RT Journal Article SR Electronic T1 Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification JF bioRxiv FD Cold Spring Harbor Laboratory SP 729616 DO 10.1101/729616 A1 Hirokazu Takahashi A1 Kyohei Horio A1 Setsu Kato A1 Toshiro Kobori A1 Kenshi Watanabe A1 Tsunehiro Aki A1 Yutaka Nakashimada A1 Yoshiko Okamura YR 2019 UL http://biorxiv.org/content/early/2019/11/21/729616.abstract AB Meta-analyses using next generation sequencing is a powerful strategy for studying microbiota; however, it cannot clarify the role of individual microbes within microbiota. To know which cell expresses what gene is important for elucidation of the individual cell’s function in microbiota. In this report, we developed novel fluorescence in situ hybridization (FISH) procedure using RNase-H-assisted rolling circle amplification to visualize mRNA of interest in microbial cells without reverse transcription. Our results show that this method is applicable to both gram-negative and gram-positive microbes without any noise from DNA, and it is possible to visualize the target mRNA expression directly at the single-cell level. Therefore, our procedure, when combined with data of meta-analyses, can help to understand the role of individual microbes in the microbiota.