The awarded research has been started during my study abroad in the Netherlands, and is based on the findings obtained for the past 20 years. Bile acids are the main components of bile, and emulsify lipids, thereby helping the digestion and absorption of dietary lipid. As bile acids attack bacterial cell membrane to exhibit bactericidal activities, probiotics are required to be resistant to bile acids in intestines. Therefore, using lactic acid bacteria and bifidobacteria, mechanisms underlying bile acid resistance were first investigated and then the interactions between bile acids and bacterial cell membrane were analyzed to elucidate bactericidal mechanism of bile acids. These studies were conducted in many cases from the bioenergetics point of view. Then, these findings were applied to investigate possible roles of bile acids in the control of gut microbiota in vivo. As the results, bile acid was found to be a host factor that regulates the composition of the cecal microbiota in rats. Recently, gut microbiota has been associated with host health. Therefore, our findings have a big impact on the study to investigate the causal relationship between alterations in the gut microbiota on a high-fat diet and host disease development. In this review, trajectory of my research activities will be described including my contribution to the development of Japan Society for Lactic Acid Bacteria.
Lactobacillus rhamnosus is a probiotic lactic acid bacterium frequently isolated from human gastrointestinal mucosa of healthy individuals. We describe an analysis procedure to RNA-seq data (SRP125628 or GSE107337) on the acid stress response of L. rhamnosus GG on an integrated data analysis environment called Galaxy. Specifically, we will describe importing FASTQ files from the public database ENA to Galaxy, preprocessing using Trimmomatic, mapping to reference genome sequence using Bowtie2, and obtaining count data using htseq-count. We will also discuss about similarities of count data between the original and ours. Supplementary materials are available online at: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq2.html#about_book_JSLAB.