Site Map
Integrated Symbiology

 
 

HOME | Publications

Publications
2018  2017

Hara, Y., Yamaguchi, K., Onimaru, K., Kadota, M., Koyanagi, M., Keeley, SD., Tatsumi, K., Tanaka, K., Motone, F., Kageyama, Y., Nozu, R., Adachi, N., Nishimura, O., Nakagawa, R., Tanegashima, C., Kiyatake, I., Matsumoto, R., Murakumo, K., Nishida, K., Terakita, S., Kuratani, S., Sato, K., Hyodo, S., Kuraku, S. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. (2018) Nature Ecology and Evolution, 2, 1761-1771. doi:10.1038/s41559-018-0673-5


Shen, X.X., Opulente, D.A., Kominek, J., Zhou, X., Steenwyk, J.L., Buh, K.V., Haase, M.A.B., Wisecaver, J.H., Wang, M., Doering, D.T., Boudouris, J.T., Schneider, R.M., Langdon, Q.K., Ohkuma, M., Endoh, R., Takashima, M., Manabe, R.I,. Čadež, N., Libkind, D., Rosa, C.A., DeVirgilio, J., Hulfachor, A.B., Groenewald, M., Kurtzman, C.P., Hittinger, C.T., Rokas, A. Tempo and mode of genome evolution in the budding yeast subphylum. (2018) Cell, (available online 8 November 2018) doi: 10.1016/j.cell.2018.10.023


Nakajima, A., A. Vogelzang, M. Maruya, M. Miyajima, M. Murata, A. Son, T. Kuwahara, T. Tsuruyama, S. Yamada, M. Matsuura, H. Nakase, D.A. Peterson, S. Fagarasan, and K. Suzuki. 2018. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J Exp Med 215:2019-2034. doi:10.1084/jem.20180427


Sergey P. Laptenok , Agnieszka A. Gil, Christopher R. Hall, Andras Lukacs, James N. Iuliano, Garth A. Jones, Gregory M. Greetham, Paul Donaldson, Atsushi Miyawaki, Peter J. Tonge, Stephen R. Meech (2018) Infrared spectroscopy reveals multi-step multi-timescale photoactivation in the photoconvertible protein archetype dronpa. Nature Chemistry 10, 845-852. doi:10.1038/s41557-018-0073-0


Otaka, J., Shimizu, T., Futamura, Y., Hashizume, D., Osada, H. Structures and synthesis of hitoyopodins: bioactive aromatic sesquiterpenoids produced by the mushroom Coprinopsis cinerea. (2018) Organic Letters, 20, 6294-6297. doi: 10.1021/acs.orglett.8b02788


Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET. Core microbiomes for sustainable agroecosystems. Nature Plants 4: 247-257. (2018) doi:10.1038/s41477-018-0139-4


Ostria-Gallardo E, Ranjan A, Ichihashi Y, Corcuera L, Sinha N. Decoding the gene co-expression network underlying the ability of Gevuina avellana to live in diverse light conditions. New Phytologist 220(1): 278-287. (2018) doi:10.1111/nph.15278


Iwano, S., Sugiyama, M., Hama, H., Watakabe, A., Hasegawa, N., Kuchimaru, T., Tanaka K.Z., Takahashi, M., Ishida, Y., Hata, J., Shimozono, S., Namiki, K., Fukano, T., Kiyama, M., Okano, H., Kizaka-Kondoh, S., McHugh T.J., Yamamori, T., Hioki, H., Maki, S., Miyawaki, A. Single-cell bioluminescence imaging of deep tissue in freely moving animals. (2018) Science, 359, 935-939. doi:10.1126/science.aaq1067 


Myung, J., Schmal, C., Hong, S., Tsukizawa, Y., Rose, P., Zhang, Y., Holtzman, M.J., De Schutter, E., Herzel, H., Bordyugov, G., Takumi, T. The choroid plexus is an important circadian clock component. (2018) Nature Communications, 9, 1062. doi: 10.1038/s41467-018-03507-2.


Costea, PI., Hildebrand, F., Manimozhiyan, A., Bäckhed, F., Blaser, MJ., Bushman, FD., de Vos, WM., Ehrlich, SD., Fraser, CM., Hattori, M., Huttenhower, C., Jeffery, IB., Knights, D., Lewis, JD., Ley, RE., Ochman, H., O'Toole, PW., Quince, C., Relman, DA., Shanahan, F., Sunagawa, S., Wang, J., Weinstock, GM., Wu, GD., Zeller, G., Zhao, L., Raes, J., Knight, R., Bork, P. Enterotypes in the landscape of gut microbial community composition. (2018) Nat. Microbiol., 3, 8-16. doi: 10.1038/s41564-017-0072-8.


Takumi, T., Tamada, K. CNV biology in neurodevelopmental disorders. (2018)Current Opinion in Neurobiology, 48, 183-192. doi: 10.1016/j.conb.2017.12.004.


Suzuki S, Endo R, Manabe R, Ohkuma M, Hirakawa Y. Multiple losses of photosynthesis and convergent reductive genome evolution in the colorless green algae Prototheca. (2018) Scientific Reports, 8, 940. doi: 10.1038/s41598-017-18378-8


Kaizuka, T., Takumi, T. Postsynaptic density proteins and their involvement in neurodevelopmental disorders. (2018)Journal of Biochemistry, doi: 10.1093/jb/mvy022.


Wu, M., Takemoto, M., Luo, H., Xu, J.J., Lu, M.H., Kameyama, M., Takumi, T., Song, W.J. A novel role of the antitumor agent tricyclodecan-9-yl-xanthogenate as an open channel blocker of KCNQ1/KCNE1. (2018) European Journal of Pharmacology, doi: 10.1016/j.ejphar.2018.02.013.


Koizumi T, Hattori M, Nara K. Ectomycorrhizal fungal communities in alpine relict forests of Pinus pumila on Mt. Norikura, Japan.(2018) Mycorrhiza, 28, 129-145. doi: 10.1007/s00572-017-0817-5.


Chiou, TY., Suda, W., Oshima, K., Hattori, M., Matsuzaki, C., Yamamoto, K., Takahashi, T. Lactobacillus kosoi sp. nov., a fructophilic species isolated from kôso, a Japanese sugar-vegetable fermented beverage. (2018) Antonie Van Leeuwenhoek, in press. doi:10.1007/s10482-018-1019-7.


Kumagai, Y., Yoshizawa, S., Nakajima, Y., Watanabe, M., Fukunaga, T., Ogura, Y., Hayashi, T,, Oshima, K., Hattori, M., Ikeuchi, M., Kogure, K., DeLong, EF., Iwasaki, W. Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. (2018) ISME J., in press. doi:10.1038/s41396-018-0058-4.


Nanki, K., Mizuno, S., Matsuoka, K., Ono, K., Sugimoto, S., Kiyohara, H., Arai, M., Nakashima, M., Takeshita, K., Saigusa, K., Senoh, M., Fukuda, T., Naganuma, M., Kato, H., Suda, W., Hattori, M., Kanai, T. Fecal microbiota transplantation for recurrent Clostridium difficile infection in a patient with ulcerative colitis.(2018) Intest. Res., 16, 142-146. doi: 10.5217/ir.2018.16.1.142


Mori, K., Nakamura, H., Kurooka, H., Miyachi, H., Tamada, K., Sugai, M., Takumi, T., Yokota, Y. Id2 determines intestinal identity through repression of the foregut transcription factor, Irx5. (2018)Molecluar and Cellular Biology, doi: 10.1128/MCB.00250-17.


Onimaru, K., Motone, F., Kiyatake, I., Nishida, K., Kuraku, S. A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum). (2018) Developmental Dynamics, accepted. doi:10.1002/dvdy.24623


Onimaru, K., Kuraku, S. Inference of the ancestral vertebrate phenotype through vestiges of the whole genome duplications. (2018) Briefings in Functional Genomics, accepted. doi: 10.1093/bfgp/ely008


Nogawa, T,. Kato, N., Shimizu, T., Okano, A., Futamura, Y., Takahashi, S., Osada, H. Wakodecalines A and B, new decaline metabolites isolated from a fungus Pyrenochaetopsis sp. RK10-F058 (2018) Journal of Antibiotics, 71, 123–128. doi: 10.1038/ja.2017.103


Kawaichi, S., Yamada, T., Umezawa, A., McGlynn, E. S., Suzuki, T., Dohme, N., Yoshida, T., Sako, Y., Matsushita, N., Hashimoto, K., Nakamura, R., Anodic and cathodic extracellular electron transfer by the filamentous bacterium Ardenticatena maritima 110S (2018) Front. Microbiol., doi: 10.3389/fmicb.2018.00068.


Iriki A, McCairn K. (2018) Brain mechanisms of tool-use that advance our knowledge beyond the border ~Neural correlates of “proto-language” in the monkey brain~, In: B Gulyás, J W Vasbinder, (Eds.), Cultural Patterns and Neurocognitive Circuits II: East-West Connections, World Sci Pub, Singapore, pp 73-111. doi: 10.1142/9789813230484_0004


Woodward A, Hashikawa T, Maeda M, Kaneko T, Hikishima K, Iriki A, Okano H, Yamaguchi Y. The Brain/MINDS digital marmoset brain atlas.(2018) Sci Data, 5,180009. doi: 10.1038/sdata.2018.9


Kato M, Yokoyama C, Kawasaki A, Takeda C, Koike T, Onoe H, Iriki A. Individual identity and affective valence in marmoset calls: in vivo brain imaging with vocal sound playback. (2018) Anim Cogn, in press. doi:10.1007/s10071-018-1169-z


Iriki A, Okano HJ, Sasaki E, Okano H. (Eds.), Hashikawa T, Hikishima K, Nakatomi R. (Contributors). The 3-Dimensional Atlas of the Marmoset Brain: Reconstructible in Stereotaxic Coordinates. (2018) Springer, Tokyo, in press. doi: 10.1007/978-4-431-56612-0


Kumazawa-Manita N, Hashikawa T, Iriki A. The 3D Stereotaxic Brain Atlas of the Degu (Octodon degu): with MRI and Histology Digital Model with a Freely Rotatable Viewer. (2018) Springer, Tokyo, in press. doi: 10.1007/978-4-431-56615-1


Kosugi A, Takemi M, Tia b, Castagnola E, Ansaldo A, Sato K, Awiszus F, Seki K, Ricci D, Fadiga L, Iriki A, Ushiba J. Accurate motor mapping using micro-electrocorticographic stimulation and stochastic threshold-hunting algorithm: a common marmoset study.(2018) J Neural Eng, in press. doi: 10.1088/1741-2552/aab307


Noda, S., Shimizu, D., Yuki, M., Kitade, O., Ohkuma, M. Host- symbiont co-speciation of termite-gut cellulolytic protist of the genera Teranympha and Eucomonympha and their Treponema endosymbionts. (2018) Microbes and Environments, 33, 26-33. doi: 10.1264/jsme2.ME17096


Utami, Y.D., Kuwahara, H., Murakami, T., Morikawa, T., Sugaya, K., Kihara, K., Yuki, M., Lo, N., Deevong, P., Hasin, S., Boonriam, W., Inoue, T., Yamada, A., Ohkuma, M., Hongoh, Y. Phylogenetic diversity and single-cell genome analysis of “Melainabacteria”, a non-photosynthetic cyanobacterial group, in the termite gut. (2018) Microbes and Environments, 33: 50-57. doi: 10.1264/jsme2.ME17137


Yuki M, Sakamoto M, Nishimura Y, Ohkuma M. Lactococcus reticulotermitis sp. nov., isolated from the gut of thesubterranean termite Reticulitermes speratus. (2018)impactInternational Journal of Systematic and Evolutionary Microbiology, 68, 596-601. 10.1099/ijsem.0.002549


Takashima M, Sriswasdi S, Manabe R, Ohkuma M, Sugita T, Iwasaki W. A Trichosporonales genome tree based on 27 haploid and three evolutionary conserved ‘natural’ hybrid genomes. (2018) Yeast, 35, 99-111. doi:10.1002/yea.3284


Wardell, CP., Fujita, M., Yamada, T., Simbolo, M., Fassan, M., Karlic, R., Polak, P., Kim, J., Hatanaka, Y., Maejima, K., Lawlor, RT., Nakanishi, Y., Mitsuhashi, T., Fujimoto, A., Furuta, M., Ruzzenente, A., Conci, S., Oosawa, A., Sasaki-Oku, A., Nakano, K., Tanaka, H., Yamamoto, Y., Kubo, M., Kawakami, Y., Aikata, H., Ueno, M., Hayami, S., Gotoh, K., Ariizumi, S., Yamamoto, M., Yamaue, H., Chayama, K., Miyano, S., Getz, G., Scarpa, A., Hirano, S., Nakamura, T., and Nakagawa, H. Genomic characterization of biliary tract cancers identifies their driver genes and predisposing mutations. (2018) J Hepatol, in press. doi: 10.1016/j.jhep.2018.01.009


Furuta, M., Tanaka, H., Shiraishi, Y., Unida, T., Imamura, M., Fujimoto, A., Fujita, M., Oku-Sasaki, A., Maejima, K., Nakano, K., Kawakami, Y., Arihiro, K., Aikata, H., Ueno, M., Hayami, S., Ariizumi, S., Yamamoto, M., Gotoh, K., Ohdan, H., Yamaue, H., Miyano, S., Chayama, K., and Nakagawa, H. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected liver. (2018) Oncotarget, in press.


VanderWeele, DJ., Finney, R., Katayama, K., Gillard, M., Paner, G., Imoto, S., Yamaguchi, R., Wheeler, D., Cam, M., Pontier, A., Maejima, K., Sasaki-Oku, A., Nakano, K., Tanaka, H., Kubo, K., Ratain, MJ., Miyano, S., and Nakagawa, H. Genomic heterogeneity within individual prostate cancer foci impacts predictive biomarkers of targeted therapy. (2018) Eur Urol Focus, in press. doi:10.1016/j.euf.2018.01.006


Kanaya, T., Sakakibara, S., Jinnohara, T., Hachisuka, M., Tachibana, N., Hidano, S., Kobayashi,T., Kimura, S., Iwanaga, T., Nakagawa, T., Katsuno, T., Kato, N., Akiyama, T., Sato, T., Williams, I. R., Ohno, H. Development of intestinal M cells and follicle-associated epithelium is regulated by TRAF6-mediated NF-kB signaling. (2018) J. Exp. Med. 215:501-519.doi: 10.1084/jem.20160659.


Kato, N., Furutani, S., Otaka, J., Noguchi, A., Kinugasa, K., Kai, K., Hayashi, H., Ihara, M., Takahashi, S., Matsuda, K., Osada, H. Biosynthesis and structure-activity relationship studies of okaramines that target insect glutamate-gated chloride channels.(2018) ACS Chem. Biol.,13 (3): 561-566. doi: 10.1021/acschembio.7b00878


Takagi, H., Nogawa, T., Futamura, Y., Takahashi, S., and Osada, H. Kinanthraquinone, a new anthraquinone carboxamide isolated from Streptomyces reveromyceticus SN-593-44.(2018) J. Antibiot. in press. doi: 10.1038/s41429-017-0020-0


Date, Y. and Kikuchi, J. Application of a deep neural network to metabolomics studies and its performance in determining important variables. (2018) Anal. Chem. 90, 1805-1810. doi: 10.1021/acs.analchem.7b03795


Asakura, T., Sakata, K., Date, Y. and Kikuchi, J. Application of ensemble deep neural network to metabolomics studies. (2018) Anal. Chim. Acta. in press. doi: 10.1016/j.aca.2018.02.045


Wei, F., Sakata, K., Asakura, T., Date, Y. and Kikuchi, J. Systemic Homeostasis in Metabolome, Ionome and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem. (2018) Sci. Rep. 8, 3478. doi: 10.1038/s41598-018-20120-x


Kikuchi, J., Ito, K. and Date, Y. Environmental metabolomics with data science as investigation of ecosystem homeostasis. (2018) Progress in NMR Spectroscopy 104, 56-88. doi: 10.1016/j.pnmrs.2017.11.003


菊地淳、武部孝行 “エコインフォマティクスによる難養殖魚種の持続的生産管理構想” (2018)アグリバイオ 28, 344-347


Yamaya-Ito, H., Shimoda, Y., Hakoyama, T., Sato, S., Kaneko, T., Hossain, M.S., Shibata, S., Kawaguchi, M., Hayashi, M., Kouchi, H., Umehara, Y. Loss-of-function of ASPARTIC PEPTIDASE NODULE- INDUCED 1 (APN1) in Lotus japonicus restricts efficient nitrogen-fixing symbiosis with specific Mesorhizobium loti strains. (2018) Plant J. 93: 5-16. doi: 10.1111/tpj.13759


Germond, A., Ichimura, T., Horinouchi, T., Fujita, H., Furusawa, C., Watanabe, T.M. Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli. Communication Biology (2018) 1:85. doi:10.1038/s42003-018-0093-8




Germond, A., Ichimura, T., Chiu, L., Fujita, K., Watanabe, T.M., Fujita, H. Cell type discrimination based on image features of molecular component distribution. Scientific Reports, volume 8, Article number: 11726 (2018) doi: 10.1038/s41598-018-30276-1


Iritani S, Torii Y, Habuchi C, Sekiguchi H, Fujishiro H, Yoshida M, Go Y, Iriki A, Isoda M, Ozaki N. (2018) The neuropathological investigation of the brain of a monkey model of autism spectrum disorder with ABCA13 deletion, Int J Dev Neurosci, 71, 130-139. doi:10.1016/j.ijdevneu.2018.09.002


Iriki A (2018) On Cognitive Evolution, Inference: International Review of Science, <http://inference- review.com/article/on-cognitive-evolution>


Onimaru, K., Tatsumi, K., Shibagaki, K., Kuraku, S. A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra. (2018) Scientific Data, 5,180197. doi: 10.1038/sdata.2018.197


Tanegashima, C., Nishimura, O., Motone, F., Tatsumi, K., Kadota, M., Kuraku, S. Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei. (2018) Scientific Data, 5, 180200. doi: 10.1038/sdata.2018.200


Hara, Y., Takeuchi, M., Kageyama, Y., Tatsumi, K., Hibi, M., Kiyonari, H., Kuraku, S. Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes. (2018) BMC Biology, 16, 40. doi: 10.1186/s12915-018-0509-4


Furuta M, Tanaka H, Shiraishi Y, Unida T, Imamura M, Fujimoto A, Fujita M, Oku-Sasaki A, Maejima K, Nakano K, Kawakami Y, Arihiro K, Aikata H, Ueno M, Hayami S, Ariizumi S, Yamamoto M, Gotoh K, Ohdan H, Yamaue H, Miyano S, Chayama K*, and Nakagawa H*. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected liver. Oncotarget9:25075-25088 (2018) doi: 10.18632/oncotarget.25308


Boot A, Huang MN, Ng AW, Ho SC, Lim JQ, Kawakami Y, Chayama K, Teh BT, Nakagawa H, and Rozen SG. In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. Genome Res 28: 654-665 (2018) doi:10.1101/gr.230219.117


Kato, N., Nogawa, T., Takita, R., Kinugasa, K., Kanai, M., Uchiyama, M., Osada, H., Takahashi, S. Control of the stereochemical course of [4+2] cycloaddition during trans-decalin formation by Fsa2-family enzymes. (2018) Angewandte Chemie International Edition in English, 57, 9754-9758. doi: 10.1002/anie.201805050


Qi, J., Cheng, L., Sun, Y., Hirata, Y., Ushida, N., Ma, Z., Osada, H., Nishikawa, T., Xiang, L. Identification of an asexual reproduction inducer of phytopathogenic and toxigenic Fusarium. (2018) Angewandte Chemie International Edition in English, 57, 8100-8104. doi: 10.1002/anie.201803329


Maeda, K., Ichikawa, H., Nakajima, Y., Motoyama, T., Ohsato, S., Kanamaru, K., Kobayashi, T., Nishiuchi, T., Osada, H., Kimura, M. Identification and characterization of small molecule compounds that modulate trichothecene production by Fusarium graminearum. (2018) ACS Chemical Biology, 13, 1260-1269. doi: 10.1021/acschembio.8b00044


He, D., Li, Y., Ooka, H., Go, Y. K., Jin, F., Kim, S. H., Nakamura, R. Selective electrocatalytic reduction of nitrite to dinitrogen based on decoupled proton-electron transfer. (2018) J. Am. Chem. Soc., 140, 2012-2015. doi:10.1021/jacs.7b12774


Sato K, Kadota Y, Gan P, Bino T, Uehara T, Yamaguchi K, Ichihashi Y, Maki N, Iwahori H, Suzuki T, Shigenobu S, Shirasu K. High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O. Genome Announc. 6(26): e00519-18. (2018) doi:10.1128/genomeA.00519-18


Nakata,TM, Sato M, Wakazaki M, Sato N, Kojima K, Sekine A, Nakamura S, Shikanai T, Toyooka K, Tsukaya H and Horiguchi G. Plastid translation is essential for lateral root stem cell patterning in Arabidopsis thaliana. Biology Open (2018) doi: 10.1242/bio.028175


Hamada T, Yako M, Minegishi M, Sato M, Kamei Y, Yanagawa Y, Toyooka K, Watanabe Y, Hara-Nishimura I. Stress granule formation is induced by a threshold temperature rather than a temperature difference in Arabidopsis. J Cell Sci 131, doi: 10.1242/jcs.216051


Cui Y, Cao W, He Y, Zhao Q, Wakazaki M, Zhuang X, Gao J, Zeng Y, Gao C, Ding Y, Wong H-Y, Wong W-S, Lam H-K, Wang P, Ueda T, Rojas-Pierce M, Toyooka K, Kang B-K, Jiang L. Whole cell electron tomography reveals the nature and biogenesis of vacuoles in Arabidopsis root cells. Nature Plants (in press)


Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. Computer-guided design of optimal microbial consortia for immune system modulation. (2018) Elife, Apr 17; 7. pii: e30916. doi: 10.7554/eLife.30916


Kato, N., Furutani, S., Otaka, J., Noguchi, A., Kinugasa, K., Kai, K., Hayashi, H., Ihara, M., Takahashi, S., Matsuda, K., Osada, H. Biosynthesis and structure-activity relationship studies of okaramines that target insect glutamate-gated chloride channels.(2018) ACS Chem. Biol.,13 (3), 561-566, 2018. doi: 10.1021/acschembio.7b00878


Kato N., Nogawa T., Takita R., Kinugasa K., Kanai M., Uchiyama M., Osada H., Takahashi S. Control of the stereochemical course of [4+2] cycloaddition during trans-decalin formation by Fsa2-family enzymes. Angew. Chem. Int. Ed., 57, 1-6, 2018. doi: 10.1002/anie.201805050


Jang J.-P., Hwang G.J., Kwon M.C., Ryoo I.-J., Jang M., Takahashi S., Ko S.K., Osada H., Jang J.H., Ahn J.S. Pentaminomycins A and B, Hydroxyarginine-Containing Cyclic Pentapeptides from Streptomyces sp. RK88-1441. J. Nat. Prod., 81(4), 806-810, 2018. doi: 10.1021/acs.jnatprod.7b00882


Jang J.-P.,Hwang G.J., Jang M., Takahashi S., Ko S.K., Osada H., Jang J.H., Ahn J.S. Aturanosides A and B, Glycosylated Anthraquinones with Antiangiogenic Activity from a Soil-Derived Streptomyces Species. J. Nat. Prod., 81(9), 2004-2009, 2018. doi: 10.1021/acs.jnatprod.8b00307


Son S., Hong Y.S., Futamura Y., Jang M., Lee J.K., Heo K.T., Ko S.K., Lee J.S., Takahashi S., Osada H., Jang J.H., Ahn J.S. Catenulisporolides, Glycosylated Triene Macrolides from the Chemically Underexploited Actinomycete Catenulispora Species. Org Lett. in press. Oct 31. doi: 10.1021/acs.orglett.8b03160


Kitashima DY, Kobayashi T, Woodring T, Idouchi K, Doebel T, Voisin B, Adachi T, Ouchi T, Takahashi H, Nishifuji K, Kaplan DH, Clausen BE, Amagai M, Nagao K. Langerhans Cells Prevent Autoimmunity via Expansion of Keratinocyte Antigen-Specific Regulatory T Cells. EBioMedicine 27 293-303, 2017. doi:10.1016/j.ebiom.2017.12.022


Yanagiya, K., Maejima, Y., Nakat,a H., Tokuda, M., Moriuchi, R., Dohra, H., Inoue, K., Ohkuma, M., Kimbara, K., Shintani, M. Novel self-transmissible and broad-host-range plasmids exogenously captured from anaerobic granules or cow manure. (2018) Frontiers in Microbiology, 9, 2602. doi: 10.3389/fmicb.2018.02602


Tanizawa, Y., Tada, I., Kobayashi, H., Endo, A., Maeno, S., Toyoda, A., Arita, M., Nakamura, Y., Sakamoto, M., Ohkuma, M., Tohno, M. Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 3512-3517. doi: 10.1099/ijsem.0.003020


Sujarit, K., Kudo, T., Ohkuma, M., Pathom-Aree, W., Lumyong, S. Streptomyces venetus sp. nov., an actinomycete with a blue aerial mycelium. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 3333-3339. doi: 10.1099/ijsem.0.002995


Kato, S., Yuki, M., Itoh, T., Ohkuma, M. Complete genome sequence of Ferriphaselus amnicola strain OYT1, a neutrophilic, stalk-forming, iron-oxidizing bacterium. (2018) Microbiology Resource Announcements,7, e00911-18. doi: 10.1128/MRA.00911-18


Tanimura, A., Sugita, T., Endoh, R., Ohkuma, M., Kishino, S., Ogawa, J., Shima, J., Takashima, M. Lipid production via simultaneous conversion of glucose and xylose by a novel yeast, Cystobasidium iriomotense. (2018) PLoS ONE,13, e0202164. doi: 10.1371/journal.pone.0202164


Sakamoto, M., Iino, T., Yuki, M., Ohkuma, M. Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 2074-2081. doi: 10.1099/ijsem.0.002800


Kinjo, Y., Bourguignon, T., Tong, K.J., Kuwahara, H., Lim, S.J., Yoon, K.B., Shigenobu, S., Park, Y.C., Nalepa, C.A., Hongoh, Y., Ohkuma, M., Lo, N., Tokuda, G. Parallel and gradual genome erosion in the Blattabacterium endosymbionts of Mastotermes darwiniensis and Cryptocercus wood roaches. (2018) Genome Biology and Evolution, 10,1622-1630. doi: 10.1093/gbe/evy110


Sakamoto, M., Ikeyama, N., Yuki, M., Ohkuma, M. Draft Genome Sequence of Lawsonibacter asaccharolyticus JCM 32166T, a Butyrate-Producing Bacterium, Isolated from Human Feces. (2018) Genome Announcements, 6, e00563-18. doi: 10.1128/genomeA.00563-18


Noda, S., Aihara, C., Yuki, M., Ohkuma, M. Draft genome sequence of Lactococcus sp. strain NtB2 (JCM 32569T), isolated from the gut of the higher termite Nasutitermes takasagoensis. (2018) Genome Announcements, 6, e00445-18. doi: 10.1128/genomeA.00445-18


Chiba, M., Itabashi, T., Hirai, K., Sakamoto, M., Ohkuma, M., Ishige, T., Kawasaki, S. Lactobacillus metriopterae sp. nov., a novel lactic acid bacterium isolated from the gut of grasshopper Metrioptera engelhardti. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 1484-1489. doi: 10.1099/ijsem.0.002694


Penkhrue, W., Sujarit, K., Kudo, T., Ohkuma, M., Masaki, K., Aizawa, T., Pathom-Aree, W., Khanongnuch, C., Lumyong, S. Amycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 1448-1454. doi: 10.1099/ijsem.0.002682


Sakamoto, M.. Iino, T., Hamada, M., Ohkuma, M. Parolsenella catena gen. nov., sp. nov., isolated from human faeces. (2018) International Journal of Systematic and Evolutionary Microbiology, 68, 1165-1172. doi: 10.1099/ijsem.0.002645


Kaizuka T, Takumi T. Postsynaptic density proteins and their involvement in neurodevelopmental disorders. (2018) J Biochem. 163, 447-455. doi: 10.1093/jb/mvy022


Horder J, Petrinovic MM, Mendez MA, Bruns A, Takumi T, Spooren W, Barker GJ, Künnecke B, Murphy DG. Glutamate and GABA in autism spectrum disorder-a translational magnetic resonance spectroscopy study in man and rodent models. (2018) Transl Psychiatry. 8, 106. doi: 10.1038/s41398-018-0155-1


Jha A, Dhungel S, Takumi T. Role of selective 5-HT2c ligands on maternal separation induced ultrasonic vocalization and c-fos expression in paternal duplicated mouse pups. (2018)Open Access J Transl Med Res, 2, 73-76. doi: 10.15406/oajtmr.2018.02.00040


Nakai N, Takumi T, Nakai J, Sato M. Common Defects of Spine Dynamics and Circuit Function in Neurodevelopmental Disorders: A Systematic Review of Findings From in Vivo Optical Imaging of Mouse Models. (2018) Front Neurosci. 12, 412. doi: 10.3389/fnins.2018.00412


Nagano M, Takumi T, Suzuki H. Critical roles of serotonin-oxytocin interaction during the neonatal period in social behavior in 15q dup mice with autistic traits. (2018) Sci Rep. 8, 13675. doi: 10.1038/s41598-018-32042-9


Nakamura T, Nakajima K, Ohnishi T, Yoshikawa T, Nakanishi M, Takumi T, Tsuboi T, Kato T. Quantitative evaluation of incomplete preweaning lethality in mice by using the CRISPR/Cas9 system. (2018) Sci Rep. 8, 16025. doi: 10.1038/s41598-018-34270-5


Oita, A., Oshima, T., Tsuboi, Y., Moriya, S., Date, Y. and Kikuchi, J. Profiling physicochemical and planktonic features from discretely/continuously sampled surface water. Sci. Total Environ. (2018) 636, 12-19. doi:10.1016/j.scitotenv.2018.04.156


Mekuchi, M., Sakata, K., Asakura, T., Yamaguchi, T., Teruya, K. and Kikuchi, J. Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus). PLoS One 13, e0197256 (2018). doi:10.1371/journal.pone.0197256


Asakura, T., Sakata, K., Date, Y. and Kikuchi, J. Regional feature extraction of various fishes based on chemical and microbial variable selection using machine learning. Anal. Methods (2018) 17, 16-26. doi:10.1039/C8AY00377G


Shiokawa, Y., Date, Y. and Kikuchi, J. Application of kernel principal component analysis and machine learning computation to an exploration of metabolites strongly associated with human lifestyles. Sci. Rep. 8, 3426 (2018). doi:10.1038/s41598-018-20121-w


Ito, K., Obuchi, Y., Chikayama, E., Date, Y. and Kikuchi, J. Exploratory machine-learned theoretical chemical shifts can closely predict metabolic mixture signals. Chem. Sci. (in press). doi:10.1039/C8SC03628D


Mekuchi, M., Asakura, T. and Kikuchi, J. New aquaculture technology based on host-symbiotic co-metabolism. Marine Metagenomics (in press).


Kato, T., Yamazaki, K., Nakajima, M., Date, Y., Kikuchi, J., Hase, K., Ohno, H., Yamazaki K. Oral administration of Porphyromonas gingivalis alters the gut microbiome and serum metabolome. (2018) mSphere 3. e00460-18. doi: 10.1128/mSphere.00460-18.


Iwasawa K, Suda W, Tsunoda T, Oikawa-Kawamoto M, Umetsu S, Takayasu L, Inui A, Fujisawa T, Morita H, Sogo T, Hattori M. Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker. Sci Rep. (2018) 8, 5480. doi: 10.1038/s41598-018-23870-w


Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. Computer-guided design of optimal microbial consortia for immune system modulation. Elife. (2018) 7, e30916. doi: 10.7554/eLife.30916


Kurokawa S, Kishimoto T, Mizuno S, Masaoka T, Naganuma M, Liang KC, Kitazawa M, Nakashima M, Shindo C, Suda W, Hattori M, Kanai T, Mimura M. The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study. J Affect Disord. (2018) 235, 506-512. doi: 10.1016/j.jad.2018.04.038


Nakade Y, Iwata Y, Furuichi K, Mita M, Hamase K, Konno R, Miyake T, Sakai N, Kitajima S, Toyama T, Shinozaki Y, Sagara A, Miyagawa T, Hara A, Shimizu M, Kamikawa Y, Sato K, Oshima M, Yoneda-Nakagawa S, Yamamura Y, Kaneko S, Miyamoto T, Katane M, Homma H, Morita H, Suda W, Hattori M, Wada T. Gut microbiota-derived D-serine protects against acute kidney injury. JCI Insight. (2018) 3, e97957 doi: 10.1172/jci.insight.97957


Shitashima Y, Shimozawa T, Asahi T, Miyawaki A. (2018) A dual-ligand-modulable fluorescent protein based on UnaG and calmodulin. Biochem Biophys Res Commun., 496 (3): 872-879. doi:10.1016/j.bbrc.2018.01.134

2017  2018

Kim, S., Kim, H., Yim, Y.S., Ha, S., Atarashi, K., Tan, T.G., Longman, R.S., Honda, K., Littman, D.R., Choi, G.B., Huh, J.R. Maternal gut bacteria promote neurodevelopmental abnormalities in mouse offspring. (2017) Nature. Sep 28;549(7673):528-532. doi:10.1038/nature23910. Epub 2017 Sep 13. PMID: 28902840


Atarashi, K., Suda, W., Luo, C., Kawaguchi, T., Motoo, I., Narushima, S., Kiguchi, Y., Yasuma, K., Watanabe, E., Tanoue, T., Thaiss, C.A., Sato, M., Toyooka, K., Said, H.S., Yamagami, H., Rice, S.A., Gevers, D., Johnson, R.C., Segre, J.A., Chen, K., Kolls, J.K., Elinav, E., Morita, H., Xavier, R.J., Hattori, M., Honda, K. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. (2017) Science, 358, 359-365. doi:10.1126/science.aan4526


Piotrowski, J. S., Li, S. C., Deshpande, R., Simpkins, S. W., Nelson, J., Yashiroda, Y., Barber, J. M., Safizadeh, H., Wilson, E., Okada, H., Gebre, A. A., Kubo, K., Torres, N. P., LeBlanc, M. A., Andrusiak, K., Okamoto, R., Yoshimura, M., van Leeuwen, J., Shirahige, K., Baryshnikova, A., Brown, G. W., Hirano, H., Costanzo, M., Andrews, B., Ohya, Y., Osada, H., Yoshida, M., Myers, C. L., Boone, C. Functional Annotation of Chemical Libraries across Diverse Biological Processes. (2017) Nature Chemical Biology, 13, 982-993. doi:10.1038/nchembio.2436


Sakaue-Sawano A, Yo M, Komatsu N, Hiratsuka T, Kogure T, Hoshida T, Goshima N, Matsuda M, Miyoshi H, Miyawaki A. Genetically Encoded Tools for Optical Dissection of the Mammalian Cell Cycle. (2017) Molecular Cell, 68: 626-640. doi: 10.1016/j.molcel.2017.10.001


Chai JN, Peng Y, Rengarajan S, Solomon BD, Ai TL, Shen Z, Perry JSA, Knoop KA, Tanoue T, Narushima S, Honda K, Elson CO, Newberry RD, Stappenbeck TS, Kau AL, Peterson DA, Fox JG, Hsieh CS. Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation. (2017) Science Immunol. 2(13). pii: eaal5068. doi: 10.1126/sciimmunol.aal5068. PMID: 28733471


Miyamoto A, Lee S, Cooray NF, Lee S, Mori M, Matsuhisa N, Jin H, Yoda L, Yokota T, Itoh A, Sekino M, Kawasaki H, Ebihara T, Amagai M, Someya T. Inflammation-free, gas-permeable, lightweight, stretchable on-skin electronics with nanomeshes. (2017) Nature Nanotechnol,12: 907-913. doi: 10.1038/nnano.2017.125


Costea, PI., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, FE., Kultima, JR., Hayward, MR., Coelho, LP., Allen-Vercoe, E., Bertrand, L., Blaut, M., Brown, JRM., Carton, T., Cools-Portier, S., Daigneault, M., Derrien, M., Druesne, A., de Vos, WM., Finlay, BB., Flint, HJ., Guarner, F., Hattori, M., Heilig, H., Luna, RA., van Hylckama Vlieg, J., Junick, J., Klymiuk, I., Langella, P., Le Chatelier, E., Mai, V., Manichanh, C., Martin, JC., Mery, C., Morita, H., O'Toole, PW., Orvain, C., Patil, KR., Penders, J., Persson, S., Pons, N., Popova, M., Salonen, A., Saulnier, D., Scott, KP., Singh, B., Slezak, K., Veiga, P., Versalovic, J., Zhao, L., Zoetendal, EG., Ehrlich, SD., Dore, J., Bork, P. Towards standards for human fecal sample processing in metagenomic studies. (2017) Nat Biotechnol., 35, 1069-1076. doi: 10.1038/nbt.3960.


Chujo, T., Yamazaki, T., Kawaguchi, T., Kurosaka, S., Takumi, T., Nakagawa, S., Hirose, T. Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. (2017) EMBO Journal, 36, 1447-1462. doi: 10.15252/embj.201695848.


Shimokawa, C., Kanaya, T., Hachisuka, M., Ishiwata, K., Hisaeda, H., Kurashima, Y., Kiyono, H., Yoshimoto, T., Kaisho, T., Ohno, H. Mast Cells Are Crucial for Induction of Group 2 Innate Lymphoid Cells and Clearance of Helminth Infections. (2017) Immunity 46, 863-874. doi: 10.1016/j.immuni.2017.04.017.


Nakanishi, M., Nomura, J., Ji, X., Tamada, K., Arai, T., Takahashi, E., Bućan, M., Takumi, T. Functional significance of rare neuroligin 1 variants found in autism. (2017)PLoS Genetics, 13, e1006940. doi: 10.1371/journal.pgen.1006940.


Azzi, A., Evans, J.A., Leise, T., Myung, J., Takumi, T., Davidson, A.J., Brown, S.A. Network dynamics mediate circadian clock plasticity. (2017)Neuron, 93, 441-450. doi: 10.1016/j.neuron.2016.12.022.


Kuwahara, H., Yuki, M., Izawa, K., Ohkuma, M., Hongoh, Y. Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in sa tripartite symbiotic system within a protist cell in the termite gut. (2017) The ISME Journal, 11, 766-776. doi: 10.1038/ismej.2016.143


Nakazawa, S., Haramiishi, A., Fukuda, K., Kanayama, Y., Watanabe, T., Yuki, M., Ohkuma, M, Takeda, K., Kimbara, K., Shintani, M. Different transferability of incompatibility (Inc) P-7 plasmid pCAR1 and IncP-1 plasmid pBP136 in stirring liquid conditions. (2017) PLoS ONE, 12, e0186248. doi: 10.1371/journal.pone.0186248


Kamo, T., Akazawa, H., Suda, W., Saga-Kamo, A., Shimizu, Y., Yagi, H., Liu, Q., Nomura, S., Naito, AT., Takeda, N., Harada, M., Toko, H., Kumagai, H., Ikeda, Y., Takimoto, E., Suzuki, JI., Honda, K., Morita, H., Hattori, M., Komuro, I. Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure. (2017) PLoS One, 12, e0174099. doi: 10.1371/journal.pone.0174099.


Takayasu, L., Suda, W., Watanabe, E., Fukuda, S., Takanashi, K., Ohno, H., Takayasu, M., Takayasu, H., Hattori, M. A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes. (2017) PLoS One, 12, e0180863. doi: 10.1371/journal.pone.0180863.


Tanaka, M., Endo, S., Kotake, F., Al-Saari, N., Amin, AKMR., Feng, G., Mino, S., Doi, H., Ogura, Y., Hayashi, T., Suda, W., Hattori, M., Yumoto, I., Sawabe, T., Sawabe, T., Araki, T. Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed. (2017) PLoS One, 12, e0180053. doi: 10.1371/journal.pone.0180053.


Nishita, M., Park, S.Y., Nishio, T., Kamizaki, K., Wang, Z., Tamada, K., Takumi, T., Hashimoto, R., Otani, H., Pazour, G.J., Hsu, V.W., Minami, Y. Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness. (2017)Scientific Reports, 7, 1. doi: 10.1038/s41598-016-0028-x.


Lewis, K.E., Sharan, K., Takumi, T., Yadav, V.K. Skeletal site-specific changes in bone mass in a genetic mouse model for human 15q11-13 duplication seen in autism. (2017)Scientific Reports, 7, 9902. doi: 10.1038/s41598-017-09921-8.


Hatanaka, F., Takumi, T. CHRONO integrates behavioral stress and epigenetic control of metabolism. (2017) Annals of Medicine, 49, 352-356. doi: 10.1080/07853890.2016.1276301.


Sarashina-Kida, H., Negishi, H., Nishio, J., Suda, W., Nakajima, Y., Yasui-Kato, M., Iwaisako, K., Kang, S., Endo, N., Yanai, H., Asagiri, M., Kida, H., Hattori, M., Kumanogoh, A., Taniguchi, T. Gallbladder-derived surfactant protein D regulates gut commensal bacteria for maintaining intestinal homeostasis. (2017) Proc Natl Acad Sci USA, 114, 10178-10183. doi: 10.1073/pnas.1712837114.


Anbutsu, H., Moriyama, M., Nikoh, N., Hosokawa, T., Futahashi, R., Tanahashi, M., Meng, XY., Kuriwada, T., Mori, N., Oshima, K., Hattori, M., Fujie, M., Satoh, N., Maeda, T., Shigenobu, S., Koga, R., Fukatsu, T. Small genome symbiont underlies cuticle hardness in beetles. (2017) Proc Natl Acad Sci USA, 114, E8382-E8391. doi: 10.1073/pnas.1712857114.


Iwasawa, K., Suda, W., Tsunoda, T., Oikawa-Kawamoto, M., Umetsu, S., Inui, A., Fujisawa, T., Morita, H., Sogo, T., Hattori, M. Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis. (2017) Gut, 66, 1344-1346. doi:10.1136/gutjnl-2016-312533.


Wang, M., Li, H., Takumi, T., Qiu, Z., Xu, X., Yu, X., Bian, W.J. Distinct defects in spine formation or pruning in two gene duplication mouse models of autism. (2017) Neuroscience Bulletin, 33, 143-152. doi: 10.1007/s12264-017-0111-8.


Nomura, J., Kannan, G., Takumi, T. Rodent models of genetic and chromosomal variations in psychiatric disorders. (2017)Psychiatry and Clinical Neurosciences, 71, 508-517. doi: 10.1111/pcn.12524.


Kishimoto, K., Nomura, J., Ellegood, J., Fukumoto, K., Lerch, J.P., Moreno-De-Luca, D., Bourgeron, T., Tamada, K., Takumi, T. Behavioral and neuroanatomical analyses in a genetic mouse model of 2q13 duplication. (2017) Genes to Cells, 22, 436-451. doi: 10.1111/gtc.12487.


Tokuda, I.T., Okamoto, A., Matsumura, R., Takumi, T., Akashi, M. Potential contribution of tandem circadian enhancers to nonlinear oscillations in clock gene expression. (2017) Molecular Biology of Cell, 28, 2333-2342. doi: 10.1091/mbc.E17-02-0129.


Nakai, N., Nagano, M., Saitow, F., Watanabe, Y., Kawamura, Y., Kawamoto, A., Tamada, K., Mizuma, H., Onoe, H., Watanabe, Y., Monai, H., Hirase, H., Nakatani, J., Inagaki, H., Kawada, T., Miyazaki, T., Watanabe, M., Sato, Y., Okabe, S., Kitamura, K., Kano, M., Hashimoto, K., Suzuki, H., Takumi, T. Serotonin rebalances cortical tuning and behavior linked to autism symptoms in 15q11-13 CNV mice. (2017) Science Advances, 3, e1603001. doi: 10.1126/sciadv.1603001.


Fukumoto, K., Tamada, K., Toya, T., Nishino, T., Yanagawa, Y., Takumi, T. Identification of genes regulating GABAergic interneuron maturation. (2017) Neuroscience Research, doi: 10.1016/j.neures.2017.11.010.


Hirota T, Nakayama T, Sato S, Yanagida N, Matsui T, Sugiura S, Takaoka Y, Hizawa N, Fujieda S, Miyatake A, Sasaki T, Amagai M, Doi S, Ito K, Ebisawa M, Tamari M. Association study of childhood food allergy with genome-wide association studies-discovered loci of atopic dermatitis and eosinophilic esophagitis. (2017) J Allergy Clin Immunol, 140:1713-1716. doi: 10.1016/j.jaci.2017.05.034


Yamazaki Y, Kawarai S, Morita H, Kikusui T, Iriki A. Faecal transplantation for the treatment of Clostridium difficile infection in a marmoset. (2017) BMC Veterinary Research, 13, 150. doi: 10.1186/s12917-017-1070-z


Tia B, Takemi M, Kosugi A, Castagnola E, Ansaldo A, Nakamura T, Ricci D, Ushiba J, Fadiga L, Iriki A. Cortical control of object-specific grasp relies on adjustments of both activity and effective connectivity: a common marmoset study. (2017) J Physiol (Lond), 595, 17203-7221. doi: 10.1113/JP274629


Takemi M, Castagnola E, Ansaldo A, Ricci D, Fadiga L, Taoka M, Iriki A, Ushiba J. Rapid identification of cortical motor areas by high-frequency automatic cortical stimulation and novel motor threshold algorithm.(2017) Front. Neurosci, 11, 580. doi: 10.3389/fnins.2017.00580


Yamazaki Y, Iriki A. Behavioral, cognitive, and neuronal changes in the acquisition of tool use.(2017) In: Watanabe S, Hifman MA, Shimizu T. (Eds.) Evolution of the Brain, Cognition, and Emotion in Vertebrates. Brain Science Series (Series Eds. Okano H. & Iriki A). Springer, Tokyo, pp 169-185. doi: 10.1007/978-4-431-56559-8_8


Nogawa, T., Ogita, N., Futamura, Y., Negishi, S., Watanabe, N., Osada, H. Trachyspic acid 19-butyl ester, a new inhibitor of Plk1 polo box domain-dependent recognition from uncharacterized fungus RKGS-F2684. (2017) Journal of Antibiotics, 70, 705-707. doi: 10.1038/ja.2016.167


Maeda, K., Nakajima, Y., Motoyama, T., Kondoh, Y., Kawamura, T., Kanamaru, K., Ohsato, S., Nishiuchi, T., Yoshida, M., Osada, H., Kobayashi, T., Kimura, M. Identification of a trichothecene production inhibitor by chemical array and library screening using trichodiene synthase as a target protein. (2017) Pesticide Biochemistry and Physiology, 138, 1-7. doi: 10.1016/j.pestbp.2017.03.006


Otaka, J., Hashizume, D., Masumoto, Y., Muranaka, A., Uchiyama, M., Koshino, H., Futamura, Y., Osada, H. Hitoyol A and B, two norsesquiterpenoids from the basidiomycete Coprinopsis cinerea. (2017) Organic Letters, 19, 4030–4033. doi: 10.1021/acs.orglett.7b01784


Nishimura, O., Hara, Y., Kuraku, S. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. (2017) Bioinformatics, 33, 3635-3637. doi: 10.1093/bioinformatics/btx445


Ogawa, T., Kryukov, K., Imanishi, T., Shiroguchi, K. The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules. (2017) Scientific Reports, 7, 13576. doi:10.1038/s41598-017-13529-3


Yun, C.S., Motoyama, T., Osada, H. Regulatory Mechanism of Mycotoxin Tenuazonic Acid Production in Pyricularia oryzae. (2017) ACS Chemical Biology, 12, 2270-2274. doi: 10.1021/acschembio.7b00353


Germond, A., Kumar, V., Ichimura, T., Moreau, J., Furusawa, C., Fujita, H., Watanabe, T.M. Raman spectroscopy as a tool for ecology and evolution. (2017) Journal of the Royal Society Interface,14, 20170174. doi:10.1098/rsif.2017.0174


Nakagome, S., Chinen, H., Iraha, A., Hokama, A., Takeyama, Y., Sakisaka, S., Matsui, T., Kidd, JR., Kidd, KK., Said, HS., Suda, W., Morita, H., Hattori, M., Hanihara, T., Kimura, R., Ishida, H., Fujita, J., Kinjo, F., Mano, S., Oota, H.
Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands. (2017) 
Hum. Genet., 136, 387-397. doi: 10.1007/s00439-017-1764-0.


Sato, A., Matsushima, K., Oshima, K., Hattori, M., Koyama, Y. Draft Genome Sequencing of the Highly Halotolerant and Allopolyploid Yeast Zygosaccharomyces rouxii NBRC 1876.
(2017) Genome Announce. 5:e01610-16. doi:10.1128/genomeA.01610-16.


Mizuno, S., Nanki, K., Matsuoka, K., Saigusa, K., Ono, K., Arai, M., Sugimoto, S., Kiyohara, H., Nakashima, M., Takeshita, K., Naganuma, M., Suda, W., Hattori, M., Kanai, T. Single fecal microbiota transplantation failed to change intestinal microbiota and had limited effectiveness against ulcerative colitis in Japanese patients. (2017) Intest. Res., 15, 68-74. doi: 10.5217/ir.2017.15.1.68


Aoki, R., Kamikado, K., Suda, W., Takii, H., Mikami, Y., Suganuma, N., Hattori, M., Koga, Y. A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation. (2017) Sci. Rep., 7, 43522. doi: 10.1038/srep43522.


Takayasu, L., Suda, W., Takanashi, K., Iioka, E., Kurokawa, R., Shindo, C., Hattori, Y., Yamashita, N., Nishijima, S., Oshima, K., Hattori, M. Circadian oscillations of microbial and functional composition in the human salivary microbiome. (2017) DNA Res., 24, 261-270. doi: 10.1093/dnares/dsx001.


Mizuno, S., Masaoka, T., Naganuma, M., Kishimoto, T., Kitazawa, M., Kurokawa, S., Nakashima, M., Takeshita, K., Suda, W., Mimura, M., Hattori, M., Kanai, T. Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome. (2017) Digestion, 96, 29-38. doi: 10.1159/000471919


Jia, S., Nakano, T., Hattori, M., Nara, K. Root-associated fungal communities in three Pyroleae species and their mycobiont sharing with surrounding trees in subalpine coniferous forests on Mount Fuji, Japan. (2017) Mycorrhiza, 27, 733-745. doi: 10.1007/s00572-017-0788-6.


Doki, N., Suyama, M., Sasajima, S., Ota, J., Igarashi, A., Mimura, I., Morita, H., Fujioka, Y., Sugiyama, D., Nishikawa, H., Shimazu, Y., Suda, W., Takeshita, K., Atarashi, K., Hattori, M., Sato, E., Watakabe-Inamoto, K., Yoshioka, K., Najima, Y., Kobayashi, T., Kakihana, K., Takahashi, N., Sakamaki, H., Honda, K., Ohashi, K. Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation. (2017) Ann Hematol., 96, 1517-1523. doi: 10.1007/s00277-017-3069-8.


Hayashi, A., Mikami, Y., Miyamoto, K., Kamada, N., Sato, T., Mizuno, S., Naganuma, M., Teratani, T., Aoki, R., Fukuda, S., Suda, W., Hattori, M., Amagai, M., Ohyama, M., Kanai, T. Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice. (2017) Cell Rep., 20, 1513-1524. doi: 10.1016/j.celrep.2017.07.057.


Shibagaki, N., Suda, W., Clavaud, C., Bastien, P., Takayasu, L., Iioka, E., Kurokawa, R., Yamashita, N., Hattori, Y., Shindo, C., Breton, L., Hattori, M. Aging-related changes in the diversity of women's skin microbiomes associated with oral bacteria. (2017) Sci Rep., 7, 0567. doi: 10.1038/s41598-017-10834-9


Yamazaki, T., Ichihara, K., Suzuki, R., Oshima, K., Miyamura, S., Kuwano, K., Toyoda, A., Suzuki, Y., Sugano, S., Hattori, M., Kawano, S. Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita. (2017) Sci Rep., 7, 11679. doi: 10.1038/s41598-017-11677-0.


Urushiyama, D., Suda, W., Ohnishi, E., Araki, R., Kiyoshima, C., Kurakazu, M., Sanui, A., Yotsumoto, F., Murata, M., Nabeshima, K., Yasunaga, S., Saito, S., Nomiyama, M., Hattori, M., Miyamoto, S., Hata, K. Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome. (2017) Sci Rep., 7, 12171. doi: 10.1038/s41598-017-11699-8.


Nakamoto, N., Amiya, T., Aoki, R., Taniki, N., Koda, Y., Miyamoto, K., Teratani, T., Suzuki, T., Chiba, S., Chu, PS., Hayashi, A., Yamaguchi, A., Shiba, S., Miyake, R., Katayama, T., Suda, W., Mikami, Y., Kamada, N., Ebinuma, H., Saito, H., Hattori, M., Kanai, T. Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice. (2017) Cell Rep., 21, 1215-1226. doi: 10.1016/j.celrep.2017.10.022.


Otsubo, T., Yamada, K., Hagiwara, T., Oshima, K., Iida, K., Nishikata, K., Toyoda, T., Igari, T., Nohara, K., Yamashita, S., Hattori, M., Dohi, T., Kawamura, YI. DNA hypermethyation and silencing of PITX1 correlated with advanced stage and poor postoperative prognosis of esophageal squamous cell carcinoma.(2017) Oncotarget, 8, 84434-84448. doi: 10.18632/oncotarget.21375.


Naganuma, M., Sugimoto, S., Mitsuyama, K., Kobayashi, T., Yoshimura, N., Ohi, H., Tanaka, S., Andoh, A., Ohmiya, N., Saigusa, K., Yamamoto, T., Morohoshi, Y., Ichikawa, H., Matsuoka, K., Hisamatsu, T., Watanabe, K., Mizuno, S., Suda, W., Hattori, M., Fukuda, S., Hirayama, A., Abe, T., Watanabe, M., Hibi, T., Suzuki, Y., Kanai, T. INDIGO Study Group: Efficacy of Indigo naturalis in a Multicenter Randomized Controlled Trial of Patients with Ulcerative Colitis. (2017) Gastroenterology, 154, 935-947. doi:10.1053/j.gastro.2017.11.024.


Lee, C.G., Iida, T., Uwagaki, Y., Otani, Y., Nakaho, K., Ohkuma, M. Comparison of prokaryotic and eukaryotic communities in soil samples with and without tomato bacterial wilt that were collected from different fields.(2017) Microbes and Environments, 32, 376-385. doi: 10.1264/jsme2.ME17131


Izawa, K., Kuwahara, H., Sugaya, K., Lo, N., Ohkuma, M., Hongoh, Y. 2017. Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites. (2017) Environmental Microbiology Reports, 9, 411-418. doi: 10.1111/1758-2229.12549


Lee, C.G., Yuki, M., Iida, T., Nakaho, K., Ohkuma, M. Draft genome sequence of Tepidibacter mesophilus strain JCM16806T isolated from soil polluted by crude oil in China. (2017) Genome Announcements,5, e01308-17. doi: 10.1128/genomeA.01308-17


Yuki. M,, Sakamoto, M., Kuwahara, H., Hongoh, Y., Ohkuma, M. Draft genome sequence ofLactococcussp. strain Rs-Y01, isolated from the gut of the lower termite Reticulitermes speratus. (2017) Genome Announcements,5, e00999-17. doi: 10.1128/genomeA.00999-17


Uzuhashi, S., Endoh, R., Manabe, R.I., Ohkuma, M. Draft genome sequences of the oomycete Pilasporangium apinafurcum strains JCM 30513 and JCM 30514, formerly classified as Pythium apinafurcum. (2017) Genome Announcements,5, e00899-17. doi: 10.1128/genomeA.00899-17


Tsuchida, S., Maruyama, F., Ogura, Y., Toyoda, A., Hayashi, T., Ohkuma, M., Ushida, K. Genomic characteristics of Bifidobacterium thermacidophilum pig isolates and wild boar isolates reveal the unique presence of a putative mobile genetic element with tetW for pig farm isolates. (2017) Frontiers in Microbiology, 8, 1540. doi: 10.3389/fmicb.2017.01540


Tashiro, Y., Hasegawa, Y., Shintani, M., Ohkuma, M., Kimbara, K., Futamata, H. Interaction of bacterial membrane vesicles with specific species and their potential for delivery to target cells. (2017) Frontiers in Microbiology,8, 571. doi:10.3389/fmicb.2017.00571


Tsuchida, S., Murata, K., Ohkuma, M., Ushida, K. Isolation of Streptococcus gallolyticus with very high degradability of condensed tannins from feces of the wild Japanese rock ptarmigan on Mt. Tateyama. (2017) Journal of Geneneral and Applied Microbiology, 63, 195-198. doi: 10.2323/jgam.2016.09.003


Haruta, S., Iino, T., Ohkuma, M., Suzuki, K., Igarashi, Y. Ca2+ in hybridization solutions for fluorescence in situ hybridization facilitates the detection of Enterobacteriaceae. (2017) Microbes and Environments, 32, 142-146. doi: 10.1264/jsme2.ME16186


Lee, C.G., Iida, T., Inoue, Y., Muramoto, Y., Watanabe, H., Nakaho, K., Ohkuma, M. Prokaryotic communities at different depths between soils with and without tomato bacterial wilt but pathogen-present in a single greenhouse. (2017) Microbes and Environments, 32, 118-124. doi: 10.1264/jsme2.ME16136


Katahira, S., Muramoto, N., Moriya, S., Nagura, R., Tada, N., Yasutani, N., Ohkuma, M., Onishi, T., Tokuhiro, K. Screening and evolution of a novel protist xylose isomerase from the termite Reticulitermes speratus for efficient xylose fermentation in Saccharomyces cerevisiae. (2017) Biotechnology for Biofuels,10, 203. doi: 10.1186/s13068-017-0890-1


Kobayashi, H., Nakasato, T., Sakamoto, M., Ohtani, Y., Terada, F., Sakai, K., Ohkuma, M., Tohno, M. Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage. (2017) International Journal of Systematic and Evolutionary Microbiology, 67, 4974-4978. doi: 10.1099/ijsem.0.002387


Tohno, M., Tanizawa, Y., Irisawa, T., Masuda, T., Sakamoto, M,. Ohkuma, M., Kobayash, H. Lactobacillussilagincolasp.nov. andLactobacilluspentosiphilussp.nov. isolated from silage.(2017) International Journal of Systematic and Evolutionary Microbiology, 67, 3639-3644.doi: 10.1099/ijsem.0.002196


Sujarit, K., Sujada, N., Kudo, T., Ohkuma, M., Pathom-Aree, W., Lumyong, S. Pseudonocardia thailandensis sp. nov., an actinomycete isolated from a subterranean termite nest. (2017) International Journal of Systematic and Evolutionary Microbiology, 67, 2773-2778. doi: 10.1099/ijsem.0.002017


Khunnamwong, P., Ribeiro, J.R.A., Garcia, K.M., Hagler, A.N., Takashima, M., Ohkuma, M., Endoh, R., Sugita, T., Jindamorakot, S., Limtong, S.Occultifur plantarum f.a., sp. nov., a novel cystobasidiomycetes yeast species(2017) International Journal of Systematic and Evolutionary Microbiology, 67, 2628-2633. doi: 10.1099/ijsem.0.001988


Minegishi, H., Enomoto, S., Echigo, A., Shimane, Y., Kondo, Y., Inoma, A., Kamekura, M., Takai, K., Itoh, T., Ohkuma, M., Ihara, K., Takahashi-Ando, N., Fukushima, Y., Ishii, S., Yoshida, Y., Usami, R. Salinarchaeum chitinilyticum sp. nov., a chitin-degrading haloarchaeon isolated from commercial salt. (2017) International Journal of Systematic and Evolutionary Microbiology, 67, 2274-2278. doi: 10.1099/ijsem.0.001941


Sripreechasak, P., Phongsopitanun, W., Supong, K., Pittayakhajonwut, P., Kudo, T., Ohkuma, M., Tanasupawat, S. Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil. (2017) International Journal of Systematic and Evolutionary Microbiology, 67, 1683-1687. doi: 10.1099/ijsem.0.001843


Sakamoto, M., Iino, T., Ohkuma, M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb.nov. (2017) International Journal of Systematic and Evolutionary Microbiology, 67, 1219-1227. doi: 10.1099/ijsem.0.001790


Jutakanoke, R., Endoh, R., Takashima, M., Ohkuma, M., Tanasupawat, S., Akaracharanya, A. Allodekkera sacchari gen. nov., sp. nov., a yeast species in the Saccharomycetales isolated from a sugar factory. (2017) International Journal of Systematic and Evolutionary Microbiology, 67, 250-255. doi: 10.1099/ijsem.0.001607


Tanizawa, Y., Kobayashi, H., Kaminuma, E., Sakamoto, M., Ohkuma, M., Nakamura, Y., Arita, M., Tohno, M. Genomic characterization reconfirms the taxonomic status ofLactobacillus parakefiri. (2017) Bioscience of Microbiota, Food and Health, 36, 129-134. doi:10.12938/bmfh.16-026


Fujita, M., Matsubara, N., Matsuda, I., Maejima, K., Oosawa, A., Yamano, T., Fujimoto, A., Furuta, M., Nakano, K., Oku-Sasaki, A., Tanaka, H., Shiraishi, Y., Mateos, RN., Nakai, K., Miyano, S., Tomita, N., Hirota, S., Ikeuchi, H., and Nakagawa, H. Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in RNF43 and Wnt signaling.(2017) Oncotarget 9:969-98. doi:10.18632/oncotarget.22867


Otagiri, M., Khalid, A., Moriya, S., Osada, H., Takahashi, S. Novel squalene-producing thraustochytrids found in mangrove water.(2017) Bioscience, Biotechnology, and Biochemistry, 81, 10, 2034-2037. doi:10.1080/09168451.2017.1359485


Jinnohara, T., Kanaya, T., Hase, K., Sakakibara, S., Kato, T., Tachibana, N., Sasaki, T., Hashimoto, Y., Sato, T., Watarai, H., Kunisawa, J., Shibata, N., Williams, I. R., Kiyono, H., Ohno, H.IL-22BP dictates characteristics of Peyer's patch follicle-associated epithelium for antigen uptake. (2017) J Exp Med 214, 1607-1618.doi: 10.1084/jem.20160770.


Date, Y., Ebisawa, M., Fukuda, S., Shima, H., Obata, Y., Takahashi, D., Kato, T., Hanazato, M., Nakato, G., Williams, I. R., Hase, K., Ohno, H. NALT M cells are important for immune induction for the common mucosal immune system. (2017)Int Immunol 29, 471-478. doi: 10.1093/intimm/dxx064.


Yanagihara S, Kanaya T, Fukuda S, Nakato G, Hanazato M, Wu XR, Yamamoto N, Ohno H. Uromodulin-SlpA binding dictates Lactobacillus acidophilus uptake by intestinal epithelial M cells. (2017) Int. Immunol. 29: 357-363. doi: 10.1093/intimm/dxx043.


Nakajima, A., Kaga, N., Nakanishi, Y., Ohno, H., Miyamoto, J., Kimura, I., Hori, S., Sasaki, T., Hiramatsu, K., Okumura, K., Miyake, S., Habu, S., Watanabe, S. Maternal High Fiber Diet during Pregnancy and Lactation Influences Regulatory T Cell Differentiation in Offspring in Mice. (2017) J. Immunol. 199: 3516-3524. doi: 10.4049/jimmunol.1700248.


Sato, K., Takahashi, N., Kato, T., Matsuda, Y., Yokoji, M., Yamada, M., Nakajima, T., Kondo, N., Endo, N., Yamamoto, R., Noiri, Y., Ohno H, Yamazaki K. Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system. (2017) Sci Rep. 7:6955. doi:10.1038/s41598-017-07196-7.


Lye, H. S., Kato, T., Low, W. Y., Taylor, T. D., Prakash, T., Lew, L. C., Ohno, H., Liong, M. T. Lactobacillus fermentum FTDC 8312 combats hypercholesterolemia via alteration of gut microbiota. (2017) J. Biotechnol. 262: 75-83. doi: 10.1016/j.jbiotec.2017.09.007.


Takayasu, L., Suda, W., Watanabe, E., Fukuda, S., Takanashi, K., Ohno, H., Takayasu, M., Takayasu, H., Hattori, M. A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes. (2017) PLoS ONE 12(8):e0180863. doi: 10.1371/journal.pone.0180863.


Khalid, A., Takagi, H., Panthee, S., Muroi, M., Chappell, J., Osada H., Takahashi S.Development of a terpenoid-production platform in Streptomyces reveromyceticus SN-593. (2017) ACS Synth. Biol. 6 (12): 2339-2349. doi: 10.1021/acssynbio.7b00249.


Amagai, K., Ikeda, H., Hashimoto, J., Kozone, I., Izumikawa, M., Kudo, F., Eguchi, T., Nakamura, T., Osada, H., Takahashi, S., Shin-ya, K., Identification of gene cluster for telomestatin biosynthesis and efficient production in heterologous host using specific promoter. (2017) Sci. Rep. 7: 3382. doi:10.1038/s41598-017-03308-5


Zhang, L., Hashimoto, T., Qin, B., Hashimoto, J., Kozone, I., Kawahara, T., Okada, M., Awakawa, T., Ito, T., Asakawa, Y., Ueki, M., Takahashi, S., Osada, H., Wakimoto, T., Ikeda, H., Shin-ya, K., Abe, I. Characterization of giant modular PKSs provides insight into genetic mechanism for structural diversification of aminopolyol polyketides. (2017) Angew. Chem. Int. Ed., 56 (7): 1740-1745. doi: 10.1002/anie.201611371


Uchimiya, M., Tsuboi, Y., Ito, K., Date, Y. and Kikuchi, J. Bacterial substrate transformation tracked by stable-isotope-guided NMR metabolomics: Application in a natural aquatic microbial community. (2017) Metabolites 7, e52. doi: 10.3390/metabo7040052


Kikuchi, J. and Yamada, S. NMR window of molecular complexity showing homeostasis in superorganisms. (2017) Analyst 142, 4161-4172. doi: 10.1039/C7AN01019B


Mekuchi, M., Sakata, K., Yamaguchi, T., Koiso, M. and Kikuchi, J. Trans-omics approaches represented used to characterize fish nutritional biorhythms in Leopard coral groupers (Plectropomus leopardus). (2017) Sci. Rep. 7, 9372. doi: 10.1038/s41598-017-09531-4

Integrated Symbiology
Riken
iSYM Official SNS (Facebook / Twitter)