2024

• Molecular diversity of green-colored microbial mats from hot springs of northern Japan
  Yangtsho Gyaltshen†, Yuu Ishii†, Sophie Charvet, Eleanor Goetz, Shinichiro Maruyama, Eunsoo Kim(2024), Extremophiles. Jun 5:e0033423. doi: 10.1007/s00792-024-01358-y †These authors contributed equally to the study.
• Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome
  
  Yuka Adachi Katayama, Ryoma Kamikawa, Takashi Yoshida
  Microb Genom. 2024;10:001285. 2024. doi: 10.1099/mgen.0.001285
• Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses
  Takebe, H., Tominaga, K., Isozaki, T., Watanabe, T., Yamamoto, K., Kamikawa, R. and Yoshida, T.
  mSystems. 2024. doi: 10.1128/msystems.00949-23.
• Draft genome of Parageobacillus thermoglucosidasius, a member of hydrogenogenic carbon monoxide utilizers, isolated from a freshwater lake sediment
  S, Nishida., J, Suzuki., M, Inoue., R, Kamikawa., T, Yoshida.
  Microbiology Resource Announcements. 13 (2), e00795-23. 2024. doi:10.1128/mra.00795-23
• Virus–prokaryote infection pairs associated with prokaryotic production in a freshwater lake.
  Shen, S., Tominaga, K., Tsuchiya, K., Matsuda, T., Yoshida, T. and Shimizu, Y.
  mSystems. 2024. doi: 10.1128/msystems.00906-23
  
• A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals.
  Sato, Y., Takebe, H., Tominaga, K., Yasuda, J.,  Kumagai, H.,  Hirooka, H. and Yoshida, T. 
  Appl. Environ. Microbiol. 2024. doi: 10.1128/aem.01581-23

2023

2022

• Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan
• Y Sato, H Takebe, K Oishi, J Yasuda, H Kumagai, H Hirooka, T Yoshida
• Microbes and environments 37 (4), ME22039
• Tight association between microbial eukaryote and giant virus communities in the Arctic Ocean.
  Xia, J., Kameyama, S., Prodinger, F., Yoshida, T., Cho, K.-H., Jung, J., Kang, S.-H., Yang, E.-J., Ogata, H. and Endo, H.
  Limnol. Oceanogr., 67, 1343-1356, 2022. 10.1002/lno.12086.
• Viral nature of the aquatic ecosystems.
  Morimoto, D., Tominaga, K., Takebe, H., Šulčius, S. and Yoshida, T.
  In The biological role of a virus (eds. Christon J. Hurst). Adv. Environ. Microbiol.9:3-25, Springer, Cham., 2022.
• Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases.
  Inoue, M., Omae, K., Nakamoto, I., Kamikawa, R., Yoshida, T., Sako, Y. (2022).
  Extremophiles, 26, 9, 10.1007%2Fs00792-022-01259-y.
• An enigmatic stramenopile sheds light on early evolution in Ochrophyta plastid organellogenesis.
  Azuma, T., Panek, T., Tice, A.K., Kayama, M., Kobayashi, M., Miyashita, H., Suzaki, T., Yabuki, A., Brown, M.W., Kamikawa, R. (2022).
  Molecular Biology and Evolution, 39(4), msac065.
• Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida.
  Kamikawa, R., Mochizuki, T., Sakamoto, M., Tanizawa, Y., Nakayama, T., Onuma, R., Cenci, U., Moog, D., Speak, S., Sarkozi, K., Toseland, A., van Oosterhout, C., Oyama, K., Kato, M., Kume, K., Kayama, M., Azuma, T., Ishii, K., Miyashita, H., Henrissat, B., Lombard, V., Win, J., Kamoun, S., Kashiyama, Y., Mayama, S., Miyagishima, S., Tanifuji, G., Mock, T., Nakamura, Y. (2022).
  Science Advances, 8(17), eabi5075.

2021

• Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitervirales and prokaryotes in a coastal ecosystem.
  Prodinger, F., Endo, Hisashi, Takano, Y., Li, Y., Tominaga, K., Isozaki, T., Blanc-Mathieu, R., Gotoh, Y., Hayashi, T., Taniguchi, E., Nagasaki, K., Yoshida, T. and Ogata, H.
  FEMS Microbiol. Ecol., 97, fiab167, 2021., 10.1093/femsec/fiab167.
• Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing.
  Sato, Y., Takebe, H., Tominaga, K., Oishi, K., Kumagai, H., Yoshida, T. and Hirooka H.
  FEMS Microbiol. Ecol., 97, fiab152, 2021. , 10.1093/femsec/fiab152.
• Rappemonads are haptophyte phytoplankton
  Masanobu Kawachi, Takuro Nakayama, Motoki Kayama, Mami Nomura, Hideaki Miyashita, Othman Bojo, Lesley Rhodes, Stuart Sym, Richard N. Pienaar, Ian Probert, Isao Inouye, Ryoma Kamikawa (2021),
  Curr. Biol., 10.1016/j.cub.2021.03.012
• Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers
  Kimiho Omae,Tatsuki Oguro,Masao Inoue,Yuto Fukuyama,Takashi Yoshida & Yoshihiko Sako (2021),
  Extremophiles, 10.1007/s00792-020-01211-y

2020

• Calcium salts of long-chain fatty acids from linseed oil decrease methane production by altering the rumen microbiome in vitro
  Yoshiaki Sato,Kento Tominaga,Hirotatsu Aoki,Masayuki Murayama,Kazato Oishi ,Hiroyuki Hirooka,Takashi Yoshida,Hajime Kumagai. (2020),
  PLoS One, 15(11), 10.1371/journal.pone.0242158
• Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis
  Kayama M, Maciszewski K, Yabuki A, Miyashita H, Karnkowska A, Ryoma Kamikawa. (2020),
  Front. Plant Sci., 11:602455, 10.3389/fpls.2020.602455
• A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems.
  Kayama M, Chen JF, Nakada T, Nishimura Y, Shikanai T, Azuma T, Miyashita H, Takaichi S, Kashiyama Y, Ryoma Kamikawa. (2020),
  BMC Biol., 18: 126, 10.1186/s12915-020-00853-w
• Putative genome features of the relic green alga-derived nuclei in the dinoflagellates and the future perspectives as model organisms.
  Nakayama T, Takahashi K, Ryoma Kamikawa, Iwataki M, Inagaki Y, Tanifuji G. (2020),
  Comm. Integr. Biol. , 13:84-88, 10.1080/19420889.2020.1776568
• Genetic Engineering of Carbon Monoxide-Dependent Hydrogen-Producing Machinery in Parageobacillus thermoglucosidasius
  Yuka Adachi, Masao Inoue, Takashi Yoshida, Yoshihiko Sako (2020),
  Microbes Environ. , 35(4),10.1264/jsme2.ME20101
• Viruses of freshwater bloom‐forming cyanobacteria: Genomic features, infection strategies and coexistence with the host.
  Daichi Morimoto, Sigitas Šulčius, Takashi Yoshida. (2020)
  Environ. Microbiol. Rep.,10.1111/1758-2229.12872
• 次世代エネルギー・炭素循環を目指した H₂ 生成型 CO 酸化菌の包括的研究
  井上真男, 吉田天士, 左子芳彦 (2020)
  脱石油に向けた CO₂ 資源化技術―化学・生物プロセスを中心に― 第 III 編, 第 11 章, pp.331-338, シーエムシー出版
• Draft Genome Sequence of Thermanaeromonas sp. Strain C210 Isolated in the Presence of Carbon Monoxide
  Masao Inoue, Ayumi Tanimura, Yuto Fukuyama, Suguru Okunishi, HirotoMaeda, Takashi Yoshida, and Yoshihiko Sako (2020),
  Microbiol. Resour. Announc., 9:e00608-20. 10.1128/MRA.00608-20
• Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments
  Daichi Morimoto, Sigitas Šulčius, Kento Tominaga, and Takashi Yoshida (2020)
  Adv. Appl. Microbiol., 113:163-191, 10.1016/bs.aambs.2020.06.001
• Draft genome sequence of the astaxanthin-producing microalgaeHaematococcus lacustris strain NIES-144
  Daichi Morimoto, Takashi Yoshida, and Shigeki Sawayama (2020),
  Microbiol. Resour. Announc.,9:e0012820.10.1128/MRA.00128-20
• Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates
  Hiroaki Takebe, Kento Tominaga, Kentaro Fujiwara, Keigo Yamamoto, Takashi Yoshida (2020) ,
  Microbes Environ., 35, 3. 10.1264/jsme2.ME20033
• Anaerobic and hydrogenogenic carbon monoxide-oxidizing prokaryotes:Versatile microbial conversion of a toxic gas into an available energy
  Yuto Fukuyama, Masao Inoue, Kimiho Omae, Takashi Yoshida, Yoshihiko Sako (2020) ,
  Adv. Appl. Microbiol., 110, 99-148. ISBN:978-0-12-820703-1
• Carbon Monoxide-dependent Transcriptional Changes in a Thermophilic,Carbon Monoxide-utilizing, Hydrogen-evolving Bacterium Calderihabitans maritimus KKC1 Revealed by Transcriptomic Analysis
  Masao Inoue, Hikaru Izumihara, Yuto Fukuyama, Kimiho Omae, Takashi Yoshida and Yoshihiko Sako (2020),
  Extremophiles, 24, 551–564. 10.1007/s00792-020-01175-z
• In silico prediction of virus-host interactions for marine Bacteroidetes with the use of metagenome-assembled genomes
  Kento Tominaga, Daichi Morimoto, Yosuke Nishimura, Hiroyuki Ogata and Takashi Yoshida　(2020).
  Front.Microbiol.,  fmicb.2020.00738
• An optimized metabarcoding method for Mimiviridae
  Florian Prodinger, Hisashi Endo, Yasuhiro Gotoh, Yanze Li, Daichi Morimoto, Kimiho Omae, Kento Tominaga, Romain Blanc-Mathieu, Yoshihito, Takano, Tetsuya Hayashi, Keizo Nagasaki, Takashi Yoshida, Hiroyuki Ogata　(2020).
  Microorganisms, 8(4), 506. microorganisms8040506
• Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses on earth
  Francisco, M.H., Elaine, L., Tominaga, K., Ogata, H., Yoshida, T., Edward, F.D., Manuel, M.G. (2020).
  Environ Microbiol Rep., doi.org/10.1111/1758-2229.12825

2019

• Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
  Okazaki, Y., Nishimura, Y., Yoshida, T., Ogata, H., Nakano, S. (2019).
  Environ Microbiol., doi.org/10.1111/1462-2920.14816
• Draft Genome Sequences of Two Thermophilic Bacteria Moorella spp., Isolated from an Acidic Hot Spring in Japan
  Fukuyama, Y., Tanimura, A., Inoue, M., Omae, K., Yoshida, T., Sako, Y. (2019).
  Microbiol. Resour. Announc., DOI:10.1128/MRA.00663-19
• Co-occurrence of broad and narrow host-range viruses infecting the toxic bloom-forming cyanobacterium Microcystis aeruginosa.
  Morimoto, D., Tominaga, K., Nishimura, Y., Yoshida, N., Kimura, S., Sako, Y., Yoshida, T. (2019).
  Appl. Environ. Microbiol., doi.org/10.1128/AEM.01170-19
• The earth is small for “leviathans”: long distance dispersal of giant viruses across aquatic environments.　
  Li, Y., Endo, H., Gotoh, Y., Watai, H., Ogawa, N., Blanc-Mathieu, R., Yoshida, T., Ogata, H. (2019).
  Microbes and Environ., Volume 34 Issue 3 Pages 334-339, jsme2.ME19037
• Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan.
  Omae, K., Fukuyama, Y., Yasuda, H., Mise, K., Yoshida, T., Sako, Y. (2019).
  Arch. Microbiol., doi.org/10.1007/s00203-019-01661-9
• Bacteria-virus interaction.
  Yoshida, T., Morimoto, D., Kimura, S. (2019).
  P.95-108, In DNA Traffic in the Environment. (eds. Nishida, T., Oshima, T.)
  Springer Nature Singapore 2019.
• Transcriptome analysis of a thermophilic and hydrogenogenic carboxydotroph Carboxydothermus pertinax
  Fukuyama, Y., Omae, K., Yoshida, T., Sako, Y. (2019).
  Extremophiles., 23, 389-398
• Draft genome sequence of Parageobacillus thermoglucosidasius strain TG4, a hydrogenogenic carboxydotrophic bacterium isolated from a marine sediment.
  Inoue, M., Tanimura, A., Ogami, Y., Hino, T., Okunishi, S., Maeda, H., Yoshida, T., Sako, Y. (2019).
  Microbiol. Resour. Announc., 8:e01666-18
• Structural and Phylogenetic Diversity of Anaerobic Carbon-monoxide Dehydrogenases.
  Inoue, M., Nakamoto, I., Omae, K., Oguro, T., Ogata H., Yoshida, T., Sako, Y. (2019).
  Front. Microbiol., fmicb.2018.03353

2018

• Minimum Information about an Uncultivated Virus Genome (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses.
  Roux S., Adriaenssens, E.M., Dutilh, B.E., Koonin, E.V., Kropinski, A.M., Krupovic, M.,Kuhn, J.H., Lavigne, R., Brister, J.R., Varsani, A., Amid, C., Aziz, R.K., Bordenstein, S.R., Bork, P., Breitbart, M., Cochrane, G.R., Daly, R.A., Desnues, C., Duhaime, M.B., Emerson, J.B., Enault, F., Fuhrman, J.A., Hingamp, P., Hugenholtz, P., Hurwitz, B.L., Ivanova, N.N., Labonte, J.M., Lee, K.-B., Malmstrom, R.R., Martinez-Garcia, M., Mizrachi, I., Ogata, H., Paez-Espino, D., Petit, M.-A., Putonti, C., Rattei, T., Reyes, A.,Rodriguez-Valera, F., Rosario, K., Schriml, L., Schulz, F., Steward, G.F., Sullivan, M.B., Sunagawa, S., Suttle, C.A., Temperton, B., Tringe, S.G., Thurber, R.V., Webster, N.S.,Whiteson, K.L., Wilhelm, S.W., Wommack, K.E., Woyke,T., Wrighton, K.C., Yilmaz, P., Yoshida, T., Young, M.J., Yutin, N., Zeigler-Allen, L., Kyrpides, N.C., Eloe-Fadrosh,E.A. (2018).
  Nature Biotechnology
• Degenerate PCR primers to reveal the diversity of giant viruses in coastal waters.
  Yanze Li, Pascal Hingamp, Hiroyasu Watai, Hisashi Endo, Takashi Yoshida and Hiroyuki Ogata. (2018).
  Viruses,10, 496
• Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism in Carboxydothermus pertinax Revealed by Comparative Genome Analysis.
  Yuto Fukuyama, Kimiho Omae, Yasuko Yoneda, Takashi Yoshida, Yoshihiko Sako. (2018).
  Appl. Environ. Microbiol., 84, e00458-18
• LexA binds to transcription regulatory site of cell division gene ftsZ in toxic cyanobacterium Microcystis aeruginosa.
  Takashi Honda., Daichi Morimoto., Yoshihiko Sako and Takashi Yoshida. (2018).
  Mar Biotechnol.,  s10126-018-9826-4
• Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.
  Yoshida, T., Nishimura, Y., Watai, H., Haruki, N., Morimoto, D., Kaneko, H., Honda, T., Yamamoto, K., Hingamp, P., Sako, Y., Goto, S., Ogata, H. (2018).
  The ISME Journal, 82, s41396-018-0052-x
• Transcriptome Analysis of a Bloom-Forming Cyanobacterium Microcystis aeruginosa during Ma-LMM01 Phage Infection.
  Morimoto, D., Kimura, S., Sako, Y., Yoshida, T. (2018).
  Front. Microbiol. 9, fmicb.2018.00002
• Incomplete selective sweeps of Microcystis population detected by the leader-end CRISPR fragment analysis in a natural pond.
  Kimura, S., Uehara, M., Morimoto, D., Yamanaka, M., Sako, Y., Yoshida, T. (2018).
  Front. Microbiol. fmicb.2018.00425
• Anodic and Cathodic Extracellular Electron Transfer by the Filamentous Bacterium Ardenticatena maritima 110S.
  Kawaichi, S., Yamada, T., Umezawa, A., Shawn E. McGlynn, Suzuki, T., Dohmae, N., i Yoshida, T., Sako, Y., Matsushita, N., Hashimoto, K., Nakamura, R. (2018).
  Front. Microbiol. fmicb.2018.00068

2017

• Genomic analysis of Calderihabitans maritimus KKC1, a thermophilic hydrogenogenic carboxydotrophic bacterium isolated from marine sediment.
  Omae, K., Yoneda, Y., Fukuyama, Y., Yoshida, T., Sako, Y. (2017).
  Appl. Environ. Microbiol., 00832-17
• ViPTree: the viral proteomic tree server.
  Nishimura, Y., Yoshida, T., Kuronishi, M., Uehara, H., Ogata, H. and Goto, S. (2017).
  Bioinformatics 33, 2379?2380
• Draft genome sequences of two hydrogenogenic carboxydotrophic bacteria, Carboxydocella sp. strains JDF658 and ULO1, isolated from two distinct volcanic fronts in Japan.
  Fukuyama, Y., Oguro, T., Omae, K., Yoneda, Y., Yoshida, T., Sako, Y. (2017).
  Genome announcements 5, e00242-17
• Environmental viral genomes shed new light on virus-host interactions in the ocean.
  Nishimura, Y., Watai, H., Honda, T., Mihara, T., Omae, K., Roux, S., Blanc-Mathieu, R., Yamamoto, K., Hingamp, P., Sako, Y., Sullivan, M. B., Goto, S., Ogata, H., Yoshida, T. (2017).
  mSphere 2, e00359-16.
• Draft genome sequences of Carboxydothermus pertinax and C. islandicus, hydrogenogenic carboxydotrophic bacteria.
  Fukuyama, Y., Omae, K., Yoneda, Y., Yoshida, T., Sako, Y. (2017).
  Genome announcements 5, e01648-16.

2016

• Spatial and temporal variability of unicellular diazotrophic cyanobacteria in the eastern Seto Inland Sea.
  Hashimoto, R., Watai, H., Miyahara, K., Sako, Y. and Yoshida, T. (2016).
  Fish. Sci. 82, 459-471.

2015

• Development of a real-time PCR assay for the quantification of Ma-LMM01-type Microcystis cyanophages in a natural pond.
  Kimura-Sakai, S.,  Sako, Y. and Yoshida, T. (2015).
  Lett. Appl. Microbiol. 60, 400-408.
• The ocean sampling day consortium.
  Kopf, A. 他167名.
  GigaScience 2015, 4, 27.
• Detection of anaerobic carbon monoxide-oxidizing thermophiles in hydrothermal environments.
  Yoneda, Y., Kano, S. I., Yoshida, T., Ikeda, E., Fukuyama, Y., Omae, K., Kimura-Sakai, S., Daifuku, T., Watanabe, T. & Sako, Y. (2015).
  FEMS Microbiol. Ecol., 91, fiv093.
• Draft genome sequence of a heterotrophic facultative anaerobic thermophilic bacterium, Ardenticatena maritima strain 110ST. 
  Kawaichi, S., Yoshida, T., Sako, Y. & Nakamura, R. (2015).
  Genome announcements, 3, e01145-15.
• 環境におけるシアノバクテリアとウィルスのせめぎ合い―シアノバクテリアとウィルスの共進化
  吉田天士. (2015).
  生物の科学 遺伝, 69, 278-283.
• 古細菌ゲノム進化とウィルス―生命の起源といわれる熱水環境における共進化過程の解明に期待
  大福高史, 弓矢真穂, 左子芳彦. (2015).
  生物の科学 遺伝, 69, 326-31.

2014

• Characterization of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus: Enzymatic activity and active site structure.
  Terasaka, E., Okada, N., Sato, N., Sako, Y., Shiro, Y. and Tosha,T. (2014).
  Biochim. Biophys. Acta 1837, 1019-1026.
• Over-expression of carbon monoxide dehydrogenase-I with an accessory protein co-expression: a key enzyme for carbon dioxide reduction.
  Inoue, T., Takao, K., Fukuyama, Y., Yoshida, T. and Sako, Y. (2014).
  Biosci. Biotechnol. Biochem., 78, doi.org/ 10.1080/ 09168451. 2014.890027
• Genetic diversity of Microcystis cyanophages in two different freshwater environments.
  Nakamura, G., Kimura, S., Sako, Y. and Yoshida, T. (2014).
  Arc. Microbiol. 196, 401-409.
• Membrane-like protein involved in phage adsorption associated with phage-sensitivity in the bloom-forming cyanobacterium Microcystis aeruginosa.
  Yoshida, T., Kamiji, R., Nakamura, G., Kaneko, T. and Sako, Y. (2014).
  Harmful Algae. 34, 69-75.
• Diversification of CRISPR within coexisting genotypes in a natural population of the bloom-forming cyanobacterium Microcystis aeruginosa.
  Kuno, S., Sako, Y. and Yoshida, T. (2014).
  Microbiology, mic.0.073494-0.

2013

• Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.
  Sato, N., Ishii, S., Sugimoto, H., Hino, T., Fukumori, Y., Sako, Y., Shiro, Y. and Tosha, T. (2013).
  Proteins. 10, 1002.
• Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes.
  Kamikawa, R., Brown, M. W., Nishimura, Y., Sako, Y., Heiss, A., Yubuki, N., Gawryluk,
  R., Simpson, A. G. B., Roger, A. J., Hashimoto, T. and Inagaki, Y. (2013).
  BMC Evol. Biol. 13, 131.
• Host vector system in Thermophiles.
  Inoue, T. and Sako, Y.  (2013).
  P.351-373. In Thermophilic Microbes in Environmental and Industrial Biotechnology. (eds. Satyanarayana, T., Littlechild, J.,  Kawarabayasi, Y.)
  Springer, Heidelberg.
• Gene expression of Microcystis aeruginosa during infection of cyanomyovirus Ma-LMM01.
  Honda, T., Takahashi, H., Sako, Y. and Yoshida, T.
  Fish. Sci., 80, 93-91.
• Cystein 295 indirectly affects Ni coordination of carbon monoxide dehydrogenase-II C-cluster.
  Inoue, T., Takao, K., Yoshida, T., Wada, K., Daifuku, T., Yoneda, Y., Fukuyama, K. and Sako, Y. (2013).
  Biochem. Biophys. Res. Commun., 441, 13-7.
• Genome variation in the hyperthermophilic archaeon Aeropyrum.
  Daifuku, T., Yoshida, T. and Sako, Y. (2013).
  Mob. Genet. Elements., 3, e26833.
• Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum.
  Daifuku, T., Yoshida, T., Kitamura, T., Kawaichi, S., Inoue, T., Nomura, K., Yoshida, Y., Kuno, S. and Sako, Y. (2013).
  Appl. Environ. Microbiol., 79, 5891-5898.
• A novel thermophilic, hydrogenogenic, and carboxydotrophic bacterium Calderihabitans maritimus gen. nov., sp. nov. from a marine sediment core of an undersea caldera.
  Yoneda, Y., Yoshida, T., Yasuda, H., Imada, C. and Sako, Y. (2013).
  Int. J. Syst. Evol. Microbiol., 63, 3602-3608
• Imaging fully hydrated whole cells by coherent x-ray diffraction microscopy.
  Nam, D., Park, J., Gallagher-Jones, M., Kim, S., Kim, S., Kohmura, Y., Naitou, H., Kunishima, N., Yoshida, T., Ishikawa, T. and Song, C. (2013).
  Phys. Rev. Lett., 110, 098103.
• Quantitative Detection of Carboxydotrophic Bacteria Carboxydothermus in a hot aquatic environment.
  Yoneda, Y., Yoshida, T., Daifuku, T., Kitamura, T., Inoue, T., Kano, S. and Sako, Y. (2013).
  Fundam. Appl. Limnol., 182, 161-170
• Rapid Microcystis cyanophages gene diversification revealed by long- and short-term genetic analysis of the tail sheath gene in a natural pond.
  Kimura, S., Sako, Y. and Yoshida, T. (2013).
  Appl. Environ. Microbiol., 79, 2789-2795.
• Ardenticatena maritima gen.nov., sp. nov., a ferric iron-reducing lineage of the phylum Chloroflexi isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov.
  Kawaichi, S., Ito N., Kamikawa, R., Sugawara, T., Yoshida, T. and Sako, Y. (2013).
  Int. J. Syst. Evol. Microbiol., 63, 2992-3002.
• Bacterial and archaeal diversity in an iron-rich coastal hydrothermal field in Yamagawa, Kagoshima, Japan.
  Kawaichi, S., Ito N., Yoshida, T. and Sako, Y. (2013).
  Microbes and Environments., 28, 405-413.

2012

• The first assessment of cyanobacterial and diazotrophic diversities in the Japan Sea.
  Hashimoto, R., Yoshida, T., Kuno, S., Nishikawa, T. and Sako, Y. (2012).
  Fish. Sci., 78, 1293-1300
• Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring.
  Yoneda, Y., Yoshida, T., Kawaichi, S, Daifuku, T., Takabe, K. and Sako, Y. (2012).
  Int J Syst Evol Microbiol., 62, 1692-97.
• Intricate Interactions between the Bloom-Forming Cyanobacterium Microcystis aeruginosa and Foreign Genetic Elements Revealed by Diversified CRISPR Signatures.
  Kuno, S., Yoshida, T., Kaneko, T. and Sako, Y. (2012).
  Appl. Environ. Microbiol., 78, 5353-60.
• Diurnal infection patterns and impact of Microcystis cyanophage in a Japanese pond.
  Kimura, S., Yoshida, T., Hosoda, N., Honda, T., Kuno, S., Kamiji, R., Hashimoto, R. and Sako, Y. (2012).
  Appl. Environ. Microbiol., 78, 5805-11.
• Cyanophage infection in the bloom-forming cyanobacteria Microcystis aeruginosa in surface freshwater.
  Yoshida-Takashima, Y., Yoshida, M., Ogata, H., Nagasaki, K., Hiroishi, S. and Yoshida, T. (2012).
  Microbes Environ., 27, 350-355.
• Thermotomaculum hydrothermale　gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough.
  Izumi, H., Nunoura,T., Miyazaki, M., Mino, S., Toki, T., Takai, K., Sako, Y., Sawabe, T. and Nakagawa, S. (2012).
  Extremophiles, 16, 245-253.
• Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome.
  Mochizuki, T., Krupovic, M., Pehau-Arnaudet, G., Sako, Y., Forterre, P. and Prangishvili, D. (2012).
  Proc. Natl. Acad. Sci., 109, 13386-13391.

2011

• A protein binding to an upstream sequence of ftsZ involved in coordination of DNA replication and cell division in Microcystis aeruginosa.
  Honda, T., Yoshida, T., Hiroishi, S. and Sako, Y. (2011).
  Fish. Sci., 78, 375-379.
• Provirus Induction in Hyperthermophilic Archaea: Characterization of Aeropyrum pernix Spindle-Shaped Virus 1 and Aeropyrum pernix Ovoid Virus 1.
  Mochizuki, T., Sako, Y. and Pranqishvili, D. (2011).
  J. Bacteriol., 193, 5412-5419.
• Contribution of Anammox Bacteria to Benthic Nitrogen Cycling in Mangrove Forest and Shrimp Pond, Haiphong, Vietnam.
  Amano, T., Yoshinaga, I., Yamagishi, T., Thuoc, C. V., Thu, P. T., Ueda, S., Kato, K., Sako, Y. and Suwa Y. (2011).
  Microbes Environ., 26, 1-6.
• Distribution and Diversity of Anaerobic Ammonium Oxidation (Anammox) Bacteria in the Sediment of a Eutrophic Freshwater Lake, Lake Kitaura, Japan.
  Yoshinaga, I., Amano, T., Yamagishi, T., Okada, K., Ueda, S., Sako, Y. and Suwa, Y. (2011).
  Microbes Environ., 26, 189-197.
• dehydrogenaseⅡ from thermophilic bacterium Carboxydothermus hydrogenoformans.
  Inoue, T., Yoshida, T., Wada, K., Daifuku, T., Fukuyama, K. and Sako, Y. (2011).
  Biosci. Biotechnol. Biochm., 75, 1392-4.
• Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.
  Yoshida, T., Claverie, J.-M., and Ogata, H. (2011).
  Virol J., 8, 427.
• The functional effect of Gly209 and Ile213 substitutions on lysozyme activity of family 19 chitinase encoded by cyanophage Ma-LMM01.
  Hosoda, N., Kurokawa, Y., Sako, Y., Nagasaki, K., Yoshida, T. and Hiroishi, S. (2011).
  Fish. Sci., 77, 665-670.

2010

• Genetic diversity and expression of carbon monoxide dehydrogenase from Aeropyrum pernix.
  Nishimura, H., Sato, N., Nomura, Y., Iwata, E. and Sako, Y. (2010).
  Fish. Sci., 77, 135-141.
• Mitochondrial genomes from two red tide forming raphidophycean algae Heterosigma akashiwo and Chattonella marina var. marina.
  Masuda, I., Kamikawa, R., Ueda, M., Oyama, K., Yoshimatsu, S., Inagaki, Y. and Sako, Y. (2010).
  Harmful Algae, 10, 130-137.
• The Distribution of a Phage-Related Insertion Sequence Element in the Cyanobacterium, Microcystis aeruginosa.
  Kuno, S., Yoshida, T., Kamikawa, R., Hosoda, N. and Sako, Y. (2010).
  Microbes Environ., 25, 295-301.
• Purification and characterization of carbon monoxide dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix.
  Nishimura, H., Nomura, Y., Iwata, E., Sato, N. and Sako, Y. (2010).
  Fish. Sci., 76, 999-1006.
• Purification and characterization of membrane-associated hydrogenase from the deep-sea epsilonproteobacterium Hydrogenimonas thermophila.
  Nishimura, H., Kitano, Y., Inoue, T., Nomura, K. and Sako, Y. (2010).
  Biosci. Biotechnol. Biochem., 74, 1624-1630.
• Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family \”Clavaviridae\”.
  Mochizuki, T., Yoshida, T., Tanaka, R., Forterre, P., Sako, Y. and Prangishvili, D. (2010).
  Virology, 402, 347-352.
• Algicidal bacteria in particle-associated form and in free-living form during a diatom bloom in the Seto Inland Sea, Japan.
  Park, J.-H., Yoshinaga, I., Nishikawa, T. and Imai, I. (2010).
  Aquat. Microb. Ecol., 60, 151-161.
• Genetic diversity of the ciguatera fish poisoning dinoflagellates Gambierdiscus spp. (Gonyaulacales, Dinophyceae) in Japanese coastal aera.
  Kuno, S., Kamikawa, R., Yoshimatsu, S., Sagara, T., Nishio, S. and Sako, Y. (2010).
  Phycol. Res., 58, 44-52.
• Real-Time PCR Detection of Host-Mediated Cyanophage Gene Transcripts during Infection of a Natural Microcystis aeruginosa Population.
  Yoshida, M., Yoshida, T., Yoshida-Takashima, Y., Kashima, A. and Hiroishi, S. (2010).
  Microbes Environ., 25, 211-215.

2009

• Analysis of the mitochondrial genome, transcripts, and electron transport activity in the dinoflagellate Alexandrium catenella (Gonyaulacales, Dinophyceae).
  Kamikawa, R., Nishimura, H. and Sako, Y. (2009).
  Phycol. Res., 57, 1-11.
• Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene.
  Yokobori, S., Itoh, T., Yoshinari, S., Nomura, N., Sako, Y., Yamagishi, A., Oshima, T., Kita, K. and Watanabe, Y. (2009).
  BMC Evol. Biol., 9, 198.
• Isolation of a Bacterium Possessing a Haloacid Dehalogenase from a Marine Sediment Core.
  Chiba, Y., Yoshida, T., Ito, N., Nishimura, H., Imada, C., Yasuda, H. and Sako, Y. (2009).
  Microbes. Environ., 24, 276-279.
• Mitochondrial groupII intronsin the Raphidophycean flagellate Chattonella spp. suggest a diatom-to-Chattonella Lateral groupII intron transfer.
  Kamikawa, R., Matsuda, I., Demura, M., Oyama, K., Yoshimatsu, S., Kawaichi, M. and Sako, Y. (2009).
  Protist., 160, 364-375.
• Purification and characterization of the oxygen-thermostable hydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum camini.
  Nishimura, H. and Sako, Y. (2009).
  J. Biosci. Bioeng., 108, 299-303.
• Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes.
  Kamikawa, R., Sanchez-perez, G. F., Sako, Y., Roger, A. J. and Inagaki, Y. (2009).
  Mol. Phylogenet. Evol., 5, 565-570.

2008

• Development of a novel molecular marker on mitochondrial genome in the toxic dinoflagellate Alexandrium spp., and its application in single cell PCR.
  Kamikawa, R., Hosoi-Tanabe, S., Yoshimatsu, S., Oyama, K., Masuda, I. and Sako, Y. (2008).
  J. Appl. Phycol., 20, 153-159.
• Direct phylogenetic evidence for lateral transfer of elongation factor-like gene.
  Kamikawa, R., Inagaki, Y. and Sako, Y. (2008).
  Proc. Natl. Acad. Sci., 105, 6965-6969.
• Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies.
  Yoshida, T., Nagasaki, K., Takashima, Y., Shirai, Y., Tomaru, Y., Takao, Y., Sakamoto, S., Hiroishi, S. and Ogata, H. (2008).
  J. Bacteriol., 190, 1726-1772.
• Intra-specific phenotypic and genotypic variation in toxic cyanobacterial Microcystis strains.
  Yoshida, M., Yoshida, T., Satomi, M., Takashima, Y., Hosoda, N. and Hiroishi, S. (2008).
  J. Appl. Microbiol., 105, 407-415.
• Ecological dynamics of the toxic bloom-forming cyanobacterium Microcystis aeruginosa and its cyanophages in freshwater.
  Yoshida, M., Yoshida, T., Kashima, A., Takashima, Y., Hosoda, N., Nagasaki, K. and Hiroishi, S. (2008).
  Appl. Environ. Microbiol., 74, 3269-3273.

2007

• Genetic variation in mitochondrial genes and intergenic spacer region in harmful algae Chattonella species.
  Kamikawa,R., Masuda, T., Oyama, K., Yoshimatsu, S. and Sako, Y. (2007).
  Fish Sci., 73, 871-880.
• Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polarnetworks to thermostability.
  Nakayama, H., Shimamura, T., Imagawa, T., Shirai, N., Itoh, T., Sako, Y., Miyano, M., Sakuraba, H., Ohshima, T., Nomura, N. and Tsuge, H. (2007).
  J. Mol. Biol., 365, 362-378.
• Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolatemitochondria.
  Kamikawa, R., Inagaki, Y. and Sako, Y. (2007). Protist., 158, 239-245.
• Application of real-time PCR assay for detection and quantification of Alexandrium tamarense and A. catenella.
  Kamikawa, R., Nagai, S., Hosoi-Tanabe, S., Itakura, S., Yamaguchi, M., Uchida, Y., Baba, T. and Sako, Y. (2007).
  Harmful Algae, 6, 413-420.
• Proposal of Pseudochattonella verruculosa gen. nov., comb. nov. (Dictyochophyceae) for a formar raphidophycean alga Chattonella verruculosa, based on 18S rDNA phylogeny and ultrastructura characteristics.
  Hosoi-Tanabe, S., Honda, D., Fukaya, S., Otake, I., Inagaki, Y. and Sako, Y. (2007).
  Phycol. Res., 55, 185-192.
• Detection of Anammox Activity and Diversity of Anammox Bacteria-related 16S rRNA Genes in Coastal Marine Sediment in Japan.
  Amano, T., Yoshinaga, I., Okada, K., Yamagishi, T., Ueda, S., Obuchi, A., Sako, Y. and Suwa, Y. (2007).
  Microbes Environ., 22, 232-242.
• Dynamics of microcystin-producing and non-microcystin-producing Microcystis populations are correlated with nitrogen concentrations in a Japanese lake.
  Yoshida, M., Yoshida, T., Takashima, Y., Hosoda, N. and Hiroishi, S. (2007).
  FEMS Microbiol. Lett., 266, 49-53.
• Development of a competitionmodel for two cyanobacteria species Lake Mikata.
  Sang-Ho, B., Otake, S., Yoshida, Y. and Hiroishi, S. (2007).
  Fisheries Engineering, 44, 1-9.
• Cryopreservation of a myovirus infecting the toxin-producing cyanobacterium Microcystis aeruginosa.
  Takashima, Y., Yoshida T., Kashima, A., Hiroishi, S. and Nagasaki, K. (2007).
  Microbes Environ., 22, 297-299.
• Development and application of quantitative detection of cyanophages phylogenetically related to cyanophage Ma-LMM01 infecting Microcystis aeruginosa in fresh water.
  Takashima, Y., Yoshida, T., Yoshida M., Shirai Y., Tomaru Y., Takao Y., Hiroishi, S. and Nagasaki, K. (2007).
  Microbes Environ., 22, 207-213.

2006

• Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field.
  Tanaka, R., Kawaichi, S., Nishimura, H. and Sako, Y. (2006).
  Int. J. Syst. Evol. Microbiol., 56, 1531-1534.
• Microbial community in black rust exposed to hot ridge flank crustal fluids.
  Nakagawa, S., Inagaki, F., Suzuki, Y., Steinsbu, B.O., Lever, M.A., Takai, K., Engelen, B., Sako, Y., Wheat, C.W., Horikoshi, K. et al. (2006).
  Appl. Environ. Microbiol., 72, 6789-6799.
• Development and application of fluorescence in situ hybridization (FISH) method for simple and rapid identification of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella in cultured and natural seawater.
  Hosoi-Tanabe, S. and Sako, Y. (2006).
  Fish. Sci., 72, 77-82.
• Application of a real-time PCR assay to a comprehensive method for monitoring harmful algae.
  Kamikawa, R., Asai, J., Miyahara, T., Murata, K., Oyama, K., Yoshimatsu, S., Yoshida, T. and Sako, Y. (2006).
  Microbes Environ., 21, 163-173.
• Genetic differentiation in the marine dinoflagellates Alexandrium tamarense and Alexandrium catenella based on DNA-DNA hybridization.
  Hosoi-Tanabe, S. and Sako, Y. (2006).
  Plankton Benthos Res., 1, 138-146.
• Isolation and Characterization of a Cyanophage Infecting the Toxic Cyanobacterium Microcystis aeruginosa.
  Yoshida, T., Takashima, Y., Tomaru, Y., Shirai, Y., Takao, Y., Hiroishi, S. and Nagasaki, K. (2006).
  Appl. Environ. Microbiol., 72, 1239-1247.

2005

• ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1.
  Nomura, N., Morinaga, Y., Shirai, N. and Sako, Y. (2005).
  Nucleic Acid Res., 33, e116
• Species-Specific Detection and Quantification of Toxic Marine Dinoflagellates Alexandrium tamarense and A. catenella by Real-Time PCR Assay.
  Hosoi-Tanabe, S. and Sako, Y. (2005).
  Marine Biotechnol., 7, 506-514
• Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field.
  Nakagawa, S. Takai, K., Inagaki, F., Hirayama, H., Nunoura, T., Horikoshi, K. and Sako,Y. (2005).
  Environ. Microbiol., 7, 1619-1632.
• Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase separation.
  Nakagawa, S., Takai, K., Inagaki, F., Chiba, H., Ishibashi, J., Kataoka, S., Hirayama, H., Nunoura, T., Horikoshi, K. and Sako, Y. (2005).
  FEMS Microbiol. Ecol., 54, 141-155.
• Nitratiraputor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the e-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough.
  Nakagawa, S., Takai, K., Inagaki, F., Horikoshi, K. and Sako, Y. (2005).
  Int. J. Syst. Evol. Microbiol., 55, 925-933.
• Thioreductor micantilosi gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the e-Proteobacteria isolated from hydrothermal sediments in the Mid-Okinawa Trough.
  Nakagawa, S., Inagaki, F., Takai, K., Horikoshi, K. and Sako, Y. (2005).
  Int. J. Syst. Evol. Microbiol., 55, 599-605.
• Cytochrome aa3 in facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense.
  Nunoura, T., Sako, Y., Wakagi, T. and Uchida, A. (2005).
  Can. J. Microbiol., 51, 621-627.
• Development of molecular identification method for genus Alexandrium (Dinophyceae) using whole-cell FISH.
  Kim, C.J., Kim, C.H. and Sako, Y. (2005).
  Marine Biotechnol., 7, 215-222.
• Identification of a gene induced in conjugation-promoted cells of toxic marine dinoflagellates Alexandrium tamarense and Alexandrium catenella using differential display analysis.
  Hosoi-Tanabe, S., Tomishima, S., Nagai, S. and Sako, Y. (2005).
  FEMS Microbiol. Lett., 251, 161-168.
• Paralytic shellfish poisoning toxin analysis of the genus Alexandrium (Dinophyceae) occurring in Korea coastal waters.
  Kim, C.-J., Kim, C-H. and Sako, Y. (2005).
  Fish. Sci., 71, 1-11.
• Genetic diversity of the toxic cyanobacterium Microcystis in Lake Mikata. Environ.
  Takashima, Y., Kondo, R. and Hiroishi, S. (2005).
  Toxicol., 20, 229-234.
• High toxicity of the novel bloom-forming species Chattonella ovata (Raphidophyceae) to cultured fish.
  Hiroishi, S., Okada, H., Imai, I. and Yoshida, T. (2005).
  Harmful Algae., 4, 783-787.
• Coordination of DNA replication and cell division in Cyanobacteria Microcystis aeruginosa.
  Yoshida, T., Maki, M., Okamoto,H. and Hiroishi, S. (2005).
  FEMS Microbiol. Lett., 251, 149-154.
• Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterophilic sulfuroxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense.
  Nakagawa, S., Shtaih, Z., Banta, A., Beveridge, T. J., Sako, Y. and Reysenbach, A.-L. (2005).
  Int. J. Syst. Evol. Microbiol., 55, 2263-2268.