Achievements

Microbial and Genetic Resources Research Group

Recent publications (Since 2005)

2023

  1. Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng KY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK: Identification and cultivation of anaerobic bacterial scavengers of dead cells, The ISME J, 17, pages 2279–2289 (2023), DOI:10.1038/s41396-023-01538-2.
  2. Kuroda K, Tomita S, Kurashita H, Hatamoto M, Yamaguchi T, Hori T, Aoyagi T, Sato Y, Inaba T, Habe H, Tamaki H, Hagihara Y, Tamura T, Narihiro T: Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems, Water Res. X, 100196 (2023), DOI:10.1016/j.wroa.2023.100196.
  3. Suda K, Sakamoto S, Iguchi A, Tamaki H: Novel quantitative method for individual isotopomer of organic acids from 13C tracer experiments determines carbon flow in acetogenesis, Talanta 257, 124328 (2023), DOI:10.1016/j.talanta.2023.124328.
  4. Nishioka T, Morinaga K, Tamaki H: Complete Genome Sequence of Dyella sp. Strain GSA-30, a Predominant Endophytic Bacterium of Dendrobium Plants, Microbiol. Resour. Announc. 12: e01338-22 (2023), DOI:10.1128/mra.01338-22.
  5. Nishioka T, Morinaga K, Tamaki H: Complete Genome Sequence of Flavobacterium sp. Strain GSB-24, Isolated from inside Dendrobium Roots, Microbiol. Resour. Announc. 12: e01343-22 (2023), DOI:10.1128/mra.01343-22.
  6. Okazaki Y, Nguyen TT, Nishihara A, Endo H, Ogata H, Nakano S, Tamaki H: A Fast and Easy Method to Co-extract DNA and RNA from an Environmental Microbial Sample, Microbes Environ., 38: ME22102 (2023), DOI:10.1264/jsme2.ME22102.
  7. Ishizawa H, Kaji Y, Shimizu Y, Kuroda M, Inoue D, Makino A, Nakai R, Tamaki H, Morikawa M, Ike M: Spontaneous Cell Lysis by Pelomonas saccharophila MRB3 Provides Plant-Available Macronutrients in Hydroponic Growth Media and Accelerates Biomass Production of Duckweed, Journal of Water and Environment Technology, 21: 49-58 (2023), DOI:10.2965/jwet.22-054.
  8. Nobu MK, Nakai R, Tamazawa S, Mori H, Toyoda A, Ijiri A, Suzuki S, Kurokawa K, Kamagata Y, Tamaki H: Unique H2-utilizing lithotrophy in serpentinite-hosted systems, ISME J. 17, 95-104 (2023), DOI:10.1038/s41396-022-01197-9.

2022

  1. Nishioka T and Tamaki H: Improved Cultivation and Isolation of Diverse Endophytic Bacteria Inhabiting Dendrobium Roots by Using Simply Modified Agar Media, Microbiology Spectrum 10, e02238-22 (2022), DOI:10.1128/spectrum.02238-22.
  2. Morinaga K, Kusada H, Sakamoto S, Murakami T, Toyoda A, Mori H, Meng XY, Takashino M, Murotomi K, Tamaki H: Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae, Int. J. Syst. Evol. Microbiol.,72: 005596 (2022), DOI:10.1099/ijsem.0.005596.
  3. Morinaga K, Kusada H, Tamaki H: Bile salt hydrolases with extended substrate specificity confer a high level of resistance to bile toxicity on atopobiaceae bacteria, International Journal of Molecular Sciences 23 (18), 10980 (2022), DOI:10.3390/ijms231810980.
  4. Okazaki Y, Nakano S, Toyoda A, Tamaki H: Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes, mSystems 7, e00433-22 (2022), DOI:10.1128/msystems.00433-22.
  5. Makino A, Nakai R, Yoneda Y, Toyama T, Tanaka Y, Meng XY, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H: Isolation of Aquatic Plant Growth-Promoting Bacteria for the Floating Plant Duckweed (Lemna minor), Microorganisms, 10: 1564 (2022), DOI:10.3390/microorganisms10081564.
  6. Imai T, Inoue R, Nishida A, Yokota Y, Morishima S, Kawahara M, Kusada H, Tamaki H, Andoh A: Features of the gut prokaryotic virome of Japanese patients with Crohn’s disease, J. Gastroenterology, 57: 559-570 (2022), DOI:10.1007/s00535-022-01882-8.
  7. Kusada H, Arita M, Tohno M, Tamaki H: Bile salt hydrolase degrades β-lactam antibiotics and confers antibiotic resistance on Lactobacillus paragasseri, Frontiers in Microbiology, 13: 858263 (2022), DOI:10.3389/fmicb.2022.858263.
  8. Suda K, Aze T, Miyairi Y, Yokoyama Y, Matsui Y, Ueda H, Saito T, Sato T, Sawaki Y, Nakai R, Tamaki H, Takahashi H, Morikawa N, Ono S: The origin of methane in serpentinite-hosted hyperalkaline hot spring at Hakuba Happo, Japan: Radiocarbon, methane isotopologue and noble gas isotope approaches, Earth and Planetary Science Letters 585: 117510 (2022), DOI:10.1016/j.epsl.2022.117510.
  9. Yamamoto K, Yoneda Y, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H: Complete Genome Sequence of Luteitalea sp. Strain TBR-22, Microbiol. Resour. Announc. 11: e00455-21 (2022), DOI:10.1128/mra.00455-21.
  10. Kusada H, Arita M, Tohno M, Tamaki H: Isolation of a highly thermostable bile salt hydrolase with broad substrate specificity from Lactobacillus paragasseri, Frontiers in Microbiology, 13: 810872 (2022), DOI:10.3389/fmicb.2022.810872.
  11. Yamamoto K, Yoneda Y, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H: Draft Genome Sequence of Bryobacteraceae Strain F-183, Microbiol. Resour. Announc. 11: e00453-21 (2022), DOI:10.1128/mra.00453-21.
  12. Tomita S, Kusada H, Kojima N, Ishihara S, Miyazaki K, Tamaki H, Kurita R: Polymer-based chemical-nose systems for optical-pattern recognition of gut microbiota, Chemical Science, 13: 5830-5837 (2022), DOI:10.1039/D2SC00510G.

2021

  1. Hashimoto T, Hashimoto J, Kagaya N, Nishimura T, Suenaga H, Nishiyama M, Kuzuyama T, Shin-ya K:A novel oxazole-containing tetraene compound, JBIR-159, produced by heterologous expression of the cryptic trans-AT type polyketide synthase biosynthetic gene cluster, J. Antibiot., 74, 354–358 (2021), DOI:10.1038/s41429-021-00410-9.
  2. Julia M. Kurth, Nobu MK, Tamaki H, Jong ND, Berger Jetten SM, Yamamoto K, Mayumi D, Sakata S, Bai L, Cheng L, Nielsen JL, Kamagata Y, Wagner T, Welte CU: Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds, The ISME J.,15: 3549-3565 (2021), DOI:10.1038/s41396-021-01025-6.
  3. Saini MK, Yoshida S, Sebastian A, Hara E, Tamaki H, Soulier NT, Albert I, Hanada S, Tank M, Bryant DA: Elioraea tepida, sp. nov., a Moderately Thermophilic Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Mat Community of an Alkaline Siliceous Hot Spring in Yellowstone National Park, WY, USA, Microorganisms, 10: 80 (2021), DOI:10.3390/microorganisms10010080.
  4. Okazaki Y, Fujinag S, Salcher MM, Callieri C, Tanaka A, Kohzu A, Oyagi H, Tamaki H, Nakano S: Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing, Microbiome 9: 1-15 (2021), DOI:10.1186/s40168-020-00974-y.
  5. Morinaga K, Kusada H, Watanabe M, Tamaki H: Complete Genome Sequence of Lactobacillus helveticus JCM 1004, an Aminopeptidase-Producing Lactic Acid Bacterium, Microbiol. Resour. Announc. 10: e00641-21 (2021), DOI:10.1128/MRA.00641-21.
  6. Nakai R, Kusada H, Sassa F, Morigasaki A, Hayashi H, Takaya N, Tamaki H: Draft Genome Sequence of Novel Filterable Rhodospirillales Bacterium Strain TMPK1, Isolated from Soil, Microbiol. Resour. Announc. 10: Microbiol. Resour. Announc. 10: e00393-21 (2021), DOI:10.1128/MRA.00393-21.
  7. Nakai R, Naganuma T, Tazato N, Kunihiro T, Morohoshi S, Koide T, Kusada H, Tamaki H, Narihiro T: Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales), Diversity, 13: 422 (2021), DOI:10.3390/d13090422.
  8. Watanabe Y, Takeuchi N, Yang J, Obana N, Morinaga K, Kusada H, Tamaki H, Fukuda S, Arakawa K: Complete Genome Sequence of Atopobiaceae Bacterium Strain P1, Isolated from Mouse Feces, Microbiol. Resour. Announc. 10: e00627-21 (2021), DOI:10.1128/MRA.00627-21.
  9. Yoneda Y, Yamamoto K, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H: Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds, Microorganisms 9(6), 1133 (2021), DOI:10.3390/microorganisms9061133.
  10. Kusada H, Morinaga K, Tamaki H: Identification of Bile Salt Hydrolase and Bile Salt Resistance in a Probiotic Bacterium Lactobacillus gasseri JCM1131T, Microorganisms 9(5), 1011 (2021), DOI:10.3390/microorganisms9051011.
  11. Morinaga K, Kusada H, Watanabe M, Tamaki H: Complete Genome Sequence of Anaerostipes caccae Strain L1-92T, a Butyrate-Producing Bacterium Isolated from Human Feces, Microbiol. Resour. Announc. 10(16), e00056-21 (2021), DOI:10.1128/MRA.00056-21.
  12. Yamamoto K, Kusada H, Kamagata Y, Tamaki H: Parallel Evolution of Enhanced Biofilm Formation and Phage-Resistance in Pseudomonas aeruginosa during Adaptation Process in Spatially Heterogeneous Environments, Microorganisms 9 (3), 569 (2021), DOI:10.3390/microorganisms9030569.
  13. Iwashita T, Tanaka Y, Tamaki H, Nakai R, Yoneda Y, Makino A, Toyama T, Kamagata Y, Morikawa M, Mori K: Isolation and Characterization of Novel Plant Growth-Promoting Bacteria from the Fronds of Duckweed, Jpn. J. Water Treat. Biol., 57: 1-9 (2021), https://www.jstage.jst.go.jp/article/jswtb/57/1/57_1/_pdf.
  14. Suda K, Ikarashi M, Tamaki H, Tamazawa S, Sakata S, Maeda H, Kamagata Y, Kaneko M, Ujiie T, Shinotsuka Y, Wakayama T, Iwama H, Osaka N, Mayumi D, Yonebayashi H: Methanogenic crude oil degradation induced by an exogenous microbial community and nutrient injections, J. Pet. Sci. Eng.,201: 108458 (2021), DOI:10.1016/j.petrol.2021.108458.
  15. Ueno A, Tamazawa S, Tamamura S, Murakami T, Kiyama T, Inomata H, Amano Y, Miyakawa K, Tamaki H, Naganuma T, Kaneko K: Desulfovibrio subterraneus sp. nov. , a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation, Int. J. Syst. Evol. Microbiol., 71: 004683 (2021), DOI:10.1099/ijsem.0.004683.
  16. Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N, Kamagata Y, Tamaki H: Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes, Syst Appl Microiol, 44: 126154 (2021), DOI:10.1016/j.syapm.2020.126154.
  17. Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, Kohzu A, Oyagi H, Tamaki H, Nakano S: Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing, Microbiome, 9: 569 (2021), DOI:10.1186/s40168-020-00974-y.

2020

  1. Ueoka R, Hashimoto J, Kozone I, Hashimoto T, Kudo K, Kagaya N, Suenaga H, Ikeda H, Shin-ya K: A novel methymycin analog, 12-ketomethymycin N-oxide, produced by the heterologous expression of the large pikromycin/methymycin biosynthetic gene cluster of Streptomyces sp. AM4900, Biosci. Biotechnol. Biochem., 85 (4), 890-894 (2021), DOI:10.1093/bbb/zbaa111.
  2. Hashimoto T, Kozone I, Hashimoto J, Suenaga H, Fujie M, Satoh N, Ikeda H, Shin-ya K: Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin, J. Antibiot., 73, 650-654 (2020), DOI:10.1038/s41429-020-0319-0.
  3. Kudo K, Hashimoto T, Hashimoto J, Kozone I, Kagaya N, Ueoka R, Nishimura T, Komatsu M, Suenaga H, Ikeda H, Shin-ya K: In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives, Nat. Commun., 11, 4022 (2020), DOI:10.1038/s41467-020-17769-2.
  4. Saeki N, Eguchi Y, Kintaka R, Makanae K, Shichino Y, Iwasaki S, Kanno M, Kimura N, Moriya H: N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae, Sci. Rep., 10, 9500 (2020). DOI:10.1038/s41598-020-66307-z.
  5. Katayama T, Nobu MK, Kusada H, Meng XY, Hosogi N, Uematsu K, Yoshioka H, Kamagata Y, Tamaki H: Isolation of Atribacteria reveals a unique cell membrane structure, Nature Communications, 11: 1-9 (2020), DOI:10.1038/s41467-020-20149-5.
  6. Kato S, Takashino M, Igarashi K, Mochimaru H, Mayumi D, Tamaki H: An iron corrosion-assisted H2-supplying system: A culture method for methanogens and acetogens under low H2 pressures, Sci Rep, 10: 1-9 (2020), DOI:10.1038/s41598-020-76267-z.
  7. Iwashita T, Tanaka Y, Tamaki H, Yoneda Y, Makino A, Tateno Y, Li Y, Toyama T, Kamagata Y, Mori K: Comparative Analysis of microbial communities in fronds and roots of three duckweed species: Spirodela polyrhiza, Lemna minor, and Lemna aequinoctialis, Microbes Environ., 35: ME20081 (2020), DOI=10.1264/jsme2.ME20081.
  8. Ellegaard K, Suenami S, Miyazaki R, Engel P: Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species. Curr Biol. 30, 2520-2531.e7(2020), DOI=10.1016/j.cub.2020.04.070.
  9. Koto A, Nobu MK, Miyazaki R: Deep sequencing uncovers caste-associated diversity of symbionts in the social ant Camponotus japonicus. mBio. 11: (2020), DOI=10.1128/mBio.00408-20.
  10. Preiner M, Igarashi K, Muchowska KB, Yu M, Varma SJ, Kleinermanns K, Nobu MK, Kamagata Y, Tuysuz H, Moran J, Martin WF: A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism. Nat Ecol Evol. 4: 534-542 (2020), DOI=10.1038/s41559-020-1125-6.
  11. Liu M, Nobu MK, Ren J, Jin X, Hong G, Yao H: Bacterial compositions in inhalable particulate matters from indoor and outdoor wastewater treatment processes. J Hazard Mater. 385: 121515 (2020), DOI=10.1016/j.jhazmat.2019.121515.
  12. Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K: Isolation of an archaeon at the prokaryote-eukaryote interface. Nature. 577: 519-52>5 (2020), DOI=10.1038/s41586-019-1916-6.
  13. Gou M, Wang H, Li J, Sun Z, Nie Y, Nobu MK, Tang Y: Different inhibitory mechanisms of chlortetracycline and enrofloxacin on mesophilic anaerobic degradation of propionate. Environ Sci Pollut Res Int. 27: 1406-1416 (2020), DOI=10.1007/s11356-019-06705-7.
  14. Li J, Wang HZ, Yi Y, Gou M, Nobu MK, Chen YT, Tang YQ: Response of Isovalerate-Degrading Methanogenic Microbial Community to Inhibitors. Applied biochemistry and biotechnology. (2020), DOI=10.1007/s12010-020-03234-9.
  15. Mei R, Nobu MK, Liu WT: Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. Environ Microbiol Rep. 12: 173-184 (2020), DOI=10.1111/1758-2229.12821.
  16. Wang HZ, Li J, Yi Y, Nobu MK, Narihiro T, Tang YQ: Response to inhibitory conditions of acetate-degrading methanogenic microbial community. J Biosci Bioeng. 129: 476-485 (2020), DOI=10.1016/j.jbiosc.2019.10.006.
  17. Iwano H, Hatohara S, Tagawa T, Tamaki H, Li YY, Kubota K: Effect of treated sewage characteristics on duckweed biomass production and microbial communities, Water Science and Technology, wst2020168 (2020), DOI=10.2166/wst.2020.168.
  18. Hirose S, Tank M, Hara E, Tamaki H, Mori K, Takaichi S, Haruta S, Hanada S: Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria, Int. J. Syst. Evol. Microbiol., 70: 596-603 (2020), DOI=10.1099/ijsem.0.003798.
  19. Hashimoto T, Kozone I, Hashimoto J, Ueoka R, Kagaya N, Fujie M, Sato N, Ikeda H, Shin-ya K: Novel macrolactam compound produced by the heterologous expression of a large cryptic biosynthetic gene cluster of Streptomyces rochei IFO12908, J. Antibiot., 73, 171-174 (2020), DOI:10.1038/s41429-019-0265-x.

2019

  1. Habe H, Koike H, Sato Y, Iimura Y, Hori T, Kanno M, Kimura N, Kirimura K: Identification and characterization of levulinyl-CoA synthetase from Pseudomonas citronellolis, which differs phylogenetically from LvaE of Pseudomonas putida, AMB Express, 9:127 (2019), DOI=10.1186/s13568-019-0853-y.
  2. Suenami S, Nobu MK, Miyazaki R: Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima. Sci Rep., 9: 9830 (2019), DOI=10.1038/s41598-019-46388-1.
  3. 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, PLoS Genet., 15:e1008445 (2019), DOI=10.1371/journal.pgen.1008445.
  4. Wang HZ, Lv XM, Yi Y, Zheng D, Gou M, Nie Y, Hu B, Nobu MK, Narihiro T, Tang YQ: Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats, Sci. Rep., 9:17396 (2019), DOI=10.1038/s41598-019-53849-0.
  5. Yamamoto K, Hackley KC, Kelly WR, Panno SV, Sekiguchi Y, Sanford RA, Liu WT, Kamagata Y, Tamaki H: Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States, Sci. Rep., 9:13484 (2019), DOI=10.1038/s41598-019-49996-z.
  6. Zheng D, Wang HZ, Gou M, Nobu MK, Narihiro T, Hu B, Nie Y, Tang YQ: Identification of novel potential acetate-oxidizing bacteria in thermophilic methanogenic chemostats by DNA stable isotope probing, Appl. Microbiol. Biotechnol., 103:8631-8645 (2019), DOI=10.2323/jgam.2017.12.006.
  7. Ziels RM, Nobu MK, Sousa DZ: Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics, mSystems, 4: (2019), DOI=10.1128/mSystems.00159-19.
  8. Chen SC, Weng CY, Lai MC, Tamaki H, Narihiro T: Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus, Mar Genomics, 47:100673 (2019), DOI:10.1016/j.margen.2019.03.008.
  9. Kakizawa S.: A Multiplex-PCR Method for Diagnosis of AY-Group Phytoplasmas. In: Musetti R, Pagliari L, editors. Phytoplasmas: Methods and Protocols, New York, NY: Springer New York; 143-9, (2019), DOI:10.1007/978-1-4939-8837-2_11.
  10. Kusada H, Zhang Y, Tamaki H, Kimura N, Kamagata Y: Novel N-Acyl Homoserine Lactone-Degrading Bacteria Isolated From Penicillin-Contaminated Environments and Their Quorum-Quenching Activities, Front. Microbiol., 10:455 (2019), DOI:10.3389/fmicb.2019.00455.
  11. Leng L, Nobu MK, Narihiro T, Yang P, Amy Tan GY, Lee PH: Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: pathways and mechanisms, Water Res., 148:281-291 (2019), DOI:10.1016/j.watres.2018.10.063.
  12. Nakahara N, Nobu MK, Takaki Y, Miyazaki M, Tasumi E, Sakai S, Ogasawara M, Yoshida N, Tamaki H, et al.: Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi, Int J Syst Evol Microbiol., 69(4):1185-94 (2019), DOI:10.1099/ijsem.0.003291.
  13. Narihiro T, Nobu MK, Hori T, Aoyagi T, Sato Y, Inaba T, et al.: Effects of the Wastewater Flow Rate on Interactions between the Genus Nitrosomonas and Diverse Populations in an Activated Sludge Microbiome, Microbes Environ., 34(1):89-94 (2019), DOI:10.1264/jsme2.ME18108.
  14. Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, et al.: Microbial basis of Fusarium wilt suppression by Allium cultivation, Sci Rep., 9(1):1715 (2019), DOI:10.1038/s41598-018-37559-7.
  15. Sun H, Narihiro T, Ma X, Zhang XX, Ren H, Ye L: Diverse aromatic-degrading bacteria present in a highly enriched autotrophic nitrifying sludge, Sci. Total Environ., 666:245-251 (2019), DOI:10.1016/j.scitotenv.2019.02.172.
  16. Tamaki, H: Cultivation renaissance in the post-metagenomics era: combining the new and old, Microbes Environ. 34:117-120 (2019), DOI:10.1264/jsme2.ME3402rh.
  17. Ueno A, Tamazawa S, Tamamura S, Aramaki N, Badrul AKMA, Murakami T, Yamaguchi S, Yamagishi J, Tamaki H, Mayumi D, Naganuma T, Kaneko K: Improvement of terrestrial groundwater sampling method affects microbial community analysis, Geomicrobiol. J., 36:303-316 (2019), DOI:10.1080/01490451.2018.1534900.

2018

  1. Harada J, Yamada T, Giri S, Hamada M, Nobu MK, Narihiro T, Tsuji 1H, Daimon H: Draft Genome Sequence of Moorella sp. Strain Hama-1, a Novel Acetogenic Bacterium Isolated from a Thermophilic Digestion Reactor, Genome Announc., 6(24) (2018), DOI:10.1128/genomeA.00517-18.
  2. Hidalgo-Ahumada CAP, Nobu MK, Narihiro T, Tamaki H, Liu WT, Kamagata Y, Stams AJM, Imachi H, Sousa DZ: Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism, Environ. Microbiol., 20(12):4503-11 (2018), DOI:10.1111/1462-2920.14388.
  3. Kato S, Yamagishi A, Daimon S, Kawasaki K, Tamaki H, Kitagawa W, Abe A, Tanaka M, Sone T, Asano K, Kamagata Y: Isolation of Previously Uncultured Slow-Growing Bacteria by Using a Simple Modification in the Preparation of Agar Media, Appl. Environ. Microbiol., 84(19) (2018), DOI:10.1128/AEM.00807-18.
  4. Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, Gonzalez-Gonzalez L, Broto A, Querol E, Senar ML, Lambea CP, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, Hutchison CA, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y: Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells. ACS Synth. Biol., 7(6):1538-52 (2018), DOI:10.1021/acssynbio.8b00028.
  5. Mei R, Nobu MK, Narihiro T, Yu J, Sathyagal A, Willman E, Liu WT: Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Res., 147:403-12 (2018), DOI:10.1016/j.watres.2018.10.026.
  6. 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. Sci Rep. 8(1):5550 (2018), DOI:10.1038/s41598-018-23858-6.
  7. Narihiro T, Nobu MK, Bocher BTW, Mei R, Liu WT: Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environ Microbiol Rep. 10(6):673-85 (2018), DOI:10.1111/1758-2229.12689.
  8. Takeshita K, Tamaki H, Ohbayashi T, Meng XY, Sone T, Mitani Y, Peeters C, Kikuchi Y, Vandamme P: Burkholderia insecticola sp. nov., a gut symbiotic bacterium of the bean bug Riptortus pedestris. Int. J. Syst. Evol. Microbiol., 68(7):2370-4 (2018), DOI:10.1099/ijsem.0.002848.
  9. Tanaka Y, Tamaki H, Tanaka K, Tozawa E, Matsuzawa H, Toyama T, Kamagata Y, Mori K.: “Duckweed-Microbe Co-Cultivation Method” for Isolating a Wide Variety of Microbes Including Taxonomically Novel Microbes, Microbes Environ., 33(4):402-6 (2018), DOI:10.1264/jsme2.ME18067.

2017

  1. Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR: The hidden life of integrative and conjugative elements. FEMS Microbiol Rev. 41:512-537 (2017).
  2. Habe H, Kondo S, Sato Y, Hori T, Kanno M, Kimura N, Koike H, Kirimura K: Electrodialytic separation of levulinic acid catalytically synthesized from woody biomass for use in microbial conversion. Biotechnology progress. 33:448-453 (2017).
  3. Mei R, Nobu MK, Narihiro T, Kuroda K, Muñoz Sierra J, Wu Z, Ye L, Lee PKH, Lee PH, van Lier JB, McInerney MJ, Kamagata Y, Liu WT: Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Res. 124:77-84 (2017).
  4. Nobu MK, Narihiro T, Liu M, Kuroda K, Mei R, Liu WT: Thermodynamically diverse syntrophic aromatic compound catabolism. Environ. Microbiol. 18: 2495-2506 (2017).
  5. Okamoto T, Aino K, Narihiro T, Matsuyama H, Yumoto I: Analysis of microbiota involved in the aged natural fermentation of indigo. World J. Microbiol. Biotechnol. 33:70 (2017).
  6. Narihiro T, Kamagata Y: Genomics and metagenomics in microbial ecology: recent advances and challenges. Microbes Environ. 32:1-4 (2017).
  7. Browne P, Tamaki H, Kyrpides N, Woyke T, Goodwin L, Imachi H, Brauer S, Yavitt J, Liu WT, Zinder SH and Cadillo-Quiroz H: Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments, The ISME J, 11: 87-99 (2017)
  8. Kusada H, Tamaki H, Kamagata Y, Hanada S, Kimura N: A Novel Quorum-Quenching N-Acylhomoserine Lactone Acylase from Acidovorax sp. Strain MR-S7 Mediates Antibiotic Resistance, Appl. Environ. Microbiol. 83: e00080-17 (2017)
  9. Tanaka Y, Matsuzawa H, Tamaki H, Tagawa M, Toyama T, Kamagata Y, Mori K: Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method, Microbes Environ., 32: 288-292 (2017)
  10. Tamazawa S, Mayumi D, Mochimaru H, Sakata S, Maeda H, Wakayama T, Ikarashi M, Kamagata Y, Tamaki H: Petrothermobacter organivorans gen. nov., sp. nov., a novel thermophilic, strictly anaerobic bacterium of the phylum Deferribacteres isolated from a deep subsurface oil reservoir, Int. J. Syst. Evol. Microbiol., 67: 3982-3986 (2017)
  11. Kusada H, Kameyama K, Meng XY, Kamagata Y, Tamaki H: Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with the occurrence of type 2 diabetes in mice, Sci Rep. 7(1):18087 (2017)
  12. Suenaga H, Yamazoe A, Hosoyama A, Shimodaira J, Kimura K, Hirose J, Watanabe T, Fujihara H, Futagami T, Goto M, and Furukawa K: Complete genome sequence of the polychlorinated biphenyl-degrading bacterium Pseudomonas putida KF715 (NBRC 110667) isolated from biphenyl-contaminated soil, Genome announcement, 5: e01624-16 (2017)
  13. Tsujimoto Y, Saito R, Sahara T, Kimura N, Tsuruoka N, Shigeri Y, Watanabe K: Draft genome sequence of Caenibacillus caldisaponilyticus B157T, a thermophilic and phospholipase-producing bacterium isolated from acidulocompost, Genome announcement, 5: e00089-17 (2017)

2016

  1. Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT: Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microbes Environ. 31:288-292 (2016).
  2. Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Liu WT: Draft Genome sequence of Syntrophomonas wolfei subsp. methylbutyratica strain 4J5T (JCM 14075), a mesophilic butyrate- and 2-methylbutyrate-degrading syntroph. Genome Announc. 4: pii: e00047-16 (2016).
  3. Narihiro T, Kusada H, Yoneda Y, Tamaki H: Draft genome sequences of Methanoculleus horonobensis strain JCM 15517, Methanoculleus thermophilus strain DSM 2373, and Methanofollis ethanolicus strain JCM 15103, hydrogenotrophic methanogens belonging to the family Methanomicrobiaceae. Genome Announc. 4: pii: e00199-16 (2016).
  4. Narihiro T, Kanosue Y, Hiraishi A: Cultural, transcriptomic, and proteomic analyses of water-stressed cells of actinobacterial strains isolated from compost: Ecological implications in the fed-batch composting process. Microbes Environ. 31:127-136 (2016).
  5. Kamagata Y, Narihiro T: Symbiosis studies in microbial ecology. Microbes Environ. 31: 201-203 (2016).
  6. Narihiro T: Microbes in the water infrastructure: underpinning our society. Microbes Environ. 31:89-92 (2016).
  7. Mei R, Narihiro T, Nobu MK, Liu WT: Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate. Lett. Appl. Microbiol. 63: 356-362. (2016).
  8. Nobu MK, Narihiro T, Kuroda K, Mei R, Liu WT: Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J. 10:2478-87 (2016).
  9. Mei R, Narihiro T, Nobu MK, Kuroda K, Liu WT: Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Sci Rep. 6:34090 (2016).
  10. Kuroda K, Nobu MK, Mei R, Narihiro T, Bocher BT, Yamaguchi T, Liu WT: A single-granule-level approach reveals ecological heterogeneity in an upflow anaerobic sludge blanket reactor. PLoS One 11: e0167788 (2016).
  11. Shinzato N, Aoyama H, Saitoh S, Nikoh N, Nakano K, Shimoji M, Shinzato M, Satou K, Teruya K, Hirano T, Yamada T, Nobu MK, Tamaki H, Shirai Y, Park S, Narihiro T, Liu WT, Kamagata Y: Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum. Genome Announc. 4: pii: e01032-16 (2016).
  12. Kanno M, Constant P, Tamaki H, Kamagata Y: Detection and isolation of plant‐associated bacteria scavenging atmospheric molecular hydrogen. Environmental Microbiology. 18: 2495-2506 (2016).
  13. Sato Y, Koike H, Kondo S, Hori T, Kanno M, Kimura N, Morita T, Kirimura K, Habe H: Draft genome sequence of Burkholderia stabilis LA20W, a trehalose producer that uses levulinic acid as a substrate. Genome Announc. 4(4) e00795-16 (2016).
  14. Mayumi D, Mochimaru H, Tamaki H(co-1st author), Yamamoto K, Yoshioka H, Suzuki Y, Kamagata Y and Sakata S: Methane production from coal by a single methanogen, Science, 354:222-225 (2016).
  15. Tamazawa S, Yamamoto K, Takasaki K, Mitani Y, Hanada S, Kamagata Y, Tamaki H: In situ gene expression responsible for sulfide oxidation and CO2 fixation of an uncultured large sausage-shaped Aquificae bacterium in a sulfidic hot spring, Microbes Environ. 31: 194-198 (2016).
  16. Sun L, Toyonaga M, Ohashi A, Matsuura N, Tourlousse DM, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y: Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi, Int. J. Syst. Evol. Microbiol., 66: 988-996 (2016).
  17. Sun L, Toyonaga M, Ohashi A, Tourlousse DM, Matsuura N, Tourlousse DM, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y: Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov., Int. J. Syst. Evol. Microbiol., 66: 2635-2642 (2016).
  18. Mochimaru H, Tamaki H, Katayama T, Imachi H, Sakata S, Kamagata Y: Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field, Int. J. Syst. Evol. Microbiol., 66: 1-5 (2016)
  19. Kimura N, Kamagata Y: A thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach. Microbes Environ. , in press
  20. Tsujimoto Y, Saito R, Furuya H, Ishihara D, Sahara T, Kimura N, Nishino T, Tsuruoka N, Shigeri Y, Watanabe K: Caenibacillus caldisaponilyticus gen. nov., sp. nov., a thermophilic, spore-forming and phospholipid-degrading bacterium isolated from acidulocompost. Int. J. Syst. Evol. Microbiol., 66: 2684-90 (2016).
  21. Matsuzawa T, Kimura N, Suenaga H, Yaoi K: Screening, identification, and characterization of α-xylosidase from a soil metagenome. J. Biosci. Bioeng., 122: 393-9 (2016).
  22. Guangwei H, W., Takahashi S, Liu H, Saito T, Kimura N: Characterization of soil bacterial diversity in relation to irrigation water: a case study in China. J. Water Resource Protection, 8: 1090-1102 (2016).
  23. Habe H, Kondo S, Sato Y, Hori T, Kanno M, Kimura N, Kirimura K, and Koike H: Electrodialytic separation of levulinic acid catalytically synthesized from woody biomass for the use of microbial conversion. Biotechnology Progress, in press
  24. Watanabe T, Fujihara H, Hirose J, Suenaga H, Kimura N: Use of biphenyl/polychlorinated biphenyl-degrading bacteria for the production of useful aromatic compounds, Sustainable Humanosphere 12: 5 (2016).
  25. Sato Y, Koike H, Kondo S, Hori T, Kanno M, Kimura N, Morita T, Kirimura K, Habe H: Draft genome sequence of Burkholderia stabilis LA20W, a trehalose producer that uses levulinic acid as a substrate. Genome Announc. 4(4) e00795-16 (2016).

2015

  1. Kanno M, Tamaki H, Mitani Y, Kimura N, Hanada S, Kamagata Y: pH-Induced change in cell susceptibility to butanol in a high butanol-tolerant bacterium, Enterococcus faecalis strain CM4A. Biotechnology for Biofuels. 8, 69-74 (2015).
  2. Mao D, Graham DW, Tamaki H, Zhang T: Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants, Scientific Reports 5: 11857 (2015).
  3. Fujiwara H, Yamazoe A, Hosoyama A, Suenaga H, Kimura N, Hirose J, Watanabe T, Futagami T, Goto M, Furukawa K: Draft genome sequence of Pseudomonas aeruginosa KF702 (NBRC110665), a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil. Genome Announcements, 3 (3) e00517-15　(2015).
  4. Fujiwara H, Yamazoe A, Hosoyama A, Suenaga H, Kimura N, Hirose J, Watanabe T, Futagami T, Goto M, Furukawa K: Draft genome sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil. Genome Announcements, 3 (3) e00517-15 (2015).
  5. Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y: Isolation of microorganisms involved in reduction of crystalline iron (III) oxides in natural environments. Frontiers in Microbiol, 6: e368 (2015).
  6. Puspita ID, Kitagawa W, Kamagata Y, Tanaka M, Nakatsu CH: Increase in bacterial colony formation from a erpmafrost ice wedge dosed with a Tomitella biformata recombinant resuscitation-promoting factor protein. Microb Environ published ahead of printing in Apr (2015).
  7. Katayama T, Yoshioka H, Muramoto Y, Usami J, Fujiwara K, Yoshida S, Kamagata Y, Sakata S: Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. ISME J. 9: 436-446 (2015).
  8. Kato S, Yumoto I, Kamagata Y: Isolation of acetogenic bacteria that induce biocorrrosion by utilizing metallic irons as the sole electron donor. Appl Environ Microbiol, 81: 67-73 (2015).
  9. 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. Environ Microbiol. 17: 91-104 (2015). This article was selected in “Faculty of 1000”(http://f1000.com/prime/718378367).
  10. 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 W, 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. Front Microbiol. 6:101 (2015).
  11. Suenaga H, Yamazoe A, Hosoyama A, Kimura N, Hirose J, Watanabe T, Fujihara H, Futagami T, Goto M, and Furukawa K: Draft genome sequence of the polychlorinated biphenyl-degrading bacterium Pseudomonas putida KF703 (NBRC 110666) isolated from biphenyl-contaminated soil. Genome Announcements, 3 (2) e00142-15 (2015).
  12. Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT: Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. doi: 10.1038/ismej.2014.256 (2015).
  13. Suenaga H, Yamazoe A, Hosoyama A, Kimura N, Hirose J, Watanabe T, Fujihara H, Futagami T, Goto M, and Furukawa K: Draft genome sequence of the polychlorinated biphenyl-degrading bacterium Cupriavidus bacilensis KF708 (NBRC 110671). Genome Announcements, 3 (2) e00143-15 (2015).
  14. Narihiro T, Kim NK, Mei R, Nobu MK, Liu WT: Microbial community analysis of anaerobic reactors treating soft drink wastewater. PLOS ONE,10.1371/journal.pone.0119131 (2015)
  15. Kimura N, Yamazoe A, Hosoyama A, Hirose J, Watanabe T, Suenaga H, Fujihara H, Futagami T, Goto M, and Furukawa K: Draft genome sequence of Pseudomonas abietaniphila KF717 (NBRC 110669) isolated from biphenyl-contaminated soil in Japan. Genome Announcements, 3 (2) e00059-15 (2015).
  16. Takeuchi M, Yamagishi T, Kamagata Y, Oshima K, Hattori M, Katayama T, Hanada S, Tamaki H, Marumo K, Maeda H, Nedachi M, Iwasaki W, Suwa Y, Sakata S: Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions, Int. J. Syst. Evol. Microbiol., in press (2015)
  17. Kanno M, Katayama T, Morita N, Tamaki H, Hanada S, Kamagata Y: 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).
  18. Watanabe T, Yamazoe A, Hosoyama A, Fujihara H, Suenaga H, Hirose J, Futagami T, Goto M, Kimura N, and Furukawa K: Draft genome sequence of Pseudomonas toyotomiensis KF710, a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil, Genome Announcements, 3 (2) e00223-15 (2015)
  19. Watanabe T, Yamazoe A, Hosoyama A, Fujihara H, Suenaga H, Hirose J, Futagami T, Goto M, Kimura N, and Furukawa K: Draft genome sequence of Cupriavidus pauculus strain KF709, a biphenyl-utilizing bacterium isolated from biphenyl-contaminated soil, Genome Announcements, 3 (2) e00222-15 (2015).
  20. Kakizawa S, and Yoneda Y: The role of genome sequencing in phytoplasma research. Phytopathogenic Mollicutes, 5 (1):19-24 (2015).

2014

  1. Yasutake Y, Kusada H, Ebuchi T, Hanada S, Kamagata Y, Kimura N: Structural studies of β-lactam antibiotic degrading enzyme, MacQ, Photon Factory Activity Report, #31 (2014).
  2. Mori K, Kamagata Y: The challenges for studying the anaerobic world. Microb Environ 29: 335 (2014).
  3. Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y: The effects of elevated CO2 concentration on compettitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. Frontiers in Microbiol, 5 : e575 (2014).
  4. Itoh H, Aita M, Nagayama A, Meng XY, Kamagata Y, Navarro R, Hori T, Ohgiya S, Kikuchi Y: Evidence of environmental and vertical transmission of Burkholderia symbionts in the oriental chinch bug, Cavelerius saccharivorus (Heteroptera: Blissidae). Appl Environ Microbiol, 80: 5974-5983 (2014).
  5. Qiu YL, Hanada S, Kamagata Y, Guo RB, Sekiguchi Y: Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes. Int J Syst Evol Microbiol, 64: 2137-2145 (2014).
  6. Katayama T, Yoshioka H, Mochimaru H, Meng XY, Muramoto Y, Usami J, Ikeda H, Kamagata Y, Sakata S: Methanohalophilus levihalophilus sp. nov., a slightly halophilic, methylotrophic methanogen isolated from natural gas-bearing deep aquifers, and an emended description of the genus Methanohalophilus. Int J Syst Evol Microbiol, 64: 2089-2093 (2014).
  7. Suzuki S, Kuenen JG, Schipper K, van der Velde S, Ishii S, Wu A, Sorokin DY, Tenney A, Meng XY, Morrill PL, Kamagata Y, Muyzer G, Nealson KH: Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site. Nature Commun, 5: e4900 (2014).
  8. Kugo T, Kitagawa W, Shimomura Y, Yamagishi T, Tanaka M, Sone T, Asano K, Kamagata Y: Draft genome sequence of a methanol Utilizer Methylophilus sp. strain OH31, isolated from a pond sediment in Hokkaido, Japan. Genome Announcements 2: e-00274-14 (2014).
  9. Kato S, Sasaki K, Watanabe K, Yumoto I, Kamagata Y: Physiological and transcriptomic analyses of a thermophilic, aceticlastic methanogen Methanosaeta thermophila responding to ammonia stress. Microb Environ, 29: 162-167 (2014).
  10. Funo K, Kitagawa W, Tanaka M, Sone T, Asano K, Kamagata Y: Draft genome sequence of Tomitella biformata AHU 1821T, isolated from a permafrost ice wedge in Alaska. Genome Announcements 2: e-00066-14 (2014).
  11. Sahara T, Fujimori K, Nezuo M, Tsukahara M, Tochigi Y, Ohgiya S, Kamagata Y: Draft genome sequence of Saccharomyces cerevisiae IR-2, a useful industrial strain for highly efficient production of bioethanol. Genome Announcements. 2: e01160-13 (2014).
  12. Sahara T, Fujimori K, Nezuo M, Tsukahara M, Tochigi Y, Ohgiya S, Tang YQ, Kida K, Taguchi H, Akamatsu T, Kamagata Y: Draft genome sequence of Saccharomyces cerevisiae NAM34-4C, a lactic acid-assimilating industrial yeast strain. Genome Announcements 2: e-01145-13 (2014).
  13. 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. J Bacteriol. 196: 3971-3979 (2014)
  14. 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. PLoS Genet. 10: e1004441 (2014)
  15. Narihiro T, Nobu MK (equally contributed 1st author), Kim NK, Kamagata Y, Liu WT: The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey. Environ Microbiol. 2014 Sep 4. doi: 10.1111/1462-2920.12616 (2014)
  16. Narihiro T, Suzuki A (equally contributed 1st author), Yoshimune K, Hori T, Hoshino T, Yumoto I, Yokota A, Kimura N, Kamagata Y: Combining functional metagenomics and oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by cultivation-based method. Microbes Environ. 29(2):154-161 (2014)
  17. Narihiro T, Tamaki H, Akiba A, Takasaki K, Nakano K, Kamagata Y, Hanada S, Maji T: Microbial community structure of relict niter-beds previously used for saltpeter production. PLOS ONE. 9(8):e104752 (2014)
  18. Wang H, Narihiro T (equally contributed 1st author), Straub AP, Pugh CR, Tamaki H, Moor JF, Bradley IM, Kamagata Y, Liu WT, Nguyen TH.: MS2 bacteriophage reduction and microbial communities in biosand filters. Environ Sci Technol. 48(12):6702-6709 (2014)
  19. Kusada H, Hanada S, Kamagata Y, Kimura N.: The effects of N-acylhomoserine lactones, β-lactam antibiotics and adenosine on biofilm formation in the multi-β-lactam antibiotic-resistant bacterium Acidovorax sp. strain MR-S7. J Biosci Bioeng, 118 (1) 14-19 (2014).
  20. Takeuchi M, Katayama T, Yamagishi T, Hanada S, Tamaki H, Kamagata Y, Ohshima K, Hattori M, Marumo K, Nedachi M, Maeda H, Suwa Y, Sakata S: Methyloceanibacter caenitepidi gen. nov., sp. nov., a novel facultatively methylotrophic bacterium isolated from marine sediments near the hydrothermal vent area, Int. J. Syst. Evol. Microbiol., 64: 462-468 (2014).
  21. Nobu MK, Narihiro T (equally contributed 1st author), Tamaki H, Qiu YL, Sekiguchi Y, Woyke T, Goodwin L, Davenport KW, Kamagata Y, Liu WT: The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol, doi: 10.1111/1462-2920.12444 (2014)
  22. Nobu MK, Narihiro T, Tamaki H, Qiu YL, Sekiguchi Y, Woyke T, Lynne G, Davenport KW, Kamagata Y, Liu WT: Draft genome sequence of Syntrophorhabdus aromaticivorans strain UI, a mesophilic aromatic compound-degrading syntroph, Genome Announcements, 6;2(1). pii: e01064-13 (2014).
  23. Hanada S, Tamaki H, Nakamura K, Kamagata Y: Crenotalea thermophila gen. and sp. nov. isolated from a Japanese hot spring, Int. J. Syst. Evol. Microbiol., 64: 1359-1364 (2014).
  24. Teramoto K, Tamura T, Hanada S, Sato T, Kawasaki H, Suzuki K, Sato H: Simple and rapid characterization of mycolic acids from Dietzia strains by using MALDI spiral-TOFMS with ultra high mass-resolving power. J Antibiot, in press.
  25. Kosaka T, Toh H, Fujiyama A, Sakaki Y, Watanabe K, Meng X-Y, Hanada S, Toyoda A: Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2. Environmental Microbiology Reports, in press.
  26. Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann I, Flynn T, Sanford R, Krapac IG, Locke RA, Hong P, Tamaki H, Liu WT, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Mackie R, Fouke BW: Halomonas sulfidaeris-dominated Communities Inhabit 1.8km-deep Saline Sandstone Reservoirs, Environmental Microbiology, 16: 1695-1708 (2014).
  27. Katayama　T, Kanno　M, Morita　N, Hori　T, Narihiro　T, Mitani　Y, Kamagata Y： An oleaginous bacterium that intrinsically accumulates long-chain free fatty acids in its cytoplasm. Appl. Environ. Microbiol. 80, 1126-1131 (2014).
  28. Yamamoto K, Tamaki H, Cadillo-Quiroz H, Imachi H, Kyrpides N, Woyke T, Goodwin L, Zinder SH, Kamagata Y and Liu WT: Complete genome sequence of Methanoregula formicica SMSPT, a mesophilic hydrogenotrophic methanogen isolated from a methanogenic upflow anaerobic sludge blanket reactor, Genome Announcements, 2: e00870-14 (2014)
  29. Yamamoto K, Tamaki H, Cadillo-Quiroz H, Imachi H, Kyrpides N, Woyke T, Goodwin L, Zinder SH, Kamagata Y and Liu WT: Complete genome sequence of Methanolinea tarda NOBI-1T, a hydrogenotrophic methanogen isolated from methanogenic digester sludge, Genome Announcements, 2: e00876-14 (2014)
  30. Yamada K, Okuno Y, Tamaki H, Hanada S: Granulicella cerasi sp. nov., an acidophilic bacterium isolated from cherry bark, Int. J. Syst. Evol. Microbiol. 64: 2781-2785 (2014)
  31. Takeuchi M, Kamagata Y, Oshima K, Hanada S, Tamaki H, Marumo K, Maeda H, Nedachi M, Hattori M, Iwasaki W, Sakata S: Methylocaldum marinum sp. nov., a novel thermotolerant methane oxidizing bacterium isolated from marine sediments, Int. J. Syst. Evol. Microbiol. 64: 3240-3246 (2014)
  32. Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka M, Nakatsu CH, Kamagata Y: A hidden pitfall in agar media preparation undermines cultivability of microorganisms, Appl. Environ. Microbiol., 80: 7659-7666 (2014)
  33. Kakizawa S, Makino A, Ishii Y, Tamaki H, Kamagata Y: Draft genome sequence of “Candidatus Phytoplasma asteris” strain OY-V, an unculturable plant pathogenic bacterium. Genome Announcements, 2(5): e00944-14 (2014)

2013

  1. Miura T, Kusada H, Kamagata Y, Hanada S, Kimura N: Genome Sequence of the Multiple-Β-Lactam-Antibiotic-Resistant Bacterium Acidovorax sp. Strain MR-S7. Genome Anouncements, 1, e00412-13 (2013).
  2. Narihiro T, and Kamagata Y: Cultivating yet-to-be cultivated microbes: the challenge continues. Microbes Environ., 28: 163-165 (2013).
  3. Kanno M, Katayama T, Tamaki H, Mitani Y, Meng X-Y, Hori T, Narihiro T, Morita N, Hoshino T, Yumoto I, Kimura N, Hanada S, Kamagata Y: Isolation of butanol- and isobutanol-tolerant bacteria and physiological characterization of their butanol tolerance. Appl. Environ. Microbiol., 79, 6998-7005 (2013).
  4. Kakizawa S, Kamagata Y: A multiplex-PCR method for strain identification and detailed phylogenetic analysis of AY-group phytoplasmas. Plant Disease, 98:299-305 (2014)
  5. Inoue K, Miyazaki R, Ohtsubo Y, Nagata Y and Tsuda M: Inhibitory effect of Pseudomonas putida nitrogen-related phosphotransferase system on conjugative transfer of IncP-9 plasmid from Escherichia coli. FEMS Microbiol. Lett. 345: 102-109 (2013).
  6. Reinhard F, Miyazaki R (equally contributed 1st author),, Pradervand N and van der Meer JR: Cell Differentiation to ”Mating Bodies” Induced by an Integrating and Conjugative Element in Free-Living Bacteria. Curr. Biol., 23, 255-259 (2013).
  7. Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H, Nakamura K, Takamizawa K and Kamagata Y: Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic thermophilic methanogen isolated from gas-associated formation water of a natural gas field in Japan. Int. J. Syst. Evol. Microbiol., 63, 715-722 (2013).
  8. Qiu YL, Muramatsu M, Hanada S, Kamagata Y, Guo RB and Sekiguchi Y: Oligosphaera ethanolica gen. nov., sp. nov., an anaerobic, carbohydrate-fermenting bacterium isolated from methanogenic sludge, and description of the Oligosphaeria classis nov. in the bacterial phylum Lentisphaerae. Int. J. Syst. Evol. Microbiol., 63, 533-539 (2013).
  9. Li, H., Zhang Y, Yang M and Kamagata Y: Effects of hydraulic retention time on nitrification activities and population dynamics of a conventional activated sludge system. Frontiers Environ. Sci. Eng.,7, 43-48 (2013).
  10. Puspita I, Uehara M, Katayama T, Kitagawa W, Kamagata Y, Asano K, Nakatsu CH and Tanaka M: Resuscitation promoting factor (Rpf) from Tomitella biformata AHU 1821T promotes growth and resuscitates non-dividing cells. Microb. Environ., 28, 58-64 (2013).
  11. Takasaki K, Miura T, Kanno M, Tamaki H, Hanada S, Kamagata Y, Kimura N: Discovery of Glycoside Hydrolase Enzymes from an Avicel-Adapted Forest Soil Eukaryotic Community Revealed by a Metatranscriptomic Approach, PLoS One, 8, e55485 (2013)
  12. Katoh H, Tamaki H, Tokutake Y, Hanada S, Chohnan S: Identification of pantoate kinase and phosphopantothenate synthetase from Methanospirillum hungatei, J. Bioscience Bioengineering, 115, 372-376 (2013)
  13. Li H, Zhang Y, Yang M, Kamagata Y: Effects of hydraulic retention time on nitrification activities and population dynamics of a conventional activated sludge system. Frontiers of Environmental Science & Engineering, 7, 43-48 (2013)
  14. Miyazaki R and van der Meer JR: A New Large DNA Fragment Delivery System Based on Integrase Activity from an Integrative and Conjugative Element. Appl. Environ. Microbiol., 79:4440-4447 (2013).
  15. Sentchilo V, Mayer AP, Guy L, Miyazaki R, Green Tringe S, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M and van der Meer JR: Community-wide plasmid gene mobilization and selection. ISME J. 7:1173-1186 (2013).
  16. Mitani Y, Futahashi R, Niwa K, Ohba N and Ohmiya Y: Cloning and characterization of luciferase from a Fijian luminous click beetle. Photochemistry and Photobiology, DOI: 10.1111/php.12097, 89: 1163-1169 (2013).
  17. Mayumi D, Dolfing J, Sakata S, Maeda H, Miyagawa Y, Ikarashi M, Tamaki H, Takeuchi M, Nakatsu CH, Kamagata Y: Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoir, Nature Communications, 4:1998, doi: 10.1038 ncomms2998 (2013).
  18. Ishii Y, Kakizawa S, Oshima K: New ex vivo reporter assay system reveals that sigma factors of an unculturable pathogen control gene regulation involved in the host switching between insects and plants. Microbiologyopen 2(4):553-65 (2013)
  19. Ishii Y, Matsuura Y, Kakizawa S, Nikoh N, Fukatsu T: Diversity of bacterial endosymbionts associated with Macrosteles leafhoppers vectoring phytopathogenic phytoplasmas. Appl Environ Microbiol 79:5013-22 (2013)
  20. Iino T, Tamaki H, Tamazawa S, Ueno Y, Ohkuma M, Suzuki K, Igarashi Y, Haruta S: Enrichment of a novel methanogen belonging to the class Thermoplasmata from the anaerobic digested sludge, Microbes and Environ.,28: 244-250 (2013) .

2012

  1. Miyazaki R, Minoia M, Pradervand N, Sulser S, Reinhard F and van der Meer JR: Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element. PLoS Genetics, 8, e1002818 (2012).
  2. Watanabe T, Tagawa M, Tamaki H, Kanno M and Kamagata Y: Primary simple assays of cellulose-degrading fungi. Mycoscience, 53, 45-48 (2012).
  3. Tamaki H, Zhang R, Angly EF, Nakamura S, Hong P, Yasunaga T, Kamagata Y and Liu WT: Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate. Environ. Microbiol., 14, 441-452 (2012).
  4. Fujita MJ, Kimura N, Yokose H and Otsuka M: Heterologous production of bisucaberin using a biosynthetic gene cluster cloned from a deep sea metagenome. Mol. Biosyst., 8, 482-485 (2012).
  5. Narihiro T, Terada T, Ohashi A, Kamagata Y, Nakamura K and Sekiguchi Y: Quantitative detection of previously characterized syntrophic bacteria in anaerobic wastewater treatment systems by sequence-specific rRNA cleavage method. Water Res., 46, 2167-2175 (2012).
  6. Matsuura Y, Kikuchi Y, Hosokawa T, Koga R, Meng X-Y, Kamagata Y, Nikoh N and Fukatsu T: Evolution of symbiotic organs and endosymbionts in lygaeid stinkbugs. The ISME J., 6, 397-409 (2012).
  7. Mori K, Iino T, Suzuki K-I, Yamaguchi K and Kamagata Y: Aceticlastic and NaCl-requiring methanogen “Methanosaeta pelagic” sp. nov., isolated from marine tidal flat sediment. Appl. Environ. Microbiol., 78, 3416-3423 (2012).
  8. Tanaka Y, Tamaki H (equally contributed 1st author), Matsuzawa H, Nigaya M, Mori K and Kamagata Y: Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10. Microbes Environ., 27, 149-157 (2012).
  9. Puspita ID, Kamagata Y, Tanaka M, Asano K and Nakatsu CH: Are uncultivated bacteria really uncultivable? Microb. Environ., in press (2012).
  10. Kawakoshi A, Nakazawa H, Fukada J, Sasagawa M, Katano Y, Nakamura S, Hosoyama A, Sasaki H, Hanada S, Kamagata Y, Nakamura K, Yamazaki S and Fujita N: Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus. DNA Research, DNA Research, 19, 383-394 (2012).
  11. Kagawa Y, Mitani Y, Yun HY, Nakashima N, Tamura N and Tamura T: Identification of methanol-inducible promoter from Rhodococcus erythropolis PR4 and its use as an expression vector. J. Biosci. Bioeng., 113, 596-603 (2012).
  12. Nasuno E, Kimura N, Fujita MJ, Nakatsu CH, Kamagata Y and Hanada S: Phylogenetically novel LuxI/LuxR-type quorum sensing systems isolated using a metagenomic approach. Appl. Environ. Microbiol., Appl. Environ. Microbiol., 78, 8067-8074 (2012).
  13. Tamazawa S, Takasaki K, Tamaki H, Kamagata Y, Hanada S: Metagenomic and Biochemical Characterizations of Sulfur Oxidation Metabolism in Uncultured Large Sausage-Shaped Bacterium in Hot Spring Microbial Mats, PLoS One, 7, e40794 (2012)
  14. Matsui, T., Semba, H. and Hanada, S.: Citricoccus yambaruensis sp nov., a racemic phenylsuccinate stereospecifically assimilating actinomycete isolated from soil in Okinawa. J. Gen. Appl. Microbiol. 58, 373-378 (2012).

2011

  1. Miyazaki R and van der Meer JR: A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13. Mol. Microbiol., 79, 743-758 (2011).
  2. Miyazaki R and van der Meer JR: How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element? Mob. Genet. Elements, 1, 82-84 (2011).
  3. Elsaied H, Stokes H W, Kitamura K, Kurusu Y, Kamagata Y and Maruyama A: Marine integrons containing novel integrase genes, attachment sites, attI, and associated gene cassettes in polluted sediments from Suez and Tokyo Bays. The ISME J., 5, 1162-1177 (2011).
  4. Mayumi D, Mochimaru H, Yoshioka H, Sakata S, Maeda H, Miyagawa Y, Ikarashi M, Takeuchi M and Kamagata Y: Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environ. Microbiol., 13, 1995-2006 (2011).
  5. Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng X-Y, Hanada S, Mori K and Kamagata Y: Armatimonas rosea gen. nov., sp. nov., a Gram-negative, aerobic, chemoheterotrophic bacterium of a novel bacterial phylum, Armatimonadetes phyl. nov., formerly called the candidate phylum OP10. Int. J. Syst. Evol. Microbiol., 61, 1442-1447 (2011).
  6. Takeuchi M, Yoshioka H, Seo Y, Tanabe S, Tamaki H, Kamagata Y, Takahashi HA, Igari S, Mayumi D and Sakata M: A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan, Environmental Microbiology 13, 3206-3218 (2011).
  7. Yamada T, Kikuchi K, Yamauchi T, Shiraishi K, Ito T, Okabe S, Hiraishi A, Ohashi A, Harada H, Kamagata Y, Nakamura K and Sekiguchi Y: Ecophysiology of uncultured filamentous anaerobes belonging to the phylum KSB3 as causative agents of bulking in methanogenic granular sludge. Appl. Environ. Microbiol., 77, 2081-2087 (2011).
  8. Takeuchi M, Kawabe Y, Watanabe E, Oiwa T, Takahashi M, Nanba K, Kamagata Y, Hanada S, Ohko Y and Komai T: Comparative study of microbial dechlorination of chlorinated ethenes in an aquifer and a clayey aquitard. J. Contaminant Hydrology, 124, 14-24 (2011).
  9. Narihiro T, Hori T, Nagata O, Hoshino T, Yumoto I and Kamagata Y: The Impact of aridification and vegetation type on changes in the community structure of methane-cycling microorganisms in Japanese wetland soils. Biosci. Biotechnol. Biochem., 75, 1727-1734 (2011).
  10. Nakamura K, Tamaki H, Kang MS, Mochimaru H, Lee ST and Kamagata Y: A six well plate method: less laborious and effective method for cultivation of obligate anaerobic microorganisms, Microbes Environ. 26, 301-306 (2011).
  11. Kawanishi T, Shiraishi T, Okano Y, Sugawara K, Hashimoto M, Maejima K, Komatsu K, Kakizawa S, Yamaji Y, Hamamoto H, Oshima K and Namba S: New detection systems of bacteria using highly selective media designed by SMART: selective medium-design algorithm restricted by two constraints. PLoS One, 6, e16512 (2011).
  12. Nakamura H, Narihiro T, Tsuruoka N, Mochimaru H, Matsumoto R, Tanabe Y, Hagiya K, Ikeba K, Maruyama A and Hanada S: Evaluation of the aflatoxin biosynthetic genes for identification of the Aspergillus section Flavi. Microbes Environ., 26, 367-369 (2011).
  13. Oshima K, Ishii Y, Kakizawa S, Sugawara K, Neriya Y, Himeno M, Minato N, Miura C, Shiraishi T, Yamaji Y and Namba S: Dramatic transcriptional changes in an intracellular parasite enable host switching between plant and insect. PLoS One, 6, e23242 (2011).
  14. Enoki M, Shinzato N, Sato H, Nakamura K and Kamagata Y: Comparative proteomic analysis of Methanothermobacter themautotrophicus ΔH in pure culture and in co-culture with a butyrate-oxidizing bacterium. PLoS ONE, 6, e24309 (2011).
  15. Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y & Liu WT: Analysis of 16S rRNA amplicon sequencing options on the Roche/454 Next-Generation Titanium Sequencing platform, PLoS One 6, e25263 (2011).
  16. Himeno M, Neriya Y, Minato N, Miura C, Sugawara K, Ishii Y, Yamaji Y, Kakizawa S, Oshima K and Namba S: Unique morphological changes in plant pathogenic phytoplasma-infected petunia flowers are related to transcriptional regulation of floral homeotic genes in an organ-specific manner. Plant J., 67, 971-979 (2011).
  17. Neriya Y, Sugawara K, Maejima K, Hashimoto M, Komatsu K, Minato N, Miura C, Kakizawa S, Yamaji Y, Oshima K and Namba S: Cloning, expression analysis, and sequence diversity of genes encoding two different immunodominant membrane proteins in poinsettia branch-inducing phytoplasma (PoiBI). FEMS Microbiol Lett 324, 38-47 (2011).
  18. Mitrovic J, Kakizawa S, Duduk B, Oshima K, Namba S and Bertaccini A: The groEL gene as an additional marker for finer differentiation of ‘Candidatus Phytoplasma asteris’-related strains. Ann Appl Biol., 159, 41-48 (2011).
  19. Fujita MJ, Kimura N, Sakai A, Ichikawa Y, Hanyu T, Otsuka M: Cloning and heterologous expression of the vibrioferrin biosynthetic gene cluster from a marine metagenomic library. Biosci Biotechnol Biochem., 75, 2283-7 (2011).
  20. Kaiwa N, Hosokawa T, Kikuchi Y, Nikoh N, Meng XY, Kimura N, Ito M and Fukatsu T: Bacterial symbionts of the giant jewel stinkbug Eucorysses grandis (Hemiptera: Scutelleridae). Zoolog Sci., 28, 169-174 (2011).
  21. Mori K, Suzuki K, Urabe T, Sugihara M, Tanaka K, Hamada M and Hanada S: Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing bacterium of class Gammaproteobacteria isolated from the hydrothermal field in Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order of Chromatiales. Int J Syst Evol Microbiol., 61, 2412-2418 (2011).

2010

  1. Tagawa M, Tamaki H, Manome A, Koyama O and Kamagata Y: Isolation and characterization of antagonistic fungi against potato scab pathogens from potato field soils. FEMS Microbiol. Lett., 305, 136-142 (2010).
  2. Uyeno Y, Sekiguchi Y, Tajima K, Takenaka A, Kurihara M and Kamagata Y: An rRNA-based analysis for evaluating the effect of heat stress on the rumen microbial composition of Holstein heifers. Anaerobe, 16, 27-33 (2010).
  3. Gu X, Zhang Y, Zhang J, Yang M, Tamaki H, Kamagata Y and Li D: Isolation of phylogenetically diversenonylphenol ethoxylate-degrading bacteria and characterization of their corresponding biotransformation pathways. Chemosphere, 80, 216-222 (2010).
  4. Toju H, Hosokawa T, Koga R, Nikoh N, Meng XY, Kimura N and Fukatsu T: “Candidatus Curculioniphilus buchneri,” a novel clade of bacterial endocellular symbionts from weevils of the genus Curculio. Appl. Environ. Microbiol. 76, 275-82 (2010).
  5. Kouzuma A, Meng XY, Kimura N, Hashimoto K and Watanabe K: Disruption of the putative cell-surface polysaccharide biosynthesis gene SO3177 in Shewanella oneidensis MR-1 enhances the adhesiveness to electrodes and current generation in microbial fuel cells. Appl. Environ. Microbiol., 76, 4151-7 (2010).
  6. Kaiwa N, Hosokawa T, Kikuchi Y, Nikoh N, Meng XY, Kimura N, Ito M and Fukatsu T: Primary gut symbiont and secondary, Sodalis-allied symbiont of the Scutellerid stinkbug Cantao ocellatus. Appl. Environ. Microbiol., 76, 3486-94 (2010).
  7. Kimura N, Sakai K and Nakamura K: Isolation and characterization of a 4-nitrotoluene-oxidizing enzyme from activated sludge by a metagenomic approach. Microb. Environ., 25, 133-139 (2010).
  8. Kimura H, Mori K, Nashimoto H, Hanada S and Kato K: In situ biomass production of hot spring sulfur-turf microbial mat. Microbes Environ., 25, 140-143 (2010).
  9. Miyamoto-Shinohara Y, Nozawa F, Sukenobe J and Imaizumi T: Survival of yeasts stored after freeze-drying or liquid-drying. J. Gen. Appl. Microbiol., 56, 107-119 (2010).
  10. Takagi M, Tamaki H, Miyamoto Y, Leonardi R, Hanada S, Jackowski S and Chohnan S: Pantothenate kinase from thermoacidophilic archaeon Picrophilus torridus. J Bacteriol., 192, 233-241 (2010).
  11. Kimura H, Mori K, Tashiro T, Kato K, Yamanaka T, Ishibashi J and Hanada S: Culture-independent estimation of optimal and maximum growth temperatures of archaea in subsurface habitats based on the G+C content in 16S rRNA gene sequences. Geomicrobiology J., 27, 114-122 (2010).
  12. Naraoka H, Uehara T, Hanada S and Kakegawa T: δ13C-δD distribution of lipid biomarkers in a bacterial mat from a hot spring in Miyagi Prefecture, NE Japan. Organic Geochemistry, 41, 398-403 (2010).
  13. Aino K, Narihiro T, Minamida K, Kamagata Y, Yoshimune K and Yumoto I: Bacterial community characterization and dynamics of indigo fermentation. FEMS Microbiol. Ecol., 74, 174-183 (2010).
  14. Tamaki H, Matsuoka T, Yoshioka I, Imamura S, Hanada S, Kamagata Y, Nakamura K and Sakasegawa S: A novel multi-copper oxidase with urate oxidase activity from Lysobacter sp. T-15: a new member of the multi-copper oxidase family. J. Biochem., 148, 481-489 (2010).
  15. Matsuzawa H, Tanaka Y, Tamaki H, Kamagata Y and Mori K: Culture-dependent and independent analyses of the microbial communities inhabiting the giant duckweed (Spirodela polyrrhiza) rhizoplane and isolation of a variety of rarely cultivated organisms within the phylum Verrucomicrobia. Microb. Environ., 25, 302-308 (2010).
  16. Uyeno Y, Sekiguchi Y and Kamagata Y: rRNA-based analysis to monitor succession of faecal bacterial communities in Holstein calves. Lett. Appl. Microbiol., 51, 570-577 (2010).
  17. Miyaji T, Murayama S, Kouzuma Y, Kimura N, Kanostoc MR, KKramerd KKJ and Yonekura M: Molecular Cloning of A Multidomain Cysteine Protease and Protease Inhibitor Precursor Gene from the Tobacco Hornworm (Manduca sexta) and Functional Expression of the Cathepsin F-like Cysteine Protease Domain. Insect Biochemistry and Molecular Biology, 40, 835-846 (2010).
  18. Narihiro T, Kaiya S, Futamata H and Hiraishi A: Removal of polychlorinated dioxins by semi-aerobic fed-batch composting with biostimulation of “Dehalococcoides”. J. Biosci. Bioeng., 109, 249-256 (2010).
  19. Takaichi S, Maoka T, Takasaki K and Hanada S: Carotenoids in the new phylum bacterium, Gemmatimonas aurantiaca: oscillol 2,2’-dirhamnoside, its synthesis, and its related genes. Microbiology, 156, 757-763 (2010).

2009

  1. Sentchilo V, Czechowska K, Pradervand N, Minoia M, Miyazaki R and van der Meer JR: Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. Mol. Microbiol., 72, 1293-1306 (2009).
  2. Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M and Miyazaki K: Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J., 3, 1335-1348 (2009).
  3. Mochimaru H, Tamaki H, Hanada S, Imachi H, Nakamura K, Sakata S and Kamagata Y: Methanolobus profundi sp. nov., a new methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. Int. J. Syst. Evol. Microbiol., 58, 714-718 (2009).
  4. Takeuchi M, Hanada S, Tamaki H, Tanabe S, Uchiyama M, Nakazawa T, Miyachi Y, Kamagata Y, Komai T and Kimura K: Bacterial and archaeal 16S rRNA genes in Late Pleistocene to Holocene muddy sediments from the Kanto Plain of Japan. Geomicrobiol. J., 26, 104-118 (2009).
  5. Kikuchi Y, Hosokawa T, Nikoh N, Meng X-Y, Kamagata Y and Fukatsu T: Host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs. BMC Biology, 7, 2 (2009).
  6. Narihiro T, Terada T, Ohashi A, Wu J-H, Liu W-T, Araki N, Kamagata Y, Nakamura K, and Sekiguchi Y: Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method. The ISME J., 3, 522-535 (2009).
  7. Narihiro T, Terada T, Kikuchi K, Iguchi A, Ikeda M, Yamaguchi T, Shiraishi K, Kamagata Y, Nakamura K and Sekiguchi Y: Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microb. Environ., 24, 88-96 (2009).
  8. Iguchi A, Terada T, Narihiro T, Yamaguchi T, Kamagata Y and Sekiguchi Y: In situ detection and quantification of uncultured members of the phylum Nitrospirae that reside in methanogenic wastewater treatment systems in abundance. Microb. Environ., 24, 97-104 (2009).
  9. Tamaki H, Hanada S, Sekiguchi Y, Tanaka Y and Kamagata Y: Effect of gelling agent on colony formation in solid cultivation of microbial community in lake sediment. Environ. Microbiol., 11, 1827-1834 (2009).
  10. Yamada K, Akimoto H, Ogawa Y, Kinumi T, Kamagata Y and Ohmiya Y: Upregulation of immunity-related GTPase (IRG) proteins by TNF-alpha in murine astrocytes. Biochem. Biophys. Res. Commun., 382, 434-439 (2009).
  11. Kimura N and Kamagata Y: Impact of dibenzofuran / dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations. Appl. Microbiol. Biotechnol., 84, 365-473 (2009).
  12. Sakai S, Imachi H, Sekiguchi Y, I-Cheng Tseng, Ohashi A, Harada H and Kamagata Y: Cultivation of methanogens under low hydrogen conditions by using the coculture method. Appl. Environ. Microbiol., 75, 4892-4896 (2009).
  13. Kormas KA, Tamaki H, Hanada S and Kamagata Y: Apparent richness and community composition of Bacteria and Archaea in geothermal springs. Aquat. Microb. Ecol., 57, 113-122 (2009).
  14. Matsui T, Shinzato N, Tamaki H, Muramatsu M and Hanada S: Shinella yambaruensis sp. nov., a 3-methyl sulfolane assimilating bacterium isolated from soil in Okinaw. Int. J. Syst. Evol. Microbiol., 59, 536-539 (2009).
  15. Takenawa T, Yokota A, Oda M, Takahashi H and Iwakura M: Protein oxidation during long storage: Identification of the oxidation sites in dihydrofolate reductase from Escherichia coli through LC-MS and fragment studies. J. Biochem., 145(4), 517-523 (2009).
  16. Tsukatani Y, Nakayama N, Shimada K, Mino H, Itoh S, Matsuura K, Hanada S and Nagashima KV: Characterization of a blue-copper protein, auracyanin, of the filamentous anoxygenic phototrophic bacterium Roseiflexus castenholzii. Arch. Biochem. Biophys., 490(1), 57-62 (2009).
  17. Kasuno M, Torimura M, Tsukatani Y, Murakami D, Hanada S, Matsushita T and Tao H: Characterization of the photoinduced electron transfer reaction from the photosynthetic system in Rhodobacter sphaeroides to an exogenous electron acceptor. J. Electroanal. Chem., 636, 101-106 (2009).
  18. Ohko Y, Nagao Y, Okano K, Sugiura N, Fukuda A, Yang Y, Negishi N, Takeuchi M and Hanada S: Prevention of phormidium tenue biofilm formation by TiO2 photocatalysis. Microb. Environ., 24(3), 241-245 (2009).
  19. Matsuura Y, Koga R, Nikoh N, Meng XY, Hanada S and Fukatsu T: Huge symbiotic organs in giant scale insects of the genus Drosicha (Coccoidea: Monophlebidae) harbor flavobacterial and enterobacterial endosymbionts. Zoolog Sci., 26(7), 448-56 (2009).
  20. Takaichi S, Maoka T, Takasaki K and Hanada S: Carotenoids in the new phylum bacterium, Gemmatimonas aurantiaca: oscillol 2,2′-dirhamnoside, its synthesis, and its related genes. Microbiology, Online (2009).
  21. Hoshi A, Oshima K, Kakizawa S, Ishii Y, Ozeki J, Hashimoto M, Komatsu K, Kagiwada S, Yamaji Y and Namba S: A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium. Proc Natl Acad Sci U S A 106, 6416-6421 (2009).
  22. Ishii Y, Kakizawa S, Hoshi A, Maejima K, Kagiwada S, Yamaji Y, Oshima K and Namba S: In the non-insect-transmissible line of onion yellows phytoplasma (OY-NIM), the plasmid-encoded transmembrane protein ORF3 lacks the major promoter region. Microbiology 155, 2058-2067 (2009).
  23. Ishii Y, Oshima K, Kakizawa S, Hoshi A, Maejima K, Kagiwada S, Yamaji Y and Namba S: Process of reductive evolution during 10 years in plasmids of a non-insect-transmissible phytoplasma. Gene 446, 51-57 (2009).
  24. Kakizawa S, Oshima K, Ishii Y, Hoshi A, Maejima K, Jung H Y, Yamaji Y and Namba S: Cloning of immunodominant membrane protein genes of phytoplasmas and their in planta expression. FEMS Microbiol Lett 293, 92-101 (2009).

2008

  1. Miyazaki R, Ohtsubo Y, Nagata Y and Tsuda M: Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer. J. Bacteriol., 190, 6281-6289 (2008).
  2. Fuchu G, Ohtsubo Y, Ito M, Miyazaki R, Ono A, Nagata Y and Tsuda M: Insertion sequence-based cassette PCR: cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA. Appl. Microbiol. Biotechnol., 79, 627-632 (2008).
  3. Imachi H, Sakai S, Sekiguchi Y, Hanada S, Kamagata Y, Ohashi A and Harada H: Methanolinea tarda gen. nov. sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int. J. Syst. Evol. Microbiol., 58, 294-301 (2008).
  4. Uyeno Y, Sekiguchi Y and Kamagata Y: Impact of consumption of probiotic lactobacilli-containing yogurt on microbial composition in human feces. Int. J. Food Microbiol., 122, 16-22 (2008).
  5. Zhang Y, Sei K, Toyama T, Ike M, Zhang J, Yang M and Kamagata Y: Changes of catabolic genes and microbial community structures during biodegradation of nonylphenol ethoxylates and nonylphenol in natural water microcosms. Biochem. Eng. J., 39, 288-296 (2008).
  6. Qiu YL, Hanada S, Ohashi A, Harada H Kamagata Y and Sekiguchi Y: Syntrophorhabdus aromatica gen. nov., sp. nov., the first cultured representative of Syntrophorhabdaceae fam. nov. in the class Deltaproteobacteria: an anaerobe capable of degrading phenol into acetate in syntrophic associations with a hydrogenotrophic methanogen. Appl. Environ. Microbiol., 74, 2051-2058 (2008).
  7. Sakai S, Imachi H, Hanada S, Ohashi A, Harada H and Kamagata Y: Methanocella paludicola gen. nov., sp. nov., a methane producing archaeon that is the first isolate of the lineage `Rice Cluster I’ , and proposal of the new archaeal order Methanocellales ord. nov. Int. J. Syst. Evol. Microbiol., 58, 929-936 (2008).
  8. Hu J, Shi J, Chang H, Li D, Yang M and Kamagata Y: Phenotyping and genotyping of antibiotic-resistance Escherichia coli isolated from Beijing River Basin, North China. Environ. Sci. Technol., 42, 3415-3420 (2008).
  9. Yoshioka H, Sakata S and Kamagata Y: Hydrogen isotope fractionation by Methanothermobacter thermautotrophicus in coculture and pure culture conditions. Geochim. Cosmochim. Acta, 72, 2687-2694 (2008).
  10. Xin G, Zhang Y, Zhang J, Yang M, Tamaki H and Kamagata Y: Degradation behaviors of nonylphenol ethoxylates by isolated bacteria using improved isolation method. J. Environ. Sci., 20, 1025-1028 (2008).
  11. Manome A, Kageyama A, Kurata S, Yokomaku T, Koyama O, Kanagawa T, Tamaki H, Tagawa M and Kamagata Y: Quantification of potato scab pathogens in soil by quantitative competitive PCR with fluorescent quenching-based probes. Plant Pathology, 57, 887-896 (2008).
  12. Shinzato N, Enoki M, Sato H, Nakamura K, Matsui T and Kamagata Y: Specific DNA binding of a potential transcriptional regulator, IMPDH-related protein VII, to the promoter region of MCRI-coding operon retrieved from Methanothermobacter thermautotrophicus strain ΔH. Appl. Environ. Microbiol., 74, 6239-6247 (2008).
  13. Sekiguchi Y, Muramatsu M, Imachi H, Narihiro T, Ohashi A, Harada H, Hanada S and Kamagata Y: Thermodesulfovibrio aggregans and Thermodesulfovibrio fermentans sp. nov., two anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludges. Int. J. Syst. Evol. Microbiol., 58, 2541-2548 (2008).
  14. Tagawa M, Tamaki H, Manome A, Koyama O and Kamagata Y: Development of genotyping method for potato scab pathogens based on multiplex PCR. Biosci. Biotechnol. Biochem., 72, 2324-2334 (2008).
  15. Takii S, Hanada S, Hasegawa Y, Tamaki H, Uyeno Y, Sekiguchi Y and Matsuura M: Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids. Int. J. Syst. Evol. Microbiol., 58, 2454-2458 (2008).
  16. Mori K, Maruyama A, Urabe, T, Suzuki K and Hanada S: Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Int. J. Syst. Evol. Microbiol., 58(4), 810-816 (2008).
  17. Miyamoto-Shinohara Y, Sukenobe J, Imaizumi T and Nakahara T: Survival of freeze-dried bacteria. J. Gen. Appl. Microbiol., 54(1), 9 24 (2008).
  18. Arashida R, Kakizawa S, Ishii Y, Hoshi A, Jung H Y, Kagiwada S, Yamaji Y, Oshima K and Namba S: Cloning and characterization of the antigenic membrane protein (Amp) gene and in situ detection of Amp from malformed flowers infected with Japanese hydrangea phyllody phytoplasma. Phytopathology 98, 769-775 (2008).
  19. Arashida R, Kakizawa S, Hoshi A, Ishii Y, Jung H Y, Kagiwada S, Yamaji Y, Oshima K and Namba S: Heterogeneic dynamics of the structures of multiple gene clusters in two pathogenetically different lines originating from the same phytoplasma. DNA Cell Biol 27, 209-217 (2008).
  20. Maejima K, Himeno M, Komatsu K, Kakizawa S, Yamaji Y, Hamamoto H and Namba S: Complete nucleotide sequence of a new double-stranded RNA virus from the rice blast fungus, Magnaporthe oryzae. Arch Virol 153, 389-391 (2008).

2007

  1. Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y and Tsuda M: Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl. Microbiol. Biotechnol., 74, 501-510 (2007).
  2. Mochimaru H, Yoshioka H, Tamaki H, Nakamura K, Kaneko N, Sakata S, Imachi H, Sekiguchi Y, Hoaki T, Uchiyama H and Kamagata Y: Microbial diversity and methanogenic potential in a high temperature natural gas field in Japan. Extremophiles, 11, 453-461 (2007).
  3. Mochimaru H, Yoshioka H, Tamaki H, Nakamura K, Imachi H, Sekiguchi Y, Hoaki T, Uchiyama H and Kamagata Y: Methanogen diversity in deep subsurface gas-associated water at Minami-kanto gas field in Japan. Geomicrobiol. J., 24, 93-100 (2007).
  4. Imachi H, Sakai S, Ohashi A, Harada H, Hanada S, Kamagata Y and Sekiguchi Y: Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic propionate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol., 57, 1487-1492 (2007).
  5. Jeong H, Lim Y-W, Yi H, Sekiguchi Y, Kamagata Y and Chun J: Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil. Int. J. Syst. Evol. Microbiol., 57, 1784-1787 (2007).
  6. Yamada T, Yamauchi T, Shiraishi S, Hugenholtz P, Ohashi A, Harada H, Kamagata Y, Nakamura K and Sekiguchi Y: Identification, distribution and diversity of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. ISME J., 1, 246-255 (2007).
  7. Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H and Kamagata Y: Isolation of key methanogens for global methane emission from rice paddy field: a novel isolate affiliated with a clone cluster, the Rice Cluster I. Appl. Environ. Microbiol., 73, 4326-4331 (2007).
  8. Morono Y, Kitagawa W, Kimura N, Noda N, Nakamura K and Kamagata Y: “Mark the gene„ : a method for non-destructive introduction of marker sequences inside the gene-frame of transgenes. Appl. Environ. Microbiol., 73, 4915-4331 (2007).
  9. Uyeno Y, Sekiguchi Y, Tajima K, Takenaka A, Kurihara M and Kamagata Y: Evaluation of group-specific, 16S rRNA-targeted scissor probes for quantitative detection of predominant bacterial populations in dairy cattle rumen. J. Appl. Micobiol., 103, 1995-2005 (2007).
  10. Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y and Sekiguchi Y: Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int. J. Syst. Evol. Microbiol., 57, 2299-2306 (2007).
  11. Shinzato N, Watanabe I, Meng X-Y, Sekiguchi Y, Tamaki H, Matsui T and Kamagata Y: Phylogenetic analysis and fluorescence in situ hybridization detection of archaeal and bacterial endosymbionts in the anaerobic ciliate Trimyema compressum. Microbial Ecol., 54, 627-636 (2007).
  12. Nakamura T, Hoaki T, Hanada S, Maruyama A, Kamagata Y and Fuse H: Soluble and particulate methane monooxygenase gene clusters in a marine methanotroph Methylomicrobium sp. strain NI. FEMS Microbiol. Lett., 277, 157-164 (2007).
  13. Zhang Y, Dou X, Liu J, Yang M, Zhang L and Kamagata Y: Decolorization of reactive brilliant red X-3B by heterogeneous photo-Fenton reaction using an Fe-Ce bimetal catalyst. Catalysis Today, 126, 387-393 (2007).
  14. Miyata R, Noda N, Tamaki H, Kinjo I, Aoyagi H, Uchiyama H and Tanaka H: Influence of feed components on the symbiotic bacterial community structure in the gut of wood-feeding higher termite Nasutitermes takasagoensis. Biosci. Biotech. Biochem., 71, 1244-1251 (2007).
  15. Miyata R, Noda N, Tamaki H, Kinjo I, Aoyagi H, Uchiyama H and Tanaka H: Phylogenetic relationship of symbiotic Archaea in the gut of higher termite Nasutitermes takasagoensis fed with various carbon source. Microb. Environ., 22, 157-164 (2007).
  16. Takii S, Hanada S, Tamaki H, Uyeno Y, Sekiguchi Y, Ibe A and Matsuura M: Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids. Int. J. Syst. Evol. Microbiol., 57, 2320-2326 (2007).
  17. Kubota K, Imachi H, Kawakami S, Nakamur K, Harada H and Ohashi A: Evaluation of enzymatic cell treatments for application of CARD-FISH to methanogens. J. Microbiol. Methods, 72(10), 54-59 (2007).
  18. Kimura H, Ishibashi J, Masuda H, Kato K and Hanada S: Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere. Appl. Environ. Microbiol., 73(3), 2110-2117 (2007).
  19. Tani H, Kanagawa T, Kurata S, Teramura T, Nakamura K, Tsuneda S and Noda N: Quantitative method for specific nucleic acid sequences using competitive polymerase chain reaction with an alternately binding probe. Anal. Chem., 79, 974-979 (2007).
  20. Okunuki S, Nakamura K, Kawaharasaki M, Tanaka H, Uchiyama H and Noda N: Quantification of Rhodocyclus-Related and Actinobacterial Polyphosphate-Accumulating Organisms in Enhanced Biological Phosphorus Removal Process Using Quenching Probe PCR. Microb. Environ., 22, 106-115 (2007).
  21. Tani H, Teramura T, Adachi K, Tsuneda S, Kurata S, Nakamura K, Kanagawa T and Noda N: Technique for Quantitative Detection of Specific DNA Sequences Using Alternately Bind-ing Quenching Probe Competitive Assay Combined with Loop-Mediated Isothermal Amplifi-cation. Anal. Chem., 79, 5608-5613(2007).
  22. Tani H, Kanagawa T, Morita N, Kurata S, Nakamura K, Tsuneda S and Noda N: Calibration-curve-free quantitative PCR: A quantitative method for specific nucleic acid sequences without using calibration curves. Anal. Biochem., 369, 105-111 (2007)
  23. Kamimura S, Hagi T, Kurata S, Takatsu K, Sogo H, Hoshino T and Nakamura K: Evaluation of quenching probe(QProbe) – PCR assay for quantification of the Koi herpes virus (KHV). Microbes Environ., 22(3), 223-231 (2007).
  24. Mitani Y, Watanabe T, Kondo K and Tamura T: Identification of strain specific genes in Rhodococcus erythropolis using a modified HiCEP method. The Open Biotechnology Journal, 1, 66-71 (2007).
  25. Takebayashi S, Narihiro T, Fujii Y and Hiraishi A: Water availability is a critical determinant of a population shift from Proteobacteria to Actinobacteria during start-up operation of mesophilic fed-batch composting. Microbes Environ., 22, 279-289 (2007).
  26. Oshima K, Kakizawa S, Arashida R, Ishii Y, Hoshi A, Hayashi Y, Kagiwada S and Namba S: Presence of two glycolytic gene clusters in a severe pathogenic line of Candidatus Phytoplasma asteris. Mol Plant Pathol 8, 481-489 (2007).

2006

  1. Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y and Tsuda M: Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in γ-hexachlorocyclohexane degradation. Appl. Environ. Microbiol., 72, 6923-6933 (2006).
  2. Sota M, Yano H, Ono A, Miyazaki R, Ishii H, Genka H, Top EM and 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. J. Bacteriol., 188, 4057-4068 (2006).
  3. Nagata Y, Kamakura M, Endo R, Miyazaki R, Ohtsubo Y and Tsuda M: Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons of Sphingobium japonicum UT26. FEMS Microbiol Lett., 256, 112-118 (2006)
  4. Zhang T, Fan X, Hanada S, Kamagata Y and Fang HHP: Bacillus macaensis sp. nov., a long-chain bacterium isolated from a drinking water supply. Int. J. Syst. Evol. Microbiol., 56, 349-353 (2006).
  5. Nakatsu CH, Hristova K, Hanada S, Meng XY, Hanson JR, Scow KM and Kamagata Y: Methylibium petroleiphilum PM1T gen. nov., sp. nov., a new methyl tert-butyl ether (MTBE) degrading methylotroph of the beta-Proteobacteria. Int. J. Syst. Evol. Microbiol., 56, 983-989 (2006).
  6. Dinoto A, Suksomcheep A, Ishizuka S, Hanada S, Kamagata Y, Asano K, Tomita F and Yokota A: Modulation of rat cecal microbiota by the administration of raffinose and encapsulated Bifidobacterium breve. Appl. Environ. Microbiol., 72, 784-792 (2006).
  7. Kosaka T, Uchiyama T, Ishii S, Enoki M, Imachi H, Kamagata Y, Ohashi A, Harada H, Ikenaga H and Watanabe K: Genomic insights into the central catabolic pathway in a thermophilic syntrophic bacterium, Pelotomaculum thermopropionicum. J. Bacteriol., 188, 202-210 (2006).
  8. Qiu YL, Sekiguchi Y, Hanada S, Imachi H, Tseng IC, Cheng SS, Ohashi A, Harada H and Kamagata Y: Pelotomaculum terephthalicicum sp. nov. and Pelotomaculum isophthalicicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch. Microbiol., 185, 172-182 (2006).
  9. Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu YL, Hugenholtz P, Kimura N, Wagner M, Ohashi A and Harada H: Non-sulfate-reducing, syntrophic bacteria affiliated with the Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl. Environ. Microbiol., 72, 2080-2091 (2006).
  10. Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H and Kamagata Y: Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int. J. Syst. Evol. Microbiol., 56, 1331-1340 (2006).
  11. Sekiguchi Y, Imachi H, Susilorukmi A, Muramatsu M, Ohashi A, Harada H, Hanada S and Kamagata Y: Tepidanaerobacter syntrophicus gen. nov., sp. nov., a novel anaerobic, moderately thermophilic, syntrophic alcohols- and lactate-degrading bacterium isolated from thermophilic digested sludges. Int. J. Syst. Evol. Microbiol., 56, 1621-1629 (2006).
  12. Kimura N, Kitagawa W, Mori T, Nakashima N, Tamura T and Kamagata Y: Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101. Appl. Microbiol. Biotechnol., 73, 474-484 (2006).
  13. Nakamura K, Terada T, Sekiguchi Y, Shinzato N, Meng XY, Enoki M and Kamagata Y: Application of pseudomurein endoisopeptidase to fluorescence in situ hybridization of methanogens within the family Methanobacteriaceae. Appl. Environ. Microbiol., 72, 6907-6913 (2006).
  14. Li H, Yang M, Zhang Y, Yu T and Kamagata Y: Nitrification performance and microbial community dynamics in a submerged membrane bioreactor with complete sludge retention. J. Biotechnol., 123, 60-70 (2006).
  15. Kimura H, Sugihara M, Kato K and Hanada S: Selective phylogenetic analysis targeted at 16S rRNA Genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments. Appl. Environ. Microbiol., 72(1), 21-27 (2006).
  16. Kimura N: Metagenomics: Access to Unculturable Bacteria in the Environments，Microbes and Environments，21(4)，201-215 (2006).Review.
  17. Sawada MT, Tamura T, Mitani Y, Kaya M, Ito G, Hashimoto H and Sawada H: Participation of proteasome-associating complex PC500 in starfish oocyte maturation as revealed by monoclonal antibodies. Biochem. Biophis. Res. Commun, 349(2), 694-700 (2006).
  18. Mitani Y, Suzuki K, Kondo K, Okumura K and Tamura T: Gene expression analysis using a modified HiCEP method applicable to prokaryotes: A study of the response of Rhodococcus to isoniazid and ethambutol. J. Biotechnol, 123(3), 259-272 (2006).
  19. Khalid SI, Mitani Y and Tamura T: Construction of random transposition mutagenesis system in Rhodococcus erythropolis using IS1415. J. Biotechnol, 121(1), 13-22 (2006).
  20. Sekiguchi Y: Yet-to-be cultured microorganisms relevant to methane fermentation processes (mini-review). Microb. Environ., 21, 1-15 (2006).
  21. Adachi K, Noda N, Nakashige M, Tsuneda S and Kanagawa T: Affinity capillary electrophoresis with a DNA-nanoparticle conjugate as a new tool for genotyping. J. Chromatography A, 1109, 127?131 (2006).
  22. Furukawa K, Noda N, Tsuneda S, Saito T, Itayama T and Inamori Y: Highly Sensitive Real-Time PCR Assay for Quantification of Toxic Cyanobacteria Based on Microcystin Synthetase A Gene: Journal of Bioscience and Bioengineering, 102(2), 90-96(2006).
  23. Hori K, Mii J, Morono Y, Tanji Y and Unno H: Kinetic analyses of trichloroethylene cometabolism by toluene-degrading bacteria harboring a tod homologous gene. Biochem. Eng. J., 26(1), 59-64 (2006)
  24. Suzuki S, Oshima K, Kakizawa S, Arashida R, Jung H Y, Yamaji Y, Nishigawa H, Ugaki M and Namba S: Interaction between the membrane protein of a pathogen and insect microfilament complex determines insect-vector specificity. Proc Natl Acad Sci U S A 103, 4252-4257 (2006).
  25. Kakizawa S, Oshima K, Jung H Y, Suzuki S, Nishigawa H, Arashida R, Miyata S, Ugaki M, Kishino H and Namba S: Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas. J Bacteriol 188, 3424-3428 (2006).
  26. Miyamoto-Shinohara Y, Sukenobe J, Imaizumi T, Nakahara T: Survival curves for microbial species stored by freeze-drying. Cryobiology, 52, 27-32(2006).

2005

  1. Lee TH, Kurata S, Nakatsu CH and Kamagata Y: Molecular analysis of bacterial community based on 16S rDNA and functional genes in activated sludge enriched with 2,4-dichlorophenoxyacetic acid (2,4-D) under different cultural conditions. Microbial Ecol., 49, 151-162 (2005).
  2. Amachi S, Muramatsu Y, Akiyama Y, Miyazaki K, Hanada S, Kamagata Y, Shinoyama H, Bannai T and Fujii T: Isolation of iodide-oxidizing bacteria from iodide-rich natural gas brines and seawaters. Microbial Ecol., 49, 547-557 (2005).
  3. Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M and Kamagata Y: Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake as revealed by molecular and improved cultivation-based techniques. Appl. Environ. Microbiol., 71, 2162-2169 (2005).
  4. Mitani Y, Meng XY, Kamagata Y and Tamura T: Characterization of LtsA from Rhodococcus erythropolis -an enzyme with glutamine amidotransferase activity. J. Bacteriol., 187, 2582-2591 (2005).
  5. Hattori S, Galushko AS, Kamagata Y and Schink B: Operation of the CO dehydrogenase/acetyl-CoA pathway both in acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum J. Bacteriol., 187, 3471-3476 (2005).
  6. Sekiguchi Y, Uyeno Y, Sunaga A, Yoshida H and Kamagata Y: Sequence-specific cleavage of 16S rRNA for rapid and quantitative detection of a particular group of anaerobes in bioreactors. Wat. Sci. Tech., 52, 107-113 (2005).
  7. Li H, Yang M, Zhang Y, Liu X, Gao M and Kamagata Y: Comparison of nitrification performance and microbial community between submerged membrane bioreactor and conventional activated sludge system. Water Sci. Technol., 51, 193-200 (2005).
  8. Tanaka Y, Hanada S, Tamaki H, Nakamura K and Kamagata Y: Isolation and identification of bacterial strains producing diffusible growth factor(s) for Catellibacterium nectariphilum strain AST4T. Microb. Environ., 20, 110-116 (2005).
  9. Kamagata Y and Tamaki H: Cultivation of uncultured fastidious microbes. Microb. Environ., 20, 85-91 (2005).
  10. Yamada T, Fujii T, Kanai T, Amo T, Imanaka T, Nishimasu H, Wakagi H, Shoun H, Kamakura M, Kamagata Y, Kato T and Kawashima K: Expression of acetylcholine (ACh) and ACh-synthesizing activity in Archaea. Life Sci., 77, 1935-1944 (2005).
  11. Yamada T, Sekiguchi Y, Imachi H, Kamagata Y, Ohashi A and Harada H: Diversity, localization and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl. Environ. Microbiol., 71, 7493-7503 (2005).
  12. Kimura H, Sugihara M, Yamamoto H, Patel BK, Kato K and Hanada S: Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia. Extremophiles, 9, 407-414 (2005).
  13. Yamada M, Zhang H, Hanada S, Nagashima KVP, Shimada K and Matsuura K: Structural and spectroscopic properties of a reaction center complex from the chlorosome-lacking filamentous anoxygenic phototrophic bacterium Roseiflexus castenholzii. J. Bacteriol., 187(5), 1702-1709 (2005).
  14. Watanabe K, Takihana N, Aoyagi H, Hanada S, Watanabe Y, Ohmura N, Saiki H and Tanaka H: Symbiotic association in Chlorella culture. FEMS Microbiol. Ecol., 51, 187-196 (2005).
  15. Harazono K and Nakamura K: Decolorization of mixtures of different reactive textile dyes by the white-rot basidiomycete Phanerochaete sordida and inhibitory effect of polyvinyl alcohol. Chemosphere, 59, 63-68 (2005).
  16. Watanabe T and Nakamura K: Gliocephalotrichum microchlamydosporum and G. simplex in the Ryukyu Islands, Japan. Mycoscience, 46, 46-48 (2005).
  17. Tani H, Noda N, Yamada K, Kurata S, Tsuneda S, Hirata A and Kanagawa T: Quantification of genetically modified soybean by quenching probe (QProbe)-PCR. J. Agric. Food Chem., 53, 2535-2540 (2005).
  18. Yoshida N, Yagi K, Sato D, Watanabe N, Kuroishi T, Nishimoto K, Yanagida A, Katsuragi T, Kanagawa T, Kurane R and Tani Y: Bacterial communities in petroleum oil stockpiles. J. Biosci. Bioeng., 99, 143-149 (2005).
  19. Suenaga H, Liu R, Shiramasa Y and Kanagawa T: A novel approach to the quantitative detection of specific rRNA using catalytic DNA in a microbial community. Appl. Environ. Microbiol., 71, 4879-4884 (2005).

REVIEW ARTICLES AND BOOK CHAPTERS

2017

  1. Kimura N: Novel biological resources screened from uncultured bacteria by a metagenomic method. In Recent advances and perspectives in metagenomics (Edited by M. Nagarajan). Elsevier USA, in press.

2016

  1. Narihiro T, Kamagata Y: Anaerobic Cultivation, pp. 2.1.2-1-2.1.2-12. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC (2016).

2015

  1. Narihiro T, Nobu MK, Mei R, Liu WT: Microbial Community Involved in Anaerobic Purified Terephthalic Acid Treatment Process, pp. 31-48. In Fang HHP, Zhang T. (ed.), Anaerobic Biotechnology: Environmental Protection and Resource Recovery. World Scientific Publishing, Singapore (2015).
  2. Narihiro T, Sekiguchi Y: Primers: Functional Genes and 16S rRNA Genes for Methanogens, pp. 79-139. In McGenity TJ, Timmis KN, Nogales B. (ed.), Hydrocarbon and Lipid Microbiology Protocols. Springer Berlin Heidelberg, New York (2015).
  3. Kakizawa S, Yoneda Y: The role of genome sequencing in phytoplasma research. Phytopathogenic Mollicutes 5: 19-24 (2015).
  4. Kimura N: Mining novel genes and enzymes of uncultured eukaryotic microorganisms by a RNA-based approach, Metagenomics: Methods, Applications and Perspectives (Edited by Camilla Benedetti), Nova Science Publishers, Inc. (2015)

2014

  1. Kimura N: Metagenomic approaches to understanding phylogenetic diversity in quorum sensing, Virulence, 5 (3) 433-442 (2014).
  2. Hanada, S.:Phylum Chloroflexi, In The Prokaryotes 4th edition (Edited by E Rosenberg et al.). Springer In Press.

2013

  1. Hanada, S. and Sekiguchi, Y.: Phylum Gemmatimonadetes, In The Prokaryotes 4th edition (Edited by E Rosenberg et al.). Springer In Press (2013).
  2. Kimura N, W Kitagawa, and Kamagata Y: Microbial degradation of nitrophenol compounds. In Biological remediation of explosive residues (Edited by S. N. Singh). Springer-Verlag (2013).
  3. Kitagawa, W. and Kamagata Y: 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. in press (2013).

2012

  1. Miyazaki R, Minoia M, Pradervand N, Sentchilo V, Sulser S, Reinhard F and van der Meer JR: The clc Element and Related Genomic Islands in Proteobacteria. In Bacterial integrative mobile genetic elements. Edited by AP. Roberts and P. Mullany. Landes Bioscience (2012).

2011

  1. Narihiro T and Sekiguchi Y: Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea. Microb. Biotechnol., 4, 585-602 (2011).
  2. Kakizawa S, Hoshi A, Ishii Y, Kojima N, Sugawara K, Okano Y, Maejima K, Oshima K and Namba S: Unique features of a phytoplasma genome and its membrane proteins involved in host specificity. In Genome-enabled analysis of plant-pathogen interactions, pp. 103-110. Edited by T. Wolpert, T. Shiraishi, A. Collmer, K. Akimitsu and J. Glazebrook. Minnesota: APS press (2011).

2010

  1. Shinzato N and Kamagata Y: The methanogenic and archaeal endosymbionts of Trimyema In: Endosymbiotic methanogenic archaea (Edited by J.H.P. Hackstein). Springer Verlag. in press (2010).
  2. Kakizawa S, Oshima K and Namba S:Functional genomics of phytoplasmas. In Phytoplasmas: genome, plant hosts and vectors, pp. 37-50. Edited by P. G. Weintraub and P. Jones. Oxfordshire: CABI (2010).
  3. Hanada S and Nakamura K: Genus Microlunatus, Nakamura, Hiraishi, Yoshimi, Kawaharazaki, Masuda and Kamagata 1995, 21VP In: Bergey’s manual of systematic bacteriology volume 4, (Edited by Garrity G.). Springer-Verlag. (2010).

2009

  1. Kamagata Y: Genus Thermoacetogenium Hattori, Kamagata, Hanada, and Shoun 2000. In: Bergey’s manual of systematic bacteriology volume 3, (Edited by Garrity G.). Springer-Verlag. (2009).
  2. Kamagata Y: Genus Oscillospira Chatton and Perard 1913, 1159AL In: Bergey’s manual of systematic bacteriology volume 3, (Edited by Garrity G.). Springer-Verlag. (2009).
  3. Kamagata Y, Sekiguchi Y and Hanada S: Gemmatimonadetes phylum nov. In: Bergey’s manual of systematic bacteriology (Edited by Garrity G.). Springer-Verlag. (2009).
  4. Mori K and Hanada S: Genus X. Thermanaeromonas Mori, Hanada, Maruyama and Marumo 2002, 1679VP, pp. 1256-1259, In: Bergey’s Manual of Systematic Bacteriology vol. 3 (Edited by W. B. Whitman et al.,). Springer-Verlag. (2009).
  5. Mori K and Hanada S: Family II. Thermodesulfobiaceae Mori, Kim, Kakegawa and Hanada 2004, 1VP, pp. 1268-1271, In: Bergey’s Manual of Systematic Bacteriology vol. 3 (Edited by W. B. Whitman et al.,). Springer-Verlag. (2009).
  6. Okabe S and Kamagata Y: Wastewater treatment. In: Environmental Molecular Biology (Edited by W-T, Liu and Jansson J.K.). Caiser Academic Press. chapter 10 (2009).

2008

  1. Hogenhout S A, Oshima K, Ammar E-D, Kakizawa S, Kingdom H N and Namba S: Phytoplasmas: Bacteria that manipulate plants and insects. Mol Plant Pathol 9, 403-423 (2008).

2007

  1. Narihiro T and Sekiguchi Y: Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update. Curr. Opin. Biotechnol., 18, 273-278 (2007)

2006

  1. Hanada S and Beverly K. Pierson: The Family Chloroflexaceae. The Prokaryotes: A Handbook on the Biology of Bacteria 3rd edition, 7, 815-842 (2006).
  2. Kakizawa S, Oshima K and Namba S: Diversity and functional importance of phytoplasma membrane proteins. Trends Microbiol 14, 254-256 (2006).
  3. Mitani Y, Nakashima N, Sallam KI, Toriyabe T, Kondo K and Tamura T: Advances in the development of genetic tools for the genus Rhodococcus. Actinomycetologica, 20(2), 55-61 (2006).
  4. Kimura N: Metagenomics: Access to unculturable bacteria in the environments. Microbes Environ., 21, 201-215 (2006).

2005

  1. Nakashima N, Mitani Y, and Tamura T: Actinomycetes as host cells for production of recombinat proteins. Microb Cell Fact 4, 7 (2005).
  2. Narihiro T and Hiraishi A: Microbiology of fed-batch composting. Microbes Environ., 20, 1-13 (2005).