Sooin Lee

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples.

Preparation of optically active beta-amino acids from microbial polyester polyhydroxyalkanoates

An efficient method for the preparation of optically active ethyl β-aminobutyrate from the biopolymer, poly-(R)-(-)-3-hydroxybutyrate (PHB) obtained from bacterial cells has been established using chemical transformations: simple recovery of PHB from bacterial cells followed by acidic alcoholysis, tosylation, nucleophilic substitution by azide, and an indium mediated reduction.

Current challenges in bacterial transcriptomics.

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

Elucidation of Bacterial Genome Complexity Using Next-generation Sequencing

Next-generation sequencing (NGS) technologies generate higher resolution and less noise data that can allow the assembly of bacterial genome sequences. It also enables the characterization and quantification of transcriptomes, and the genome-wide profiling of DNA-protein interactions. With decreasing cost of NGS, such revolutionary advances in technology has become a powerful tool for studying bacterial genome complexity, which in turn will be used to design synthetic genome. This review describes the NGS approaches, the challenges associated with their application and the advances made so far in characterizing bacterial genomes, transcriptomes, and interactomes. We anticipate these high-throughput data to be a resourceful and broadly used for elucidating bacterial cells at the system level and furthermore, for the synthesis of intelligent biological systems for biotechnological purposes.