department of Chemical and Biological Engineering, PO Box 173980, Montana State University-Bozeman, Bozeman, Montana 59717-3980, USA.
BMC Microbiol. 2010 Nov 17;10:294. doi: 10.1186/1471-2180-10-294.
Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared rankings for a priori identified physiological marker genes between the biofilm and published data sets.
Biofilms tolerated exposure to antibiotics, harbored steep oxygen concentration gradients, and exhibited stratified and heterogeneous spatial patterns of protein synthetic activity. Transcriptional profiling was performed and the signal intensity of each transcript was ranked to gain insight into the physiological state of the biofilm population. Similar rankings were obtained from data sets published in the GEO database http://www.ncbi.nlm.nih.gov/geo. By comparing the rank of genes selected as markers for particular physiological activities between the biofilm and comparator data sets, it was possible to infer qualitative features of the physiological state of the biofilm bacteria. These biofilms appeared, from their transcriptome, to be glucose nourished, iron replete, oxygen limited, and growing slowly or exhibiting stationary phase character. Genes associated with elaboration of type IV pili were strongly expressed in the biofilm. The biofilm population did not indicate oxidative stress, homoserine lactone mediated quorum sensing, or activation of efflux pumps. Using correlations with transcript ranks, the average specific growth rate of biofilm cells was estimated to be 0.08 h(-1).
Collectively these data underscore the oxygen-limited, slow-growing nature of the biofilm population and are consistent with antimicrobial tolerance due to low metabolic activity.
采用转录组分析方法对在滴流生物膜反应器中生长 3 天的铜绿假单胞菌的生理活性进行了描述。传统的转录谱分析通常比较两个在单个实验控制变量上有所不同的配对数据集。相比之下，本研究获得了单个生物膜状态的转录组，对转录信号进行排序以揭示群体的优先顺序，并比较了生物膜与已发表数据集之间预先确定的生理标记基因的排序。
生物膜能够耐受抗生素的暴露，具有陡峭的氧气浓度梯度，并表现出分层和异质的蛋白质合成活性空间模式。进行了转录谱分析，并对每个转录本的信号强度进行了排序，以深入了解生物膜群体的生理状态。从 GEO 数据库 http://www.ncbi.nlm.nih.gov/geo 中发表的数据集获得了相似的排序。通过比较生物膜和比较数据集之间选择为特定生理活性标记的基因的排名，可以推断生物膜细菌生理状态的定性特征。从它们的转录组来看，这些生物膜似乎以葡萄糖为营养，铁充足，氧气有限，生长缓慢或表现出静止期特征。与 IV 型菌毛形成相关的基因在生物膜中强烈表达。生物膜群体没有表现出氧化应激、高丝氨酸内酯介导的群体感应或外排泵的激活。使用与转录本等级的相关性，估计生物膜细胞的平均比生长速率为 0.08 h(-1)。
这些数据共同强调了生物膜群体的氧气限制、生长缓慢的性质，并且与由于低代谢活性而导致的抗菌药物耐受性一致。
