【Labs spotlight】 Yamada Laboratory

Unravel the stability and dynamics of microbial communities

February 16, 2017

The Department has a variety of laboratories for Life Science and Technology, in which cutting-edge innovative research is being undertaken not only in basic science and engineering but also in the areas of medicine, pharmacy, agriculture, and multidisciplinary sciences.

This "Spotlight" series features a laboratory from the Department and introduces you to the laboratory's research projects and outcomes. This time we focus on Yamada Laboratory.

Associate Professor Takuji Yamada

Life Science and Technology
Associate Professor Takuji Yamada

Degree	PhD 1993, Tokyo Institute of Technology
Areas of Research	Bioinformatics, Metagenomics, Genomics
Keywords	Human microbiome, Data visualization, Database, Functional prediction
Website	Kurokawa, Nakashima and Yamada Laboratory

Research interest

Various microbial species construct functional eco-system in our intestine. Next generation sequencers and metagenomic analyses facilitate the comprehensive studies for human microbiome, including un-culturable bacteria. In particular, gut microbome studies accelerate the field of human microbiome studies because of their direct effects to human health.

Yamada-lab is mainly focusing on the human microbiome study based on bioinformatics, functional analysis, and database construction. We are also working for data visualization for biological big data, such as genome, or gene expression data.

Research findings

Selected publications

[1] Matsuki T, Yahagi K, Mori H, Matsumoto H, Hara T, Tajima S, Ogawa E, Kodama H, Yamamoto K, Yamada T, Matsumoto S, Kurokawa K. A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nat Commun. 2016 Jun 24;7:11939. doi: 10.1038/ncomms11939.
[2] Nishimoto Y, Mizutani S, Nakajima T, Hosoda F, Watanabe H, Saito Y, Shibata T, Yachida S, Yamada T . High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut 2016 Jun 23.
[3] Moriya Y, Yamada T, Okuda S, Nakagawa Z, Kotera M, Tokimatsu T, Kanehisa M, Goto S. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. J Chem Inf Model. 2016 Mar 28;56(3):510-6.
[4] Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T. DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. BMC Bioinformatics;16(1):96 (2015)
[5] Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T. FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data. PLoS One. 2015 May 14;10(5):e0126967. doi: 10.1371/journal.pone.0126967. PubMed PMID: 25974630
[6] Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol;10:766 (2014)
[7] Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen, Guarner F, Pedersen O, Dorè J, Ehrlich SD, Pons N, Le Chatelier E, Batto JM, Kennedy S, Haimet F, Winogradski Y, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K,Parkhill J, Antolin M, Casellas F, Borruel N, Varela E, Torrejon A, Denariaz G, Derrien M, van Hylckama Vlieg JE, Viega P, Oozeer R, Knoll J,Rescigno M, Brechot C, M'Rini C, Mèrieux A, Yamada T, Tims S, Zoetendal EG, Kleerebezem M, de Vos WM, Cultrone A, Leclerc M, Juste C,Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Blottière H, Maguin E, Renault P,Tap J, Mende, Bork P, Wang J. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834-41 (2014)
[8] Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Dorè J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Lèonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol.32(8):822-8 (2014)
[9] Waller, AS., Yamada, T., Kristensen, DM., Kultima, JR., Sunagawa, S., Koonin, EV., Bork, P. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J. 8(7):1391-402 (2014)
[10] Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clèment K, Dorè J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M'Rini C, Mèrieux A, Yamada T. Richness of human gut microbiome correlates with metabolic markers. Nature. 29;500(7464):541-6 (2014)
[11] *Yamada, T., Waller, A., Raes, J., Zeleznik, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. and Bork, P. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighibors; Molecular Systems Biology, 8:581 (2012)
[12] *Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. and Bork, P. iPath2.0: interactive pathway explorer; Nucleic Acids Res, 39 W412-415 (2011)
[13] Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Junwang, Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Consortium, M., Weissenbach, J., Ehrlich, S.D. and Bork, P. Enterotypes of the human gut microbiome. Nature. 473 (7346), 174-180 (2011)
[14] Raes, J., Letunic, I., Yamada, T., Jensen, L.J. and Bork, P. (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol, 7, 473 (2011).
[15] Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K., Bauer, D.J., Caceres, C.E., Carmel, L., Casola, C., Choi, J.H., Detter, J.C., Dong, Q., Dusheyko, S., Eads, B.D., Frohlich, T., Geiler-Samerotte, K.A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E.V., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J.R., Muller, J., Pangilinan, J., Patwardhan, R.P., Pitluck, S., Pritham, E.J., Rechtsteiner, A., Rho, M., Rogozin, I.B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y.I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J.R., Andrews, J., Crease, T.J., Tang, H., Lucas, S.M., Robertson, H.M., Bork, P., Koonin, E.V., Zdobnov, E.M., Grigoriev, I.V., Lynch, M. and Boore, J.L. The ecoresponsive genome of Daphnia pulex. Science, 331 (6017), 555-561 (2011)
[16] Qin. J., Li. R., Raes. J., Arumugam. M., Burgdorf. KS., Manichanh. C., Nielsen. T., Pons. N., Levenez. F., Yamada. T., Mende. D., Li. J., Xu. J., Li. S., Li. D., Cao. J., Wang. B., Liang. H., Zheng. H., Xie. Y., Tap. J., Lepage. P., Bertalan. M., Batto. J., Hansen. T., Paslier. DL., Linneberg. A., Nielsen. HB., Pelletier. E., Renault. P., Sicheritz-Ponten. T., Turner. K., Zhu. H., Yu. C., Li. S., Jian. M., Zhou. Y., Li. Y., Zhang. X., Li. S., Yang. H., Wang. J., Brunak. S., Dorè. J., Guarner. F., Kristiansen. K., Pedersen. O., Parkhill. J., Weissenbach. J., Consortium. M., Bork. P., Ehrlich. SD. and Wang. J; A human gut microbial gene catalog established by deep metagenomic sequencing. Nature 464 (7285), 59-65 (2010)
[17] Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.-H., Wodke, J. A. H., Guell, M., Martinez, S., Bourgeois, R., Kuhner, S., Raineri, E., Letunic, I., Kalinina, O. V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R. B., Gavin, A.-C., Bork, P., Serrano, L.; Impact of genome reduction on bacterial metabolism and its regulation. Science 326 (5957), 1263-1268 (2009)
[18] Kuhner, S., van Noort, V., Betts, M. J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., Castano-Diez, D., Chen, W.-H., Devos, D., Guell, M., Norambuena, T., Racke, I., Rybin, V., Schmidt, A., Yus, E., Aebersold, R., Herrmann, R., Bottcher, B., Frangakis, A. S., Russell, R. B., Serrano, L., Bork, P., Gavin, A.C.; Proteome organization in a genome-reduced bacterium. Science 326 (5957), 1235-1240 (2009).
[19] Guell, M., van Noort, V., Yus, E., Chen, W.-H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.-C., Bork, P., Serrano, L.; Transcriptome complexity in a genome-reduced bacterium. Science 326 (5957), 1268-1271 (2009).
[20] *Yamada T., Bork P.; Evolution of biomolecular networks - lessons from metabolic and protein interactions. Nat. Rev. Mol. Cell Biol. 10 (11):791-803 (2009).
[21] Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB; Quantifying environmental adaptation of metabolic pathways in metagenomics. PNAS USA. 2009 Feb 3; 106(5): 1374-1379 (2009)