Ryo Miyazaki Ph.D.

Research articles

Takano S, Vila JCC, Miyazaki R, Sánchez Á, Bajić D. The architecture of metabolic networks constrains the evolution of microbial resource hierarchies. 2023. Mol Biol_Evol. 40(9):msad187. doi: 10.1093/molbev/msad187.

Takano S, Takahashi H, Yama Y, Miyazaki R, Furusawa C, Tsuru S. Inference of transcriptome signatures of Escherichia coli in long-term stationary phase. 2023. Sci Rep. 13(1):5647. doi: 10.1038/s41598-023-32525-4.

Wolter L, Suenami S, Miyazaki R. Frischella japonica sp. nov., an anaerobic member of the Orbales in the Gammaproteobacteria, isolated from the gut of the eastern honey bee, Apis cerana japonica Fabricius. 2021. Int J Syst Evol Microbiol. 71(3):004712. doi: 10.1099/ijsem.0.004712.

Kosakamoto H, Yamauchi T, Akuzawa-Tokita Y, Nishimura K, Soga T, Murakami T, Mori H, Yamamoto K, Miyazaki R, Koto A, Miura M, Obata F. Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila. 2020. Cell Rep. 32(3):107938. doi:10.1016/j.celrep.2020.107938.

Ellegaard KM, Suenami S, Miyazaki R, Engel P. Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species. 2020. Curr Biol. 30(13):2520-2531. doi:10.1016/j.cub.2020.04.070.

Koto A, Nobu MK, Miyazaki R. Deep Sequencing Uncovers Caste-Associated Diversity of Symbionts in the Social Ant Camponotus japonicus. 2020. mBio. 11(2):e00408-20. doi:10.1128/mBio.00408-20.

Ellegaard KM, Suenami S, Miyazaki R, Engel P. Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species. 2020. bioRxiv. doi:10.1101/2020.01.23.916296.

Takano S, Fukuda K, Koto A, Miyazaki R. A novel system of bacterial cell division arrest implicated in horizontal transmission of an integrative and conjugative element. 2019. PLoS Genet. 15(10):e1008445. doi:10.1371/journal.pgen.1008445.

Suenami S, Konishi Nobu M, Miyazaki R. Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima. 2019. Sci Rep. 9:9830. doi:10.1038/s41598-019-46388-1.

Takano S, Koto A, Miyazaki R. Dynamics of bacterial cell proliferation inhibited by specific proteins for effective horizontal transmission of the integrative and conjugative element ICEclc. 2019. bioRxiv. doi:10.1101/512285

Suenami S, Miyazaki R, Kubo T. Detection of Phospholipase C Activity in the Brain Homogenate from the Honeybee. 2018. J Vis Exp. 139. doi:10.3791/58173

Miyazaki R, Yano H, Sentchilo V, van der Meer JR. Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. 2018. Sci Rep. 8:5550.

Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. 2015. Front Microbiol. 6:101.

Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K, Linke B, Mikulic J, Mueller L, Nicolas D, Robinson-Rechavi M, Rivolta C, Roggo C, Roy S, Sentchilo V, Siebenthal AV, Falquet L, van der Meer JR. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. 2015. Environ Microbiol. 17(1):91-104.

Pradervand N, Delavat F, Sulser S, Miyazaki R, van der Meer JR. The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer. 2014. J Bacteriol. 196(22):3971-3979.

Pradervand N, Sulser S, Delavat F, Miyazaki R, Lamas I, van der Meer JR. An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13. 2014. PLoS Genet. 10(6):e1004441.

Inoue K, Miyazaki R, Ohtsubo Y, Nagata Y, Tsuda M. Inhibitory effect of Pseudomonas putida nitrogen-related phosphotransferase system on conjugative transfer of IncP-9 plasmid from Escherichia coli. 2013. FEMS Microbiol Lett. 345(2):102-109.

Miyazaki R, van der Meer JR. A new large-DNA-fragment delivery system based on integrase activity from an integrative and conjugative element. 2013. Appl Environ Microbiol. 79(14):4440-4447.

Sentchilo V, Mayer AP, Guy L, Miyazaki R, Green Tringe S, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M, van der Meer JR. Community-wide plasmid gene mobilization and selection. 2013. ISME J. 7(6):1173-1186.

Reinhard F#, Miyazaki R#, Pradervand N, van der Meer JR. Cell differentiation to “mating bodies” induced by an integrating and conjugative element in free-living bacteria. 2013. Curr Biol. 23(3):255-259. #These authors are co-first authors. Press coverage: “Horizontal Gene Transfer: Linking Sex and Cell Gate.” 2013. Curr Biol. 23(3):R118-119. Brigid M. Davis and Matthew K. Waldor.

Miyazaki R, Minoia M, Pradervand N, Sulser S, Reinhard F, van der Meer JR. Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element. 2012. PLoS Genet. 8(7):e1002818.

Miyazaki R, van der Meer JR. How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element? 2011. Mob Genet Elements. 1(1):82-84.

Miyazaki R, van der Meer JR. A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13. 2011. Mol Microbiol. 79(3):743-758.

Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M, Miyazaki K. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. 2009. ISME J. 3(12):1335-1348.

Sentchilo V, Czechowska K, Pradervand N, Minoia M, Miyazaki R, van der Meer JR. Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. 2009. Mol Microbiol. 72(5):1293-1306.

Miyazaki R, Ohtsubo Y, Nagata Y, Tsuda M. Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer. 2008. J Bacteriol. 190(19):6281-6289.

Fuchu G, Ohtsubo Y, Ito M, Miyazaki R, Ono A, Nagata Y, Tsuda M. Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNA. 2008. Appl Microbiol Biotechnol. 79(4):627-632.

Ono A#, Miyazaki R#, Sota M, Ohtsubo Y, Nagata Y, Tsuda M. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. 2007. Appl Microbiol Biotechnol. 74(2):501-510. #These authors are co-first authors.

Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y, Tsuda M. Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. 2006. Appl Environ Microbiol. 72(11):6923-6933.

Sota M, Yano H, Ono A, Miyazaki R, Ishii H, Genka H, Top EM, Tsuda M. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. 2006. J Bacteriol. 188(11):4057-4067.

Nagata Y, Kamakura M, Endo R, Miyazaki R, Ohtsubo Y, Tsuda M. Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. 2006. FEMS Microbiol Lett. 256(1):112-118.

Reviews and books

Suenami S, Koto A, Miyazaki R. Basic structures of gut bacterial communities in eusocial insects. 2023. Insects. 14(5):444. doi: 10.3390/insects14050444.

Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR. The hidden life of integrative and conjugative elements. 2017. FEMS Microbiol Rev. 41(4):512-537.

Miyazaki R, Minoia M, Pradervand N, Sentchilo V, Sulser S, Reinhard F, van der Meer JR. The clc Element and Related Genomic Islands in Proteobacteria. 2012. Bacterial integrative mobile genetic elements. 261-272. Edited by Roberts AP, Mullany P, Eds. Landes Bioscience, Madame Curie Bioscience Database.