Computational Science Center Seminar

Enterobacter sp. 638 has been shown as a plant-promoting bacterium that lives in the soil or inside of the plant. However, the mechanisms of the plant-bacterium interaction and their beneficial effect remains to be explored. In order to fully understand how bacteria respond to their environment, it is essential to assess genome-wide transcriptional activities. The latest high-throughput sequencing technologies make it possible to query the transcriptome of an organism in an efficient and unbiased manner. In this talk, I will introduce our research work flow to study the activities of Enterobacter sp. 638 that grow in the sucrose (plant sugar) versus in the lactate (milk sugar) using mRNA-sequencing data. In our mRNA-seq experiment, 200 million 76nt-long short reads were generated, and among them, 12 million were uniquely mapped to the genome and quantified for each predicted genes. The following statistical analyses, including differentially expression analysis, enriched functional analysis and clustering analysis, were applied to the gene expression counts data to identify the potential representative genes and pathways involved in the plant-bacterium interaction. Overall, this approach provides an efficient way to survey global transcriptional activity in bacteria and enables rapid discovery of specific areas in the genome that merit further investigation.