Because of the safety and functionality, lactic acid bacteria have been intensively studied for purposes of industrial application, especially in probiotics field. Taxonomy and identification of the organisms were received poor attention during the last two decades. However, scientific names of “beneficial strains” are essential for proper use in food and feed, meaning that taxonomy and identification are also part of researches of the “beneficial strains”. This article reviews change of identification methods and taxonomy of lactic acid bacteria. Recent studies for proposal of reclassification of the genus Lactobacillus are introduced.

Movement is a fundamental attribute of all living organisms. Many bacteria swim freely in a fluid with a rotation of flagella filament. On the other hand, some tiny organisms have developed several varieties of cell motility without flagella. These mysterious movements are widespread in bacteria, and have been very attractive to many researchers for long time. But it had remained unclear how bacteria move without flagella, and what is the machinery for cell propulsion. Recent advance on the visualization techniques of optical microscopy provides us dynamic behaviors of molecular machineries at a single cellular level in detail, and the current understanding of this field have dramatically jumped in the last 10-20 years. In this review, I would like to introduce our recent study about a surprising new world of biological movements in the smallest life forms such as Spider-man like motion by the repeated cycles of extension and retraction, a caterpillar like motion by the surface flow along cell membrane, and a corkscrew like motion by mechanical drilling in high viscous environments.

Abstract

In order to elucidate the functions of uncultivable environmental bacteria, genome sequence-based analysis which does not depend on cultivation has been attracted attentions. As the development of next-generation sequencers has made it possible to obtain a large amount of sequence information at one time, genome analysis for a variety of environmental samples are currently in progress. The accumulated genome information is utilized for various analyses, and new knowledge is reported daily. In this review, recent research topics in the genome analysis of environmental bacteria using metagenomes and single-cell genomes are summarized. In particular, applications and usefulness of single-cell genome analysis using microdroplets will be described in detail.

Galaxy is an integrative data analysis environment run on the web browser. As before, we explain a topic to quantify RNA expression from an RNA-seq dataset (GSE107337) which examined the acid stress response of Lactobacillus rhamnosus GG. First, we describe a preprocessing of annotation file with GFF format and extract nucleotide sequence information of the gene regions on the genome. Next, we obtain both count and TPM values for individual genes using the Kallisto quant program. Lastly, we compare the current results with those obtained from the original study and our previous ones. Supplementary materials are available online at: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq2.html#about_book_JSLAB.