Yoichi Kamagata, Ph. D.
Asisstant Director General, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST)
Ex-Deputy Director General
Department of Life Science and Biotechnology
National Institute of Advanced Industrial Science and Technology (AIST)
Ex-Director-General
AIST Hokkaido
National Institute of Advanced Industrial Science and Technology(AIST)
Ex-director
Bioproduction Research Institute
National Institute of Advanced Industrial Science and Technology(AIST)
- April 2019
- Asisstant Director General, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST)
- April 2015
- Deputy Director General, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST)
- April 2014
- Director-General, AIST Hokkaido, National Institute of Advanced Industrial Science and Technology (AIST)
- April 2010
- Director, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- April 2006
- Director, Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST)
- September 2006 - present
- Visiting professor, Hokkaio University
- September 2004 - present
- Visiting professor, Nagaoka Institute of Technology
- April 2001- March 2006
- Group Leader, Microbial and Genetic Resources Research Group
Institute for Biological Resources and Functions
National Institute of Advanced Industrial Science and Technology (AIST)
Research interests
- Diversity of microbes in natural environment
- Syntrophy between organisms in anoxic/oxic environment
- Degradation of anthropogenic chemicals by organisms
- Molecular physiology and domestication of uncultured organisms
- Detection of target genes/organisms
- Degradation of natural polymers
Major research outcomes
- Microbial diversity in some particular environments such as wastewater treatment processes, natural gas fields, rice paddies, and rumen ecosystem have been elucidated.
- A number of methanogens, sulfate reducers, syntrophs and aerobic heterotrphs have been isolated and characterzed in conjunction with in situ physiology.
- Syntrophic relation between syntrophs and methanogens have been elucidated.
- Organisms capable of 2,4-dichloroacetate degradation were isolated from pristine environments and their physiological and genetic traits were determined.
- Bacterial methylation of iodine has been found and eludicated.
- New techniques to quantitatively determine the target genes/organisms have been developed.
LIST OF PUBLICATIONS
PEER REVIEWED PAPERS
(254) K.E. Fujimori, Kobayashi, Y., Sekine, T., T. Sahara, S. Ohgiya, Y. Kamagata: Whole genome sequence of an isogenic haploid strain Saccharomyces cerevisiae RI-2idA (MATa) established from the industrial diploid IR-2. Microbiology Resource Announcement 8: e00018-19 (2019).
(253) Sekine, T., Kobayashi, Y., T. Sahara, S. Ohgiya, Y. Kamagata, and K.E. Fujimori: Molecular evolutionary engineering of xylose isomerase to improve its catalytic activity and performance of micro-aerobic glucose/xylose co-fermentation in a recombinant Saccharomyces cerevisiae. Biotechnology for Biofuels 12:139 (2019).
(252) Takeuchi, M., H. Ozaki, S. Hiraoka, Y. Kamagata, S. Sakata, H. Yoshioka, and W. Iwasaki: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on Methylocaldum marinum S8. PLoS ONE 14: e0213535 (2019).
(251) Kusada, H., Y. Zhang, H. Tamaki, N. Kimura, and Y. Kamagata: A novel N-acylhomoserine lactone-degrading bacteria isolated from penicillin-contaminated environments and their quorum-quenching activities. Frontiers in Microbiol. 10: e455 (2019).
(250) Kato, S., K. Wada, W. Kitagawa, D. Mayumi, M. Ikarashi, T. Sone, K. Asano, and Y. Kamagata: Conductive iron oxides promote methanogenic acetate degradation by microbial communities in a high-temperature petroleum reservoir. 34: 95-98 (2019).
(249) Kobayashi, Y., T. Sahara, S. Ohgiya, Y. Kamagata, and K.E. Fujimori: Systematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae. AMB Express 8:139 (2018).
(248) Hidalgo, C.A., M.K. Nobu, T. Narihiro, H. Tamaki, W-T Liu, Y. Kamagata, A.J.M Stams, H. Imachi, and Sousa, D.Z.: Novel energy conservation strategies and behavior of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environ. Microbiol. 20: 4503-4511 (2018).
(247) Kato, S., A. Yamagishi, S. Daimon, K. Kawasaki, H. Tamaki, W. Kitagawa, A. Abe, A. Tanaka, T. Sone, K. Asano, and Y. Kamagata: Isolation of previously uncultured slow-growing bacteria by using a simple modification in preparation of agar media. Appl. Environ. Microbiol. 84: 00807-18 (2018).
(246) Mitani, Y., R. Yasuno, M. Isaka, N. Mitsuda, R. Futahashi, Y. Kamagata, and Y. Ohmiya: Novel gene encoding a unique luciferase from the fireworm Odontostyillis undecimdonta. Sci. Rep. 8: e12789 (2018).
(245) Tanka, Y., H. Tamaki, K. Tanaka, E. Tozawa, H. Matsuzawa, T. Toyama, Y. Kamagata, and K. Mori: "Duckweed-microbe co-cultivation method" for isolating a wide variety of microbes including taxonomically novel microbes. Microbe. Environ. 33: 402-406 (2018).
(244) Kusada, H., K. Kameyama, X-Y. Meng, Y. Kamagata, and H. Tamaki: Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice. Sci. Rep. 7: 18087 (2017).
(243) Kawasaki, K and Y. Kamagata : Phosphate-catalyzed hydrogen peroxide formation from agar, gellan, and κ-carrageenan and recovery of microorganisms cultivability by catalase and pyruvate. Appl. Environ. Microbiol. 83: 01366-17 (2017).
(242) Tamazawa, S., D. Mayumi, H. Mochimaru, S. Sakata, H. Maeda, T. Wakayama, M. Ikarashi, Y. Kamagata : Petrothermobacter organivorans gen. nov., sp. nov., a thermophilic, strictly anaerobic bacterium of the phylum Deferribacteres isolated from a deep subsurface oil reservoir. Int. J. Syst. Evol. Microbiol., 67: 3982-3986 (2017).
(241) Tanaka, Y., H. Matsuzawa, H. Tamaki, M. Tagawa, T. Toyama, Y. Kamagata, K. Mori : Isolation of novel bacteria including rarely cultivated phyla, Acidobacteria and Verrucomicrobia, from the toots of emergent plants by simple culturing method. Microb. Environ. 32: 288-292 (2017).
(240) Takai, R., K. Shigetomi, Y. Kamagata, M. Ubukata: Growth mechanism of actinobacterial strain Leucobacter by zinc coproporphyrin. Heterocycles 95: 145-151 (2017).
(239) Mei, R., M. K. Nobu, T. Narihiro, K. Kuroda, J. M. Sierra, Z. Wu, L. Ye, P.K.H. Lee, P-H. Lee, J.B van Lier, M.J. McInerney, Y. Kamagata, W-T. Liu: Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Wat. Res. 124: 77-84 (2017).
(238) Kobayashi, Y., T. Sahara, T. Suzuki, S. Kamachi, A. Matsushika, T. Hoshino, S. Ohgiya, Y. Kamagata, K.E. Fujimori: Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. J. Ind. Microbiol. Biotechnol. 44: 879-891 (2017).
(237) Yasutake, Y., H. Kusada, T. Ebuchi, S. Hanada, Y. Kamagata, T. Tamura, N. Kimura : Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides. Sci. Rep. 7: 8946 (2017).
(236) Kusada, H., H Tamaki, Y. Kamagata, S. Hanada, N. Kimura : A novel quorum-quenching N-acylhomoserine lactone acylase from Acidovorax sp. strain MR-S7 mediates antibiotic resistance. Appl. Environ. Microbiol. 83: e00080-17 (2017).
(235) Kato, S., Y. Kanata, W. Kitagawa, T. Sone, K. Asano, and Y. Kamagata: Restoration of the growth of Escherichia coli under K+-deficient conditions by Cs+ incorporation via the K+ transporter Kup. Sci. Rep. 7: 195 (2017).
(234) Narihiro, T. and Y. Kamagata : Genomics and metagenomics in microbial ecology: recent advances and challenges. Microb. Environ. 32: 1-4 (2017).
(233) Terashima, M., A. Yama, M. Sato, I. Yumoto, Y. Kamagata, and S. Kato : Culture-dependent and -independent identification of polyphosphate-accumulating Dechloromonas spp. predominating in a futll-scale oxidation ditch wastewater treatment plant. Microb. Environ. 31: 449-455 (2016).
(232) Tamazawa, S., K. Yamamoto, K. Takasaki, Y. Mitani, S. Hanada, Y. Kamagata, H. Tamaki : In situ gene expression responsible for sulfide oxidation and CO2 fixation of an uncultured large sausage-shaped Aquificae bacterium in a sulfidic hot spring. Microb. Environ. 31: 194-198 (2016).
(231) Iino, T., M. Ohkuma, Y. Kamagata, and S. Amachi : Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov. Int. J. Syst. Evol. Microbiol., published ahead of printing (2016).
(230) Mochimaru, H., H. Tamaki, T. Katayama, H. Imachi, S. Sakata, and Y. Kamagata : Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. Int. J. Syst. Evol. Microbiol., 66: 4873-4877 (2016).
(229) Mayumi, D., H. Mochimaru, H. Tamaki, K. Yamamoto, H. Yoshioka, Y. Suzuki, Y. Kamagata and S. Sakata : Methane production from coal by a single methanogen. Science, 354: 222-225 (2016).
(228) Kimura, N. and Y. Kamagata: A thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach. Microb. Environ., 31: 435-441. (2016).
(227) Tani, T., H. Taguchi, K. E. Fujimori, T. Sahara, S. Ohgiya, Y. Kamagata, and T. Akamatsu: Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J. Biosci. Bioeng., 122: 446-455 (2016).
(226) Shinzato, N., H. Aoyama, S. Saitoh., N. Nikoh., K. Nakano., M. Shimojo., M. Shinzato, K. Satou, K. Teruya, T. Hirano, T. Yamada, M.K. Nobu, H. Tamaki, Y. Shirai, S. Park, T. Narihiro, W-T. Liu and Y. Kamagata: Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum. Genome Announcements 5: e-01032-16 (2016).
(225) Y. Kamagata and T. Narihiro : Symbiosis studies in microbial ecology. Microb. Environ., 31: 201-202. (2016).
(224) Narihiro, T., M. K. Nobu, H. Tamaki, Y. Kamagata, Sekiguchi, Y., and W-T. Liu : Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microb. Environ., 31: 288-292. (2016).
(223) Narihiro, T., M. K. Nobu, H. Tamaki, Y. Kamagata, and W-T. Liu : Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica strain 4J5T (JCM 14075), a mesophilic butyrate- and 2-methylbutyrate-degrading syntroph. Genome Announcements 4: e-00047-16 (2016).
(222) Tani, T., H. Taguchi, K. E Fujimori, T. Sahara, S. Ohgiya, Y. Kamagata, T. Akamatsu : Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J. Biosci. Bioeng., published ahead of printing (2016).
(221) Kato, S., E. Goya, M. Tanaka, W. Kitagawa, Y. Kikuchi, K. Asano, and Y. Kamagata : Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion. Scientific Rep., 6 (2016).
(220) Nazrul Bhuiyan, M., R. Takai, S. Mitsuhashi, K. Shigetomi, Y. Tanaka, Y. Kamagata, and M. Ubukata : Novel growth factors released by Sphingopyxis sp. enable laboratory cultivation of previously uncultured Leucobacter sp. through interspecies mutualism. J. Antibiotics. 69: 97-103 (2016).
(219) Kanno, M., P. Constant, P., H. Tamaki, and Y. Kamagata : Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen. Environ. Microbiol., in press (2016).
(218) Kato, S., K. Chino, N. Kamimura, E. Masai, I. Yumoto, and Y. Kamagata : Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil. Scientific Rep., 5 (2015).
(217) Kamagata, Y. : Keys to cultivating uncultured microbes: elaborate enrichment strategies and resuscitation of dormant cells. Microb. Environ., 30: 289-290 (2015).
(216) Takeshita, K., Y. Matsuura, H. Itoh, R. Navarro, T. Hori, T. Sone, Y. Kamagata, P. Mergaert, and Y. Kikuchi : Burkholderia of plant-beneficial group are symbiotically associated with bordered plant bugs (Heteroptera: Pyrrhocoroidea: Largidae). Microb. Environ., 30: 321-329 (2015).
(215) Ohbayashi, T., K. Takeshita, W. Kitagawa, N. Nikoh, R. Koga, X-Y Meng, K. Tago, T. Hori, M. Hayatsu, K. Asano, Y. Kamagata, B-L. Lee, T. Fukatsu, and Y. Kikuchi : Insect's intestinal organ for symbiont sorting. Proc. Natl. Acad. Sci. USA, 112: E5179-5188 (2015).
(214) Nobu, M.K., T. Narihiro, H. Tamaki, Y-L. Qiu, T. Woyke, L. Goodwin, K.W. Davenport, Y. Kamagata, and W-T. Liu : The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol., 17: 4861-4872 (2015).
(213) Narihiro, T., M.K. Nobu, N-K. Kim, Y. Kamagata, and W-T. Liu : The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey. Environ Microbiol., 17: 1707-1720 (2015).
(212) Hori, T., T. Aoyagi, H. Itoh, T. Narihiro, A. Oikawa, K. Suzuki, A. Ogata, M. W. Friedrich, R. Conrad, and Y. Kamagata : Isolation of microorganisms involved in reduction of crystalline iron (III) oxides in natural environments. Frontiers in Microbiol., 6: e368 (2015).
(211) Kanno, M., T. Katayama, N. Morita, H. Tamaki, S. Hanada and Y. Kamagata : Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester. Int. J. Syst. Evol. Microbiol., 65: 805-810 (2015).
(210) Puspita, I.D., W. Kitagawa, Y. Kamagata, M. Tanaka, and C.H. Nakatsu : Increase in bacterial colony formation from a permafrost ice wedge dosed with a Tomitella biformata recombinant resuscitation-promoting factor protein. Microb. Environ., 30: 151-156 (2015).
(209) Takeuchi, M., T. Yamagishi, Y. Kamagata, K. Oshima, M. Hattori, T. Katayama, S. Hanada, H. Tamaki, K. Marumo, H. Maeda, M. Nedachi, W. Iwasaki, Y. Suwa, and S. Sakata : Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions. Int. J. Syst. Evol. Microbiol., 65: 1749-1754 (2015).
(208) Katayama, T., H. Yoshioka, Y. Muramoto, J. Usami, K. Fujiwara, S. Yoshida, Y. Kamagata, and S. Sakata : Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. ISME J., 9: 436-446 (2015).
(207) Nobu, M.K., T. Narihiro, C. Rinke, Y. Kamagata, S.G. Tringe, T. Woyke, and W-T. Liu : Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J., 9: 1710-1722 (2015).
(206) Kanno, M., H. Tamaki, Y. Mitani, N. Kimura, S. Hanada, and Y. Kamagata : pH-induced change in cell susceptibility to butanol in a high butanol-tolerant bacterium, Enterococcus faecalis strain CM4A. Biotechnology for Biofules, 8: e69 (2015).
BOOKCHAPTERS
(15) Shinzato, N. and Y. Kamagata : The methanogenic and archaeal endosymbionts in free-living anaeroibic ciliates. In: Endosymbiotic methanogenic archaea (Edited by J.H.P. Hackstein). Springer Verlag. pp. 37-53 (2018).
(14) Narihiro, T. and Y. Kamagata : Anaerobic cultivation. In: Manual of Environmental Microbiology 4th edition (Edited by Marylynn Yates). American Society of Microbiology. 2-1-2 12pp (2016).
(13) Katayama, T. and Y. Kamagata : Cultivation of Methanogens. In:Hydrocarbon and Lipid Microbiology Protocol. Springer, Heiderberg. 177-195 (2015).
(12) Y. Kamagata : Syntrophy in Anaerobic Digestion. Anaerobic Biotechnology: In: Environmental Protection and Resource Recovery (Edited by H.H.P. Fang and T. Zhang). Published ahead of printing (2015). (11) Kimura, N. W. Kitagawa and Y. Kamagata : Biodegradation of nitrophenol compounds. In: Biological Remediation of Explosive Residues (Edited by S.N. Singh). Springer International. pp. 43-57 (2014).
(10) Kitagawa, W. and Y. Kamagata : Diversity of 2,4-Dichorophenoxyacetic Acid (2,4-D)-Degradative Genes and Degrading Bacteria. In: Biodegradative Bacteria (Edited by H. Nojiri et al). Springer Verlag. pp. 43-57 (2013).
(9) Shinzato, N. and Y. Kamagata : The methanogenic and archaeal endosymbionts of Trimyema In: Endosymbiotic methanogenic archaea (Edited by J.H.P. Hackstein). Springer Verlag. (2010).
(8) Okabe, S. and Y. Kamagata : Wastewater treatment. In: Environmental Molecular Biology (Edited by W-T, Liu and Jansson J.K.). Caiser Academic Press. chapter 10 (2009).
(7) Y. Kamagata, Y. Sekiguchi, and S. Hanada : Gemmatimonadetes phylum nov. In: Bergey's manual of systematic bacteriology (Edited by Garrity G.). Springer-Verlag. (2009).
(6) Y. Kamagata : Genus Oscillospira Chatton and Perard 1913, 1159AL In: Bergey's manual of systematic bacteriology volume 3, (Edited by Garrity G.). Springer-Verlag. (2009).
(5) Y. Kamagata : Genus Thermoacetogenium Hattori, Kamagata, Hanada, and Shoun 2000. In: Bergey's manual of systematic bacteriology volume 3, (Edited by Garrity G.). Springer-Verlag. (2009).
(4) Sekiguchi, Y., and Y. Kamagata : Microbial community structure and functions in methane fermentation technology for wastewater treatment. In: Strict and facultative anaerobes: medical and environmental aspects., (Ed. by Zuber, P. and Nakano, M. M.). Horizon Scientific Press, Norfolk, UK. 361-384 (2004).
(3) Nakatsu, C.H., R. Fulthorpe, W.E. Holben, Y. Kamagata, O.V. Maltseva, V.G. Matheson, C. McGowan, Y. Suwa, J.M. Tiedje, E.M. Top, A.D. Wright, and L.J. Forney : Genetic diversity of 2,4-D catabolic genes. In Microbial diversity and genetics of biodegradation. (eds. Horikoshi, K., Fukuda, M., and Kudo, T). Japan Scientific Societies Press, Tokyo, 197-206 (1997).
(2) Tiedje, J.M., R. Fulthorpe, Y. Kamagata, C.McGowan, A. Rhodes, H. Takami : What is the global pattern of chloroaromatic degrading microbial populations. In Microbial diversity and genetics of biodegradation. (eds. Horikoshi, K., Fukuda, M., and Kudo, T). Japan Scientific Societies Press, Tokyo, 65-74 (1997).
(1) Hausinger, R.P., F. Fukumori, D.A. Hogan, T.W. Sasanella, Y. Kamagata, H. Takami, and R.E. Wallace : Biochemistry of 2,4-D degradation : Evolutionary implications. In Microbial diversity and genetics of biodegradation (eds. Horikoshi, K., Fukuda, M., and Kudo, T). Japan Scientific Societies Press, Tokyo, 35-51 (1997).
PROCEEDINGS
(13) Sekiguchi, Y., S. Hanada, and Y. Kamagata : Cultivation of yet-to-be cultured microorganisms from wastewater treatment processes. Innovative roles of Biological Resource Centers: Proceedings of the 10th International Congress for Culture Collections. ed. by Watanabe, M., Suzuki, K., and Seki, T. 107-111 (2004).
(12) Y. Kamagata : Cultivation of uncultured fastidious microbes. Innovative roles of Biological Resource Centers: Proceedings of the 10th International Congress for Culture Collections. ed. by Watanabe, M., Suzuki, K., and Seki, T. 103-106 (2004).
(11) Kimura, N. and Y. Kamagata : Microbial degradation of chlorinated dibenzo-p-dioxin by a gram-positive bacterium, Rhodococcus opacus SAO101. Organohalogen compounds. 58, 153-156 (2002).
(10) Sekiguchi, Y., Y. Kamagata, A. Ohashi, and H. Harada : Molecular and conventional analyses of microbial diversity in mesophilic and thermophilic upflow anaerobic sludge blanket granular sludges. 9th World congress on anaerobic digestion, 261-266 (2001).
(9) Y. Kamagata : Microbial community analysis of anaerobic ecosystem - significance and importance of anaerobes. Proceedings of 2001 KSAM International symposium on new horizons in microbiology and biotechnology. 24-29 (2001).
(8) Kanagawa, T., Y. Kamagata, K. Yamada, and T. Kohno : Phylogenetic analysis of type 021N strains isolated from bulking sludges. In Microbial Community and Functions in Wastewater Treatment Processes, the International Symposium of the COE, Center for Excellence, Project on Establishment and Evaluation of Advanced Water Treatment Technology Systems Using Functions of Complex Microbial Community, 75-93 (1998).
(7) Nakamura, K., M. Kawaharasaki, S. Hanada, Y. Kamagata, and T. Kanagawa : Characterization of bacterial community constructing anaerobic/aerobic activated sludge by in situ identification and cloning of 16S rDNAs. In Microbial Community and Functions in Wastewater Treatment Processes, the International Symposium of the COE, Center for Excellence, Project on Establishment and Evaluation of Advanced Water Treatment Technology Systems Using Functions of Complex Microbial Community, 75-93 (1998).
(6) Shinjoh, H., A. Miya, K. Onda, Y. Kamagata, M. Kawaharasaki, and K. Nakamura : Some properties of polyphosphate glucokinase in a polyphosphate-accumulating bacterium NM-1. IAWQ, 1993 (1994).
(5) Matsuda, K., K. Nakamura, Y. Kamagata, and E. Mikami : Isolation and characterization of an anaerobic bacterium degrading 4-chlorobutyrate. Microbiology and Biochemistry of Strict Anaerobes Involved in Interspecies Hydrogen Transfer (ed. by J-P. Belaich et al.), Plenum Press, New York, 203-212 (1990).
(4) Tasaki, M., Y. Kamagata, K. Nakamura, and E. Mikami : Isolation of propionate-using sulfate-reducing bacterium. Microbiology and Biochemistry of Strict Anaerobes Involved in Interspecies Hydrogen Transfer (ed. by J-P. Belaich et al.), Plenum Press, New York, 477-479 (1990).
(3) Y. Kamagata and E. Mikami : Diversity of acetotrophic methanogens in anaerobic digestion. Recent Advances in Microbial Ecology (ed. by T. Hattori et al.), Japan Scientific Societies Press, Tokyo, 459-464 (1989).
(2) Y. Kamagata, H. Sasaki, and S. Takao : Fractionation of extracellular cellulase produced by Penicillium purpurogenum and purification of b-glucosidase. Microbial Utilization of Renewable Resources, 4, 124-133 (1985).
(1) Sasaki, H., Y. Kamagata, S. Takao, P. Matangkasombut, and A. Bhumiratuna : Selection and classification of active cellulose-decomposing fungi. Microbial Utilization of Renewable Resources, 3, 65-76 (1983).
(254) K.E. Fujimori, Kobayashi, Y., Sekine, T., T. Sahara, S. Ohgiya, Y. Kamagata: Whole genome sequence of an isogenic haploid strain Saccharomyces cerevisiae RI-2idA (MATa) established from the industrial diploid IR-2. Microbiology Resource Announcement 8: e00018-19 (2019).
(253) Sekine, T., Kobayashi, Y., T. Sahara, S. Ohgiya, Y. Kamagata, and K.E. Fujimori: Molecular evolutionary engineering of xylose isomerase to improve its catalytic activity and performance of micro-aerobic glucose/xylose co-fermentation in a recombinant Saccharomyces cerevisiae. Biotechnology for Biofuels 12:139 (2019).
(252) Takeuchi, M., H. Ozaki, S. Hiraoka, Y. Kamagata, S. Sakata, H. Yoshioka, and W. Iwasaki: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on Methylocaldum marinum S8. PLoS ONE 14: e0213535 (2019).
(251) Kusada, H., Y. Zhang, H. Tamaki, N. Kimura, and Y. Kamagata: A novel N-acylhomoserine lactone-degrading bacteria isolated from penicillin-contaminated environments and their quorum-quenching activities. Frontiers in Microbiol. 10: e455 (2019).
(250) Kato, S., K. Wada, W. Kitagawa, D. Mayumi, M. Ikarashi, T. Sone, K. Asano, and Y. Kamagata: Conductive iron oxides promote methanogenic acetate degradation by microbial communities in a high-temperature petroleum reservoir. 34: 95-98 (2019).
(249) Kobayashi, Y., T. Sahara, S. Ohgiya, Y. Kamagata, and K.E. Fujimori: Systematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae. AMB Express 8:139 (2018).
(248) Hidalgo, C.A., M.K. Nobu, T. Narihiro, H. Tamaki, W-T Liu, Y. Kamagata, A.J.M Stams, H. Imachi, and Sousa, D.Z.: Novel energy conservation strategies and behavior of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environ. Microbiol. 20: 4503-4511 (2018).
(247) Kato, S., A. Yamagishi, S. Daimon, K. Kawasaki, H. Tamaki, W. Kitagawa, A. Abe, A. Tanaka, T. Sone, K. Asano, and Y. Kamagata: Isolation of previously uncultured slow-growing bacteria by using a simple modification in preparation of agar media. Appl. Environ. Microbiol. 84: 00807-18 (2018).
(246) Mitani, Y., R. Yasuno, M. Isaka, N. Mitsuda, R. Futahashi, Y. Kamagata, and Y. Ohmiya: Novel gene encoding a unique luciferase from the fireworm Odontostyillis undecimdonta. Sci. Rep. 8: e12789 (2018).
(245) Tanka, Y., H. Tamaki, K. Tanaka, E. Tozawa, H. Matsuzawa, T. Toyama, Y. Kamagata, and K. Mori: "Duckweed-microbe co-cultivation method" for isolating a wide variety of microbes including taxonomically novel microbes. Microbe. Environ. 33: 402-406 (2018).
(244) Kusada, H., K. Kameyama, X-Y. Meng, Y. Kamagata, and H. Tamaki: Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice. Sci. Rep. 7: 18087 (2017).
(243) Kawasaki, K and Y. Kamagata : Phosphate-catalyzed hydrogen peroxide formation from agar, gellan, and κ-carrageenan and recovery of microorganisms cultivability by catalase and pyruvate. Appl. Environ. Microbiol. 83: 01366-17 (2017).
(242) Tamazawa, S., D. Mayumi, H. Mochimaru, S. Sakata, H. Maeda, T. Wakayama, M. Ikarashi, Y. Kamagata : Petrothermobacter organivorans gen. nov., sp. nov., a thermophilic, strictly anaerobic bacterium of the phylum Deferribacteres isolated from a deep subsurface oil reservoir. Int. J. Syst. Evol. Microbiol., 67: 3982-3986 (2017).
(241) Tanaka, Y., H. Matsuzawa, H. Tamaki, M. Tagawa, T. Toyama, Y. Kamagata, K. Mori : Isolation of novel bacteria including rarely cultivated phyla, Acidobacteria and Verrucomicrobia, from the toots of emergent plants by simple culturing method. Microb. Environ. 32: 288-292 (2017).
(240) Takai, R., K. Shigetomi, Y. Kamagata, M. Ubukata: Growth mechanism of actinobacterial strain Leucobacter by zinc coproporphyrin. Heterocycles 95: 145-151 (2017).
(239) Mei, R., M. K. Nobu, T. Narihiro, K. Kuroda, J. M. Sierra, Z. Wu, L. Ye, P.K.H. Lee, P-H. Lee, J.B van Lier, M.J. McInerney, Y. Kamagata, W-T. Liu: Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Wat. Res. 124: 77-84 (2017).
(238) Kobayashi, Y., T. Sahara, T. Suzuki, S. Kamachi, A. Matsushika, T. Hoshino, S. Ohgiya, Y. Kamagata, K.E. Fujimori: Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. J. Ind. Microbiol. Biotechnol. 44: 879-891 (2017).
(237) Yasutake, Y., H. Kusada, T. Ebuchi, S. Hanada, Y. Kamagata, T. Tamura, N. Kimura : Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides. Sci. Rep. 7: 8946 (2017).
(236) Kusada, H., H Tamaki, Y. Kamagata, S. Hanada, N. Kimura : A novel quorum-quenching N-acylhomoserine lactone acylase from Acidovorax sp. strain MR-S7 mediates antibiotic resistance. Appl. Environ. Microbiol. 83: e00080-17 (2017).
(235) Kato, S., Y. Kanata, W. Kitagawa, T. Sone, K. Asano, and Y. Kamagata: Restoration of the growth of Escherichia coli under K+-deficient conditions by Cs+ incorporation via the K+ transporter Kup. Sci. Rep. 7: 195 (2017).
(234) Narihiro, T. and Y. Kamagata : Genomics and metagenomics in microbial ecology: recent advances and challenges. Microb. Environ. 32: 1-4 (2017).
(233) Terashima, M., A. Yama, M. Sato, I. Yumoto, Y. Kamagata, and S. Kato : Culture-dependent and -independent identification of polyphosphate-accumulating Dechloromonas spp. predominating in a futll-scale oxidation ditch wastewater treatment plant. Microb. Environ. 31: 449-455 (2016).
(232) Tamazawa, S., K. Yamamoto, K. Takasaki, Y. Mitani, S. Hanada, Y. Kamagata, H. Tamaki : In situ gene expression responsible for sulfide oxidation and CO2 fixation of an uncultured large sausage-shaped Aquificae bacterium in a sulfidic hot spring. Microb. Environ. 31: 194-198 (2016).
(231) Iino, T., M. Ohkuma, Y. Kamagata, and S. Amachi : Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov. Int. J. Syst. Evol. Microbiol., published ahead of printing (2016).
(230) Mochimaru, H., H. Tamaki, T. Katayama, H. Imachi, S. Sakata, and Y. Kamagata : Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field. Int. J. Syst. Evol. Microbiol., 66: 4873-4877 (2016).
(229) Mayumi, D., H. Mochimaru, H. Tamaki, K. Yamamoto, H. Yoshioka, Y. Suzuki, Y. Kamagata and S. Sakata : Methane production from coal by a single methanogen. Science, 354: 222-225 (2016).
(228) Kimura, N. and Y. Kamagata: A thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach. Microb. Environ., 31: 435-441. (2016).
(227) Tani, T., H. Taguchi, K. E. Fujimori, T. Sahara, S. Ohgiya, Y. Kamagata, and T. Akamatsu: Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J. Biosci. Bioeng., 122: 446-455 (2016).
(226) Shinzato, N., H. Aoyama, S. Saitoh., N. Nikoh., K. Nakano., M. Shimojo., M. Shinzato, K. Satou, K. Teruya, T. Hirano, T. Yamada, M.K. Nobu, H. Tamaki, Y. Shirai, S. Park, T. Narihiro, W-T. Liu and Y. Kamagata: Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum. Genome Announcements 5: e-01032-16 (2016).
(225) Y. Kamagata and T. Narihiro : Symbiosis studies in microbial ecology. Microb. Environ., 31: 201-202. (2016).
(224) Narihiro, T., M. K. Nobu, H. Tamaki, Y. Kamagata, Sekiguchi, Y., and W-T. Liu : Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microb. Environ., 31: 288-292. (2016).
(223) Narihiro, T., M. K. Nobu, H. Tamaki, Y. Kamagata, and W-T. Liu : Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica strain 4J5T (JCM 14075), a mesophilic butyrate- and 2-methylbutyrate-degrading syntroph. Genome Announcements 4: e-00047-16 (2016).
(222) Tani, T., H. Taguchi, K. E Fujimori, T. Sahara, S. Ohgiya, Y. Kamagata, T. Akamatsu : Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J. Biosci. Bioeng., published ahead of printing (2016).
(221) Kato, S., E. Goya, M. Tanaka, W. Kitagawa, Y. Kikuchi, K. Asano, and Y. Kamagata : Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion. Scientific Rep., 6 (2016).
(220) Nazrul Bhuiyan, M., R. Takai, S. Mitsuhashi, K. Shigetomi, Y. Tanaka, Y. Kamagata, and M. Ubukata : Novel growth factors released by Sphingopyxis sp. enable laboratory cultivation of previously uncultured Leucobacter sp. through interspecies mutualism. J. Antibiotics. 69: 97-103 (2016).
(219) Kanno, M., P. Constant, P., H. Tamaki, and Y. Kamagata : Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen. Environ. Microbiol., in press (2016).
(218) Kato, S., K. Chino, N. Kamimura, E. Masai, I. Yumoto, and Y. Kamagata : Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil. Scientific Rep., 5 (2015).
(217) Kamagata, Y. : Keys to cultivating uncultured microbes: elaborate enrichment strategies and resuscitation of dormant cells. Microb. Environ., 30: 289-290 (2015).
(216) Takeshita, K., Y. Matsuura, H. Itoh, R. Navarro, T. Hori, T. Sone, Y. Kamagata, P. Mergaert, and Y. Kikuchi : Burkholderia of plant-beneficial group are symbiotically associated with bordered plant bugs (Heteroptera: Pyrrhocoroidea: Largidae). Microb. Environ., 30: 321-329 (2015).
(215) Ohbayashi, T., K. Takeshita, W. Kitagawa, N. Nikoh, R. Koga, X-Y Meng, K. Tago, T. Hori, M. Hayatsu, K. Asano, Y. Kamagata, B-L. Lee, T. Fukatsu, and Y. Kikuchi : Insect's intestinal organ for symbiont sorting. Proc. Natl. Acad. Sci. USA, 112: E5179-5188 (2015).
(214) Nobu, M.K., T. Narihiro, H. Tamaki, Y-L. Qiu, T. Woyke, L. Goodwin, K.W. Davenport, Y. Kamagata, and W-T. Liu : The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol., 17: 4861-4872 (2015).
(213) Narihiro, T., M.K. Nobu, N-K. Kim, Y. Kamagata, and W-T. Liu : The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey. Environ Microbiol., 17: 1707-1720 (2015).
(212) Hori, T., T. Aoyagi, H. Itoh, T. Narihiro, A. Oikawa, K. Suzuki, A. Ogata, M. W. Friedrich, R. Conrad, and Y. Kamagata : Isolation of microorganisms involved in reduction of crystalline iron (III) oxides in natural environments. Frontiers in Microbiol., 6: e368 (2015).
(211) Kanno, M., T. Katayama, N. Morita, H. Tamaki, S. Hanada and Y. Kamagata : Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester. Int. J. Syst. Evol. Microbiol., 65: 805-810 (2015).
(210) Puspita, I.D., W. Kitagawa, Y. Kamagata, M. Tanaka, and C.H. Nakatsu : Increase in bacterial colony formation from a permafrost ice wedge dosed with a Tomitella biformata recombinant resuscitation-promoting factor protein. Microb. Environ., 30: 151-156 (2015).
(209) Takeuchi, M., T. Yamagishi, Y. Kamagata, K. Oshima, M. Hattori, T. Katayama, S. Hanada, H. Tamaki, K. Marumo, H. Maeda, M. Nedachi, W. Iwasaki, Y. Suwa, and S. Sakata : Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions. Int. J. Syst. Evol. Microbiol., 65: 1749-1754 (2015).
(208) Katayama, T., H. Yoshioka, Y. Muramoto, J. Usami, K. Fujiwara, S. Yoshida, Y. Kamagata, and S. Sakata : Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. ISME J., 9: 436-446 (2015).
(207) Nobu, M.K., T. Narihiro, C. Rinke, Y. Kamagata, S.G. Tringe, T. Woyke, and W-T. Liu : Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J., 9: 1710-1722 (2015).
(206) Kanno, M., H. Tamaki, Y. Mitani, N. Kimura, S. Hanada, and Y. Kamagata : pH-induced change in cell susceptibility to butanol in a high butanol-tolerant bacterium, Enterococcus faecalis strain CM4A. Biotechnology for Biofules, 8: e69 (2015).
BOOKCHAPTERS
(15) Shinzato, N. and Y. Kamagata : The methanogenic and archaeal endosymbionts in free-living anaeroibic ciliates. In: Endosymbiotic methanogenic archaea (Edited by J.H.P. Hackstein). Springer Verlag. pp. 37-53 (2018).
(14) Narihiro, T. and Y. Kamagata : Anaerobic cultivation. In: Manual of Environmental Microbiology 4th edition (Edited by Marylynn Yates). American Society of Microbiology. 2-1-2 12pp (2016).
(13) Katayama, T. and Y. Kamagata : Cultivation of Methanogens. In:Hydrocarbon and Lipid Microbiology Protocol. Springer, Heiderberg. 177-195 (2015).
(12) Y. Kamagata : Syntrophy in Anaerobic Digestion. Anaerobic Biotechnology: In: Environmental Protection and Resource Recovery (Edited by H.H.P. Fang and T. Zhang). Published ahead of printing (2015). (11) Kimura, N. W. Kitagawa and Y. Kamagata : Biodegradation of nitrophenol compounds. In: Biological Remediation of Explosive Residues (Edited by S.N. Singh). Springer International. pp. 43-57 (2014).
(10) Kitagawa, W. and Y. Kamagata : Diversity of 2,4-Dichorophenoxyacetic Acid (2,4-D)-Degradative Genes and Degrading Bacteria. In: Biodegradative Bacteria (Edited by H. Nojiri et al). Springer Verlag. pp. 43-57 (2013).
(9) Shinzato, N. and Y. Kamagata : The methanogenic and archaeal endosymbionts of Trimyema In: Endosymbiotic methanogenic archaea (Edited by J.H.P. Hackstein). Springer Verlag. (2010).
(8) Okabe, S. and Y. Kamagata : Wastewater treatment. In: Environmental Molecular Biology (Edited by W-T, Liu and Jansson J.K.). Caiser Academic Press. chapter 10 (2009).
(7) Y. Kamagata, Y. Sekiguchi, and S. Hanada : Gemmatimonadetes phylum nov. In: Bergey's manual of systematic bacteriology (Edited by Garrity G.). Springer-Verlag. (2009).
(6) Y. Kamagata : Genus Oscillospira Chatton and Perard 1913, 1159AL In: Bergey's manual of systematic bacteriology volume 3, (Edited by Garrity G.). Springer-Verlag. (2009).
(5) Y. Kamagata : Genus Thermoacetogenium Hattori, Kamagata, Hanada, and Shoun 2000. In: Bergey's manual of systematic bacteriology volume 3, (Edited by Garrity G.). Springer-Verlag. (2009).
(4) Sekiguchi, Y., and Y. Kamagata : Microbial community structure and functions in methane fermentation technology for wastewater treatment. In: Strict and facultative anaerobes: medical and environmental aspects., (Ed. by Zuber, P. and Nakano, M. M.). Horizon Scientific Press, Norfolk, UK. 361-384 (2004).
(3) Nakatsu, C.H., R. Fulthorpe, W.E. Holben, Y. Kamagata, O.V. Maltseva, V.G. Matheson, C. McGowan, Y. Suwa, J.M. Tiedje, E.M. Top, A.D. Wright, and L.J. Forney : Genetic diversity of 2,4-D catabolic genes. In Microbial diversity and genetics of biodegradation. (eds. Horikoshi, K., Fukuda, M., and Kudo, T). Japan Scientific Societies Press, Tokyo, 197-206 (1997).
(2) Tiedje, J.M., R. Fulthorpe, Y. Kamagata, C.McGowan, A. Rhodes, H. Takami : What is the global pattern of chloroaromatic degrading microbial populations. In Microbial diversity and genetics of biodegradation. (eds. Horikoshi, K., Fukuda, M., and Kudo, T). Japan Scientific Societies Press, Tokyo, 65-74 (1997).
(1) Hausinger, R.P., F. Fukumori, D.A. Hogan, T.W. Sasanella, Y. Kamagata, H. Takami, and R.E. Wallace : Biochemistry of 2,4-D degradation : Evolutionary implications. In Microbial diversity and genetics of biodegradation (eds. Horikoshi, K., Fukuda, M., and Kudo, T). Japan Scientific Societies Press, Tokyo, 35-51 (1997).
PROCEEDINGS
(13) Sekiguchi, Y., S. Hanada, and Y. Kamagata : Cultivation of yet-to-be cultured microorganisms from wastewater treatment processes. Innovative roles of Biological Resource Centers: Proceedings of the 10th International Congress for Culture Collections. ed. by Watanabe, M., Suzuki, K., and Seki, T. 107-111 (2004).
(12) Y. Kamagata : Cultivation of uncultured fastidious microbes. Innovative roles of Biological Resource Centers: Proceedings of the 10th International Congress for Culture Collections. ed. by Watanabe, M., Suzuki, K., and Seki, T. 103-106 (2004).
(11) Kimura, N. and Y. Kamagata : Microbial degradation of chlorinated dibenzo-p-dioxin by a gram-positive bacterium, Rhodococcus opacus SAO101. Organohalogen compounds. 58, 153-156 (2002).
(10) Sekiguchi, Y., Y. Kamagata, A. Ohashi, and H. Harada : Molecular and conventional analyses of microbial diversity in mesophilic and thermophilic upflow anaerobic sludge blanket granular sludges. 9th World congress on anaerobic digestion, 261-266 (2001).
(9) Y. Kamagata : Microbial community analysis of anaerobic ecosystem - significance and importance of anaerobes. Proceedings of 2001 KSAM International symposium on new horizons in microbiology and biotechnology. 24-29 (2001).
(8) Kanagawa, T., Y. Kamagata, K. Yamada, and T. Kohno : Phylogenetic analysis of type 021N strains isolated from bulking sludges. In Microbial Community and Functions in Wastewater Treatment Processes, the International Symposium of the COE, Center for Excellence, Project on Establishment and Evaluation of Advanced Water Treatment Technology Systems Using Functions of Complex Microbial Community, 75-93 (1998).
(7) Nakamura, K., M. Kawaharasaki, S. Hanada, Y. Kamagata, and T. Kanagawa : Characterization of bacterial community constructing anaerobic/aerobic activated sludge by in situ identification and cloning of 16S rDNAs. In Microbial Community and Functions in Wastewater Treatment Processes, the International Symposium of the COE, Center for Excellence, Project on Establishment and Evaluation of Advanced Water Treatment Technology Systems Using Functions of Complex Microbial Community, 75-93 (1998).
(6) Shinjoh, H., A. Miya, K. Onda, Y. Kamagata, M. Kawaharasaki, and K. Nakamura : Some properties of polyphosphate glucokinase in a polyphosphate-accumulating bacterium NM-1. IAWQ, 1993 (1994).
(5) Matsuda, K., K. Nakamura, Y. Kamagata, and E. Mikami : Isolation and characterization of an anaerobic bacterium degrading 4-chlorobutyrate. Microbiology and Biochemistry of Strict Anaerobes Involved in Interspecies Hydrogen Transfer (ed. by J-P. Belaich et al.), Plenum Press, New York, 203-212 (1990).
(4) Tasaki, M., Y. Kamagata, K. Nakamura, and E. Mikami : Isolation of propionate-using sulfate-reducing bacterium. Microbiology and Biochemistry of Strict Anaerobes Involved in Interspecies Hydrogen Transfer (ed. by J-P. Belaich et al.), Plenum Press, New York, 477-479 (1990).
(3) Y. Kamagata and E. Mikami : Diversity of acetotrophic methanogens in anaerobic digestion. Recent Advances in Microbial Ecology (ed. by T. Hattori et al.), Japan Scientific Societies Press, Tokyo, 459-464 (1989).
(2) Y. Kamagata, H. Sasaki, and S. Takao : Fractionation of extracellular cellulase produced by Penicillium purpurogenum and purification of b-glucosidase. Microbial Utilization of Renewable Resources, 4, 124-133 (1985).
(1) Sasaki, H., Y. Kamagata, S. Takao, P. Matangkasombut, and A. Bhumiratuna : Selection and classification of active cellulose-decomposing fungi. Microbial Utilization of Renewable Resources, 3, 65-76 (1983).
