Affiliation: University of Tokyo
- The human intestinal microbiome: a new frontier of human biologyMasahira Hattori
Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kasiwanoha, Kashiwa, Chiba 277 8561, Japan
DNA Res 16:1-12. 2009....
- Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomesKen Kurokawa
Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
DNA Res 14:169-81. 2007..In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes...
- Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adultKenshiro Oshima
Kitasato Institute for Life Sciences, Kitasato University, 1 15 1 Kitasato, Sagamihara, Kanagawa 228 8555, Japan
DNA Res 15:375-86. 2008..coli in human gut habitat...
- Complete genome sequence and comparative analysis of the fish pathogen Lactococcus garvieaeHidetoshi Morita
School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
PLoS ONE 6:e23184. 2011..The analysis also predicted other potential virulence factors such as haemolysin. The present study provides new insights into understanding of the virulence mechanisms of L. garvieae in fish...
- Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific contentFumito Maruyama
Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
BMC Genomics 10:358. 2009..While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood...
- The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor familyHiroki Goto
Division of Human Moelcular Genetics, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812 8582, Japan
BMC Evol Biol 9:224. 2009..To clarify the evolutionary dynamics and mechanisms of the GluR genes in the lineage leading to humans, we determined the complete sequences of the coding regions and splice sites of 26 chimpanzee GluR genes...
- Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomesMikihiko Kawai
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
BMC Microbiol 11:104. 2011..We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains...
- Plasma membrane-localized Al-transporter from blue hydrangea sepals is a member of the anion permease familyTakashi Negishi
Graduate School of Information Science, Nagoya University, Nagoya, Japan
Genes Cells 18:341-52. 2013..The over-expression of HmPALT2 in Arabidopsis resulted in aluminum-hypersensitivity, suggesting that HmPALT2 should work as an aluminum transporter into cells in planta...
- Chromosome painting in silico in a bacterial species reveals fine population structureKoji Yahara
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
Mol Biol Evol 30:1454-64. 2013..We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale...
- Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructureShuhei Ota
Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562 Japan Japan Science and Technology Agency JST, CREST, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562 Japan
Biotechnol Biofuels 9:13. 2016..However, further biotechnological exploitation has been hampered by a lack of genomic information...
- Bacterial population dynamics in a laboratory activated sludge reactor monitored by pyrosequencing of 16S rRNAHiroyasu Satoh
Department of Socio cultural and Environmental Studies, The University of Tokyo, Tokyo, Japan
Microbes Environ 28:65-70. 2013..It was clearly demonstrated that pyrosequencing with barcoded primers is a very effective tool to clarify the dynamics of the bacterial population in activated sludge...
- Coordinated changes in DNA methylation in antigen-specific memory CD4 T cellsShin Ichi Hashimoto
Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113 0033, Japan
J Immunol 190:4076-91. 2013..By comparing DMRs between naive and Ag-specific memory T cells, this study provides new insights into the functional status of memory T cells...
- Complete genome sequence of the denitrifying and N2O-reducing bacterium Azoarcus sp. strain KH32CTomoyasu Nishizawa
Department of Applied Biological Chemistry, The University of Tokyo, Yayoi, Bunkyo ku, Tokyo, Japan
J Bacteriol 194:1255. 2012..strain KH32C. The genome is composed of one chromosome and one megaplasmid and contains genes for plant-microbe interactions and the gene clusters for aromatic-compound degradations...
- The gut microbiome of healthy Japanese and its microbial and functional uniquenessSuguru Nishijima
Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277 8561, Japan
DNA Res 23:125-33. 2016..We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes...
- Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencingSeok Won Kim
Center for Omics and Bioinformatics, The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5 1 5, Kashiwa, Chiba 277 8561, Japan
DNA Res 20:241-53. 2013..Such OTUs were found to be individual specific and tend to be unevenly distributed in the subjects. These data, thus, suggest robustness of the gut microbiota composition in healthy adults on probiotic administration...
- Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkersHeba S Said
1Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5 1 5, Kashiwa, Chiba 277 8561, Japan
DNA Res 21:15-25. 2014..Our data demonstrate that dysbiosis of salivary microbiota is associated with inflammatory responses in IBD patients, suggesting that it is possibly linked to dysbiosis of their gut microbiota. ..
- Tonoplast- and plasma membrane-localized aquaporin-family transporters in blue hydrangea sepals of aluminum hyperaccumulating plantTakashi Negishi
Graduate School of Information Science, Nagoya University, Chikusa ku, Nagoya, Aichi, Japan
PLoS ONE 7:e43189. 2012..The overexpression of VALT and PALT1 in Arabidopsis thaliana conferred Al-tolerance and Al-sensitivity, respectively...
- Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney DiseaseMami Kikuchi
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
Nephron . 2016..In patients with chronic kidney disease (CKD), many metabolites of gut microbiota retain in the body as uremic toxins (UTs). However, the kinds of bacteria producing UTs are rarely discussed...
- Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA genePurnika Damindi Ranasinghe
Department of Socio Cultural Environmental Studies, The University of Tokyo, Japan
Water Sci Technol 66:2155-61. 2012..Thus, the pyrosequencing method provides high resolution insight into microbial community structures in activated sludge that might have been unnoticed with conventional approaches...
- Analysis of early bacterial communities on volcanic deposits on the island of Miyake (Miyake-jima), Japan: a 6-year study at a fixed siteReiko Fujimura
United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu shi, Tokyo, Japan
Microbes Environ 27:19-29. 2012..The detection of known 16S rRNA gene sequences from Fe(III)-reducing acidophiles promoted us to propose the acidity-driven iron cycle for the early microbial ecosystem on the deposit...
- Deciphering the relationship among phosphate dynamics, electron-dense body and lipid accumulation in the green alga Parachlorella kessleriShuhei Ota
Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277 8562, Japan
Sci Rep 6:25731. 2016..Our findings suggest that the dense body is a site of polyphosphate accumulation, and P. kessleri has potential as a phosphate-accumulating organism. ..
- Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunamiSatoshi Hiraoka
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277 8568, Japan
BMC Genomics 17:53. 2016..In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil...
- Inhibition of Dectin-1 Signaling Ameliorates Colitis by Inducing Lactobacillus-Mediated Regulatory T Cell Expansion in the IntestineCe Tang
Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278 0022, Japan Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo 108 8639, Japan Core Research for Evolutional Science and Technology CREST, Japan Science and Technology Agency JST, Saitama 332 0012, Japan
Cell Host Microbe 18:183-97. 2015..These observations suggest that Dectin-1 regulates the homeostasis of intestinal immunity by controlling Treg cell differentiation through modification of microbiota...
- Mutual reinforcement of inflammation and carcinogenesis by the Helicobacter pylori CagA oncoproteinNobumi Suzuki
1 Division of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan 2 Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
Sci Rep 5:10024. 2015..This work revealed that H. pylori CagA and inflammation reinforce each other in creating a downward spiral that instigates neoplastic transformation. ..
- A unique dermal dendritic cell subset that skews the immune response toward Th2Ryuichi Murakami
Laboratory of Cancer Biology and Molecular Immunology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
PLoS ONE 8:e73270. 2013..We propose that the properties of MGL2(+) dDCs, are complementary to those of CD103(+) dDCs and skew the immune response toward a Th2-type response. ..
- Birth and death of genes linked to chromosomal inversionYoshikazu Furuta
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
Proc Natl Acad Sci U S A 108:1501-6. 2011..These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells...
- Complete genome sequence of the serotype k Streptococcus mutans strain LJ23Chihiro Aikawa
Section of Bacterial Pathogenesis, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Tokyo, Japan
J Bacteriol 194:2754-5. 2012..Here we report the complete genome sequence of serotype k S. mutans strain LJ23, which was recently isolated from the oral cavity of a Japanese patient...
- Genome-wide profiling of DNA methylation in human cancer cellsKatsumi Ogoshi
Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
Genomics 98:280-7. 2011..The MSDS method has the potential to provide novel insight into the functional complexity of the human genome...
- Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysisSatoshi Ishii
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
Appl Environ Microbiol 75:7070-8. 2009..Therefore, OTUs related to Herbaspirillum are potential key players in nitrate respiration and denitrification under the conditions used...
- [Disease and metagenomics of intestinal microbiomes]Masahira Hattori
Graduate School of Frontier Sciences, The University of Tokyo
Nihon Rinsho 67:1214-8. 2009..The International Human Microbiome Project was recently launched to further promote this newly developing field, which will provide new strategies for the maintenance of human health...
- A large-scale full-length cDNA analysis to explore the budding yeast transcriptomeFumihito Miura
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
Proc Natl Acad Sci U S A 103:17846-51. 2006..The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies...
- Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2Hidehiro Toh
Advanced Science Institute, RIKEN, Yokohama, Kanagawa, Japan
J Bacteriol 192:1165-6. 2010..coli phylogenetic group B2, which includes the majority of extraintestinal pathogenic E. coli. Here, we report the finished and annotated genome sequence of this organism...