研究業績(小椋)

原著
Gotoh Y, Atsuta Y, Taniguchi T, Nishida R, Nakamura K, Ogura Y, Misawa N, Hayashi T.
Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex.
Microb Genom. 2022 May;8(5).

Xie H, Ogura Y, Suzuki Y.
Persistence of Antibiotic-Resistant Escherichia coli Strains Belonging to the B2 Phylogroup in Municipal Wastewater under Aerobic Conditions.
Antibiotics. 4;11:202. 2022.

Ono T, Taniguchi I, Nakamura K, Nagano DS, Nishida R, Gotoh Y, Ogura Y, Sato MP, Iguchi A, Murase K, Yoshimura D, Itoh T, Shima A, Dubois D, Oswald E, Shiose A, Gotoh N, Hayashi T.
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex.
Microb Genom. 8(3). 2022.

Suzuki Y, Hiroki H, Xie H, Nishiyama M, Sakamoto SH, Uemura R, Nukazawa K, Ogura Y, Watanabe T, and Kobayashi I.
Antibiotic-resistant Escherichia coli isolated from dairy cows and their surrounding environment on a livestock farm practicing prudent antimicrobial use.
Int J Hyg Environ Health. 240:113930. 2022.

Nishida R, Nakamura K, Taniguchi I, Murase K, Ooka T, Ogura Y, Gotoh Y, Itoh T, Toyoda A, Mainil JG, Piérard D, Seto K, Harada T, Isobe J, Kimata K, Etoh Y, Hamasaki M, Narimatsu H, Yatsuyanagi J, Kameyama M, Matsumoto Y, Nagai Y, Kawase J, Yokoyama E, Ishikawa K, Shiomoto T, Lee K, Kang D, Akashi K, Ohnishi M, Iyoda S, Hayashi T.
The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19.
Microb Genom. 7(12). 2021.

Tuan VP, Yahara K, Dung HDQ, Binh TT, Huu Tung P, Tri TD, Thuan NPM, Khien VV, Trang TTH, Phuc BH, Tshibangu-Kabamba E, Matsumoto T, Akada J, Suzuki R, Okimoto T, Kodama M, Murakami K, Yano H, Fukuyo M, Takahashi N, Kato M, Nishiumi S, Azuma T, Ogura Y, Hayashi T, Toyoda A, Kobayashi I, Yamaoka Y.
Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates.
Microb Genom. 7(11). 2021.

Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S, Yokota A.
Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota.
Microorganisms. 29;9:2254. 2021.

Nakae K, Ooka T, Murakami K, Hara-Kudo Y, Imuta N, Gotoh Y, Ogura Y, Hayashi T, Okamoto Y, Nishi J.
Diversification of Escherichia albertii H-Antigens and Development of H-Genotyping PCR.
Front Microbiol. 1;12:737979. 2021.

Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A.
Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species.
Front Microbiol. 6;12:740610. 2021.

Kajitani R, Noguchi H, Gotoh Y, Ogura Y, Yoshimura D, Okuno M, Toyoda A, Kuwahara T, Hayashi T, Itoh T.
MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features.
Nucleic Acids Res. 16;49:e130. 2021.

Fujikawa T, Ogura Y, Ishigami K, Kawano Y, Nagamine M, Hayashi T, Inoue K.
Unexpected genomic features of high current density-producing Geobacter sulfurreducens strain YM18.
FEMS Microbiol Lett. 9;368:fnab119. 2021.

Hirosawa Y, Tada A, Matsuura T, Mori IC, Ogura Y, Hayashi T, Uehara S, Ito-Inaba Y, Inaba T.
Salicylic Acid Acts Antagonistically to Plastid Retrograde Signaling by Promoting the Accumulation of Photosynthesis-associated Proteins in Arabidopsis.
Plant Cell Physiol. 10;62:1728-1744. 2021.

Fujikawa T, Ogura Y, Hayashi T, Inoue K.
Complete Genome Sequence of High Current-Producing Geobacter sulfurreducens Strain YM35, Isolated from River Sediment in Japan.
Microbiol Resour Announc. 19;10:e0053921. 2021.

Nakamura K, Tokuda C, Arimitsu H, Etoh Y, Hamasaki M, Deguchi Y, Taniguchi I, Gotoh Y, Ogura Y, Hayashi T.
Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli.
PeerJ. 28;9:e11871. 2021.

Nakao R, Kasama K, Boldbaatar B, Ogura Y, Kawabata H, Toyoda A, Hayashi T, Takano A, Maeda K.
The evolution of hard tick-borne relapsing fever borreliae is correlated with vector species rather than geographical distance
BMC Ecology and Evolution. 31;21:105. 2021.

Kiyoshima C, Shirasu N, Urushiyama D, Fukagawa S, Hirakawa T, Yoshikawa K, Izuchi D, Miyata K, Kurakazu M, Yotsumoto F, Hiromatsu K, Nomiyama M, Eiji O, Hirose S, Ogura Y, Hayashi T, Hata K, Nabeshima K, Yasunaga S, Miyamoto S.
MicroRNAs miR-4535 and miR-1915-5p in amniotic fluid as predictive biomarkers for chorioamnionitis.
Future Sci OA. 7:FSO686, 2021.

Fukuda K, Yamasaki K, Ogura Y, Kawanami T, Ikegami H, Noguchi S, Akata K, Katsura K, Yatera K, Mukae H, Hayashi T, Taniguchi H.
A human respiratory tract-associated bacterium with an extremely small genome.
Commun Biol. 4(1):628, 2021.

Auvray F, Perrat A, Arimizu Y, Chagneau CV, Bossuet-Greif N, Massip C, Brugère H, Nougayrède JP, Hayashi T, Branchu P, Ogura Y, Oswald E.
Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population.
Microb Genom. 7(5):mgen.0.000579, 2021.

Nakamura K, Ogura Y, Gotoh Y, Hayashi T.
Prophages integrating into prophages: A mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli.
PLoS Pathog. 17(4):e1009073, 2021.

Kinoshita-Daitoku R, Kiga K, Miyakoshi M, Otsubo R, Ogura Y, Sanada T, Bo Z, Phuoc TV, Okano T, Iida T, Yokomori R, Kuroda E, Hirukawa S, Tanaka M, Sood A, Subsomwong P, Ashida H, Binh TT, Nguyen LT, Van KV, Ho DQD, Nakai K, Suzuki T, Yamaoka Y, Hayashi T, Mimuro H.
A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment
Nat. Commun. 12(1):2085. 2021.

Ogura Y, Ueda T, Nukazawa K, Hiroki H, Xie H, Arimizu Y, Hayashi T, Suzuki Y.
The level of antimicrobial resistance of sewage isolates is higher than that of river isolates in different Escherichia coli lineages.
Sci Rep. 21;10(1):17880. 2020.

Lee JY, Shimizu H, Hagio M, Fukiya S, Watanabe M, Tanaka Y, Joe GH, Iwaya H, Yoshitsugu R, Kikuchi K, Tsuji M, Baba N, Nose T, Tada K, Hanai T, Hori S, Takeuchi A, Furukawa Y, Shirouchi B, Sato M, Ooka T, Ogura Y, Hayashi T, Yokota A, Ishizuka S.
12α-Hydroxylated bile acid induces hepatic steatosis with dysbiosis in rats
Biochim Biophys Acta Mol Cell Biol Lipids. 1865(12):158811. 2020.

Wada N, Yuasa H, Kajitani R, Gotoh Y, Ogura Y, Yoshimura D, Toyoda A, Tang SL, Higashimura Y, Sweatman H, Forsman Z, Bronstein O, Eyal G, Thongtham N, Itoh T, Hayashi T, Yasuda N.
A ubiquitous subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific.
Microbiome. 24;8(1):123. 2020.

Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T, Itoh T.
Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process.
DNA Res. 27(3):dsaa014, 2020.

Kinoshita-Daitoku R, Ogura Y, Kiga K, Maruyama F, Kondo T, Nakagawa I, Hayashi T, Mimuro H.
Complete Genome Sequence of Helicobacter pylori Strain ATCC 43504, a Type Strain That Can Infect Gerbils.
Microbiol Resour Announc. 9(18):e00105-20, 2020.

Tanaka M, Kumakura D, Mino S, Doi H, Ogura Y, Hayashi T, Yumoto I, Cai M, Zhou YG, Gomez-Gil B, Araki T, Sawabe T.
Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments.
Environ Microbiol. 22(8):3205-3217, 2020.

Kaito C, Yoshikai H, Wakamatsu A, Miyashita A, Matsumoto Y, Fujiyuki T, Kato M, Ogura Y, Hayashi T, Isogai T, Sekimizu K.
Non-pathogenic Escherichia coli acquires virulence by mutating a growth-essential LPS transporter.
PLoS Pathog. 16(4):e1008469, 2020.

Kinoshita-Daitoku R, Kiga K, Sanada T, Ogura Y, Bo Z, Iida T, Yokomori R, Kuroda E, Tanaka M, Sood A, Suzuki T, Nakai K, Hayashi T, Mimuro H.
Mutational diversity in mutY deficient Helicobacter pylori and its effect on adaptation to the gastric environment.
Biochem Biophys Res Commun 525(7):806-811, 2020.

Ikeda T, Shinagawa T, Ito T, Ohno Y, Kubo A, Nishi J, Gotoh Y, Ogura Y, Ooka T, Hayashi T.
Hypoosmotic stress induces flagellar biosynthesis and swimming motility in Escherichia albertii..
Commun Biol. 3(1):87, 2020.

Tanaka M, Kinoshita-Daitoku R, Kiga K, Sanada T, Zhu B, Okano T, Aikawa C, Iida T, Ogura Y, Hayashi T, Okubo K, Kurosawa M, Hirahashi J, Suzuki T, Nakagawa I, Nangaku M, Mimuro H.
Group A Streptococcus establishes pharynx infection by degrading the deoxyribonucleic acid of neutrophil extracellular traps.
Sci Rep. 10(1):3251, 2020.

Ishimaru K, Sasaki M, Narimatsu H, Arimizu Y, Gotoh Y, Nakamura K, Hayashi T, Ogura Y.
Escherichia coli O8:H8 Carrying a Novel Variant of the Heat-Labile Enterotoxin LT2 Gene Caused Outbreaks of Diarrhea.
Open Forum Infect Dis. 7(1):ofaa021, 2020.

Nakamura K, Murase K, Sato MP, Toyoda A, Itoh T, Mainil JG, Pierard D, Yoshino S, Kimata K, Isobe J, Seto K, Etoh Y, Narimatsu H, Saito S, Yatsuyanagi J, Lee K, Iyoda S, Ohnishi M, Ooka T, Gotoh Y, Ogura Y, Hayashi T.
Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28.
Microb Genom. 6(1):e000323, 2020.

Kasama K, Fujita H, Yamamoto S, Ooka T, Gotoh Y, Ogura Y, Ando S, Hayashi T.
Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica.
Front Microbiol. 10:2787, 2019.

Suzuki Y, Imafuku Y, Nishiyama M, Teranishi K, Jikumaru A, Nukazawa K, Ogura Y.
A highly efficient method for concentrating DNA from river water by combined coagulation and foam separation.
Separation Science and Technology. 54(18):1-7, 2019.

Hashihama F, Suwa S, Kanda J, Ehama M, Sakuraba R, Kinouchi S, Sato M, Yamaguchi T, Saito H, Ogura Y, Hayashi T, Mori H, Kurokawa K, Suzuki S, Hamasaki K.
Arsenate and microbial dynamics in different phosphorus regimes of the subtropical Pacific Ocean.
Progress in Oceanograph. 176:102115, 2019.

Ooka T, Seto K, Ogura Y, Nakamura K, Iguchi A, Gotoh Y, Honda M, Etoh Y, Ikeda T, Sugitani W, Konno T, Kawano K, Imuta N, Yoshiie K, Hara-Kudo Y, Murakami K, Hayashi T, Nishi J.
Antigen biosynthesis gene clusters of Escherichia albertii.: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method.
Microb Genom 5(11):e000314, 2019.

Okura M, Maruyama F, Ota A, Tanaka T, Matoba Y, Osawa A, Sadaat SM, Osaki M, Toyoda A, Ogura Y, Hayashi T, Takamatsu D.
Genotypic diversity of Streptococcus suis and the S. suis-like bacterium Streptococcus ruminantium in ruminants.
Vet Res 50(1):94, 2019.

Sato MP, Ogura Y, Nakamura K, Nishida R, Gotoh Y, Hayashi M, Hisatsune J, Sugai M, Takehiko I, Hayashi T.
Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes.
DNA Res. 26(5):391-398, 2019.

Arimizu Y, Kirino Y, Sato MP, Uno K, Sato T, Gotoh Y, Auvray F, Brugere H, Oswald E, Mainil JG, Anklam KS, Dopfer D, Yoshino S, Ooka T, Tanizawa Y, Nakamura Y, Iguchi A, Morita-Ishihara T, Ohnishi M, Akashi K, Hayashi T, Ogura Y*.
Large-scale genome analysis of bovine commensal Escherichia coli revealed that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains.
Genome Res. 29(9):1495-1505, 2019.

Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Watanabe H, Masuda K, Nishimoto Y, Kubo M, Hosoda F, Rokutan H, Matsumoto M, Takamaru H, Yamada M, Matsuda T, Iwasaki M, Yamaji T, Yachida T, Soga T, Kurokawa K, Toyoda A, Ogura Y, Hayashi T, Hatakeyama M, Nakagama H, Saito Y, Fukuda S, Shibata T, Yamada T.
Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.
Nat Med. 25(6):968-976, 2019.

Yoshimura D, Kajitani R, Gotoh Y, Katahira K, Okuno M, Ogura Y, Hayashi T, Itoh T.
Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP.
Microb Genom. 5(5):e000261, 2019.

Nakamura K, Shinoda N, Hiramatsu Y, Ohnishi S, Kamitani S, Ogura Y, Hayashi T, Horiguchi Y.
BspR/BtrA, an Anti-σ Factor, Regulates the Ability of Bordetella bronchiseptica. To Cause Cough in Rats.
mSphere. 4(2):e00093-19, 2019.

Fukano H, Yoshida M, Shouji M, Hatta S, Maruyama D, Izutsu K, Shiotsuka M, Ogura Y, Hayashi T, Hasegawa N, Iwata S, Hoshino Y.
Draft Genome Sequence of Mycolicibacterium sp. Strain NCC-Tsukiji, Isolated from Blood Culture of a Patient with Malignant Lymphoma.
Microbiol Resour Announc. 8(14):e01575-18, 2019.

Ito-Inaba Y, Sato M, Sato MP, Kurayama Y, Yamamoto H, Ohata M, Ogura Y, Hayashi T, Toyooka K, Inaba T.
Alternative Oxidase Capacity of Mitochondria in Microsporophylls May Function in Cycad Thermogenesis.
Plant Physiol. 180:743-756, 2019.

Takizawa N, Ogura Y, Fujita Y, Noda T, Shigematsu H, Hayashi T, Kurokawa K.
Local structural changes of the influenza A virus ribonucleoprotein complex by single mutations in the specific residues involved in efficient genome packaging.
Virology. 531:126-140, 2019.

Gotoh Y, Taniguchi T, Yoshimura D, Katsura K, Saeki Y, Hirabara Y, Fukuda M, Takajo I, Tomida J, Kawamura Y, Ogura Y, Itoh T, Misawa N, Okayama A, Hayashi T.
Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak.
Microb Genom. 4(12):e000236, 2018.

Ogura Y, Seto K, Morimoto Y, Nakamura K, Sato MP, Gotoh Y, Itoh T, Toyoda A, Ohnishi M, Hayashi T.
Genomic Characterization of β-Glucuronidase-Positive Escherichia coli O157:H7 Producing Stx2a.
Emerg Infect Dis. 24(12):2219-2227, 2018.

Wong SK, Yoshizawa S, Nakajima Y, Cuadra MJ, Nogi Y, Nakamura K, Takami H, Ogura Y, Hayashi T, Chiura HX, Hamasaki K.
Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet.
Int J Syst Evol Microbiol. 68(9):2872-2877, 2018.

Fukano H, Yoshida M, Kazumi Y, Fujiwara N, Katayama K, Ogura Y, Hayashi T, Miyamoto Y, Fujimoto N, Hongsheng W, Mizumoto C, Koizumi Y, Maeda H, Hiranuma O, Mitarai S, Ishii N, Hoshino Y.
Mycobacterium shigaense sp. nov., a slow-growing, scotochromogenic species, is a member of the Mycobacterium simiae complex.
Int J Syst Evol Microbiol. 68(8):2437-2442, 2018.

Tanaka M, Mino S, Ogura Y, Hayashi T, Sawabe T.
Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case.
PeerJ. 6:e5018, 2018.

Yoshida M, Fukano H, Ogura Y, Kazumi Y, Mitarai S, Hayashi T, Hoshino Y.
Complete Genome Sequence of Mycobacterium shigaense.
Genome Announc. 6(25):e00552-18, 2018.

Hasegawa M, Nakajima Y, Wong SK, Nakamura K, Ogura Y, Hayashi T, Kogure K, Yoshizawa S. Draft Genome Sequence of Saccharospirillum sp. Strain MSK14-1, Isolated from Surface Seawater Collected at Aburatsubo Inlet in Japan.
Genome Announc. 6(22):e00552-18, 2018.

Nakanaga K, Ogura Y, Toyoda A, Yoshida M, Fukano H, Fujiwara N, Miyamoto Y, Nakata N, Kazumi Y, Maeda S, Ooka T, Goto M, Tanigawa K, Mitarai S, Suzuki K, Ishii N, Ato M, Hayashi T, Hoshino Y.
Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic.
Sci Rep. 8(1):8218, 2018.

Inoue K, Ogura Y, Kawano Y, Hayashi T.
Complete Genome Sequence of Geobacter sulfurreducens Strain YM18, Isolated from River Sediment in Japan.
Genome Announc. 6(19):e00352-18, 2018.

Suzuki Y, Teranishi K, Matsuwaki T, Nukazawa K, Ogura Y.
Effects of bacterial pollution caused by a strong typhoon event and the restoration of a recreational beach: Transitions of fecal bacterial counts and bacterial flora in beach sand.
Sci Total Environ. 640-641:52-61, 2018.

Hirano A, Umeno J, Okamoto Y, Shibata H, Ogura Y, Moriyama T, Torisu T, Fujioka S, Fuyuno Y, Kawarabayasi Y, Matsumoto T, Kitazono T, Esaki M.
Comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis.
J Gastroenterol Hepatol. 33(9):jgh.14129, 2018.

Ke HM, Liu D, Ogura Y, Hayashi T, Urbanczyk H, Tsai IJ.
Tracing Genomic Divergence of Vibrio Bacteria in the Harveyi Clade.
J Bacteriol. 200(15):e00001-18, 2018.

Nakajima Y, Tsukamoto T, Kumagai Y, Ogura Y, Hayashi T, Song J, Kikukawa T, Demura M, Kogure K, Sudo Y, Yoshizawa S.
Presence of a Haloarchaeal Halorhodopsin-Like Cl- Pump in Marine Bacteria.
Microbes Environ. 33(1):89-97, 2018.

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.
ISME J. 12(5):1329-1343, 2018.

Oogai Y, Gotoh Y, Ogura Y, Kawada-Matsuo M, Hayashi T, Komatsuzawa H.
Small RNA repertoires and their intraspecies variation in Aggregatibacter actinomycetemcomitans.
DNA Res. 25(2):207-215, 2018.

Tawthep S, Fukiya S, Lee JY, Hagio M, Ogura Y, Hayashi T, Yokota A.
Isolation of six novel 7-oxo- or urso-type secondary bile acid-producing bacteria from rat cecal contents.
J Biosci Bioeng. 124(5):514-522, 2017.

Tsuchida S, Maruyama F, Ogura Y, Toyoda A, Hayashi T, Okuma 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.
Front Microbiol. 8:1540, 2017.

Nakajima Y, Yoshizawa S, Park S, Kumagai Y, Wong SK, Ogura Y, Hayashi T, Kogure K.
Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.
Genome Announc. 5(38):e00990-17, 2017.

Hayase E, Hashimoto D, Nakamura K, Noizat C, Ogasawara R, Takahashi S, Ohigashi H, Yokoi Y, Sugimoto R, Matsuoka S, Ara T, Yokoyama E, Yamakawa T, Ebata K, Kondo T, Hiramine R, Aizawa T, Ogura Y, Hayashi T, Mori H, Kurokawa K, Tomizuka K, Ayabe T, Teshima T.
R-Spondin1 expands Paneth cells and prevents dysbiosis induced by graft-versus-host disease.
J Exp Med. 214(12):3507-3518, 2017.

Kumagai Y, Yoshizawa S, Nakamura K, Ogura Y, Hayashi T, Kogure K.
Complete and Draft Genome Sequences of Eight Oceanic Pseudomonas aeruginosa Strains.
Genome Announc. 2;5(44). e01255-17. 2017.

Yoshida M, Miyamoto Y, Ogura Y, Hayashi T, Hoshino Y.
Complete Chromosome Sequence of a Mycolactone-Producing Mycobacterium, Mycobacterium pseudoshottsii.
Genome Announc. 5(48):e01363-17, 2017.

Ogura Y, Gotoh Y, Itoh T, Sato MP, Seto K, Yoshino S, Isobe J, Etoh Y, Kurogi M, Kimata K, Maeda E, Pierard D, Kusumoto M, Akiba M, Tominaga K, Kirino Y, Kato Y, Shirahige K, Ooka T, Ishijima N, Lee KI, Iyoda S, Mainil JG, Hayashi T.
Population structure of Escherichia coli O26:H11 with recent and repeated stx2 acquisition in multiple lineages.
Microb Genom. 3(11):e000141. 2017.

Wong SK, Park S, Lee JS, Lee KC, Ogura Y, Hayashi T, Chiura HX, Yoshizawa S, Hamasaki K.
Algibacter aquaticus sp. nov., a slightly alkaliphilic marine Flavobacterium isolated from coastal surface water.
Int J Syst Evol Microbiol. 67(7):2199-2204, 2017.

Amin AKMR, Tanaka M, Al-Saari N, Feng G, Mino S, Ogura Y, Hayashi T, Meirelles PM, Thompson FL, Gomez-Gil B, Sawabe T, Sawabe T.
Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan.
Syst Appl Microbiol. 40(5):290-296, 2017.

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.
PLoS One. 12(6):e0180053, 2017.

Lee KI, Morita-Ishihara T, Iyoda S, Ogura Y, Hayashi T, Sekizuka T, Kuroda M, Ohnishi M; EHEC Working Group in Japan.
A Geographically Widespread Outbreak Investigation and Development of a Rapid Screening Method Using Whole Genome Sequences of Enterohemorrhagic Escherichia coli O121.
Front Microbiol. 8:701, 2017.

Nakajima Y, Yoshizawa S, Nakamura K, Ogura Y, Hayashi T, Kogure K.
Draft Genome Sequences of Tersicoccus phoenicis DSM 30849T, Isolated from a Cleanroom for Spacecraft Assembly, and Tersicoccus sp. Strain Bi-70, Isolated from a Freshwater Lake.
Genome Announc. 5(13):e00079-17, 2017.

Ogawa Y, Shiraiwa K, Ogura Y, Ooka T, Nishikawa S, Eguchi M, Hayashi T, Shimoji Y.
Clonal Lineages of Erysipelothrix rhusiopathiae Responsible for Acute Swine Erysipelas in Japan Identified by Using Genome-Wide Single-Nucleotide Polymorphism Analysis.
Appl Environ Microbiol. 83(11):e00130-17, 2017.

Ishijima N, Lee KI, Kuwahara T, Nakayama-Imaohji H, Yoneda S, Iguchi A, Ogura Y, Hayashi T, Ohnishi M, Iyoda S.
Identification of a New Virulent Clade in Enterohemorrhagic Escherichia coli O26:H11/H- Sequence Type 29.
Sci Rep. 7:43136, 2017.

Akter A, Ooka T, Gotoh Y, Yamamoto S, Fujita H, Terasoma F, Kida K, Taira M, Nakadouzono F, Gokuden M, Hirano M, Miyashiro M, Inari K, Shimazu Y, Tabara K, Toyoda A, Yoshimura D, Itoh T, Kitano T, Sato MP, Katsura K, Mondal SI, Ogura Y, Ando S, Hayashi T.
Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan.
Genome Biol Evol. 9(1):124-133, 2017.

Fakih I, Thiry D, Duprez JN, Saulmont M, Iguchi A, Pierard D, Jouant L, Daube G, Ogura Y, Hayashi T, Taminiau B, Mainil JG.
Identification of Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli in diarrhoeic calves and comparative genomics of O5 bovine and human STEC.
Vet Microbiol. 202: 16-22, 2017.

Kondo Y, Ogura Y, Sato K, Imamura K, Hoshino T, Nishiguchi M, Hasuwa T, Moriuchi H, Hayashi T, Fujiwara T.
Complete Genome Sequence of Streptococcus sp. Strain NPS 308.
Genome Announc. 4(6):01349-16, 2016.

Mondal SI, Islam MR, Sawaguchi A, Asadulghani M, Ooka T, Gotoh Y, Kasahara Y, Ogura Y, Hayashi T.
Genes essential for the morphogenesis of the Shiga toxin 2-transducing phage from Escherichia coli O157:H7.
Sci Rep. 6:39036,2016.

Kaneko R, Wong SK, Ogura Y, Hayashi T, Yoshizawa S, Hamasaki K.
Draft Genome Sequences of Two Fabibacter sp. Strains Isolated from Coastal Surface Water of Aburatsubo Inlet, Japan.
Genome Announc. 4(6):01360-16, 2016.

Ogura Y, Nakayama N, Hayashi T, Ueki S.
Mitochondrial Genome Sequences of Four Strains of the Bloom-Forming Raphidophyte Heterosigma akashiwo.
Genome Announc. 4(6):e01288-16, 2016.

Amako K, Iida KI, Saito M, Ogura Y, Hayashi T, Yoshida SI.
Non-exponential growth of Mycobacterium leprae Thai-53 strain cultured in vitro.
Microbiol Immunol. 60(12):817-823, 2016.

Iwase T, Ogura Y, Hayashi T, Mizunoe Y.
Complete Genome Sequence of Klebsiella oxytoca Strain JKo3.
Genome Announc. 4(6):e01221-16. 2016.

Yoshida M, Nakanaga K, Ogura Y, Toyoda A, Ooka T, Kazumi Y, Mitarai S, Ishii N, Hayashi T, Hoshino Y.
Complete Genome Sequence of Mycobacterium ulcerans subsp. shinshuense.
Genome Announc. 4(5):e01050-16, 2016.

Ogura Y, Hayashi T, Ueki S.
Complete Genome Sequence of a Phycodnavirus, Heterosigma akashiwo Virus Strain 53.
Genome Announc. 4(6):e01279-16, 2016.

Wong SK, Yoshizawa S, Nakajima Y, Ogura Y, Hayashi T, Hamasaki K.
Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer.
Genome Announc. 4(4):e00754-16, 2016.

Kusumoto M, Ogura Y, Gotoh Y, Iwata T, Hayashi T, Akiba M.
Colistin-Resistant mcr-1-Positive Pathogenic Escherichia coli in Swine, Japan, 2007-2014.
Emerg Infect Dis. 22(7):1315-1317, 2016.

Imuta N, Ooka T, Seto K, Kawahara R, Koriyama T, Kojyo T, Iguchi A, Tokuda K, Kawamura H, Yoshiie K, Ogura Y, Hayashi T, Nishi J.
Phylogenetic analysis of enteroaggregative Escherichia coli (EAEC) isolated in Japan revealed the emergence of CTX-M-14-producing EAEC O25:H4 clones related to ST131.
J Clin Microbiol. 54(8):2128-34, 2016.

Iguchi A, Iyoda S, Seto K, Nishii H, Ohnishi M, Mekata H, Ogura Y, Hayashi T.
Six Novel O Genotypes from Shiga Toxin-Producing Escherichia coli.
Front Microbiol. 7:765, 2016.

Katahira K, Ogura Y, Gotoh Y, Hayashi T.
Draft Genome Sequences of Five Rapidly Growing Mycobacterium Species, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M. brisbanense, and M. novocastrense.
Genome Announc. 4(3):e00322-16, 2016.

Urbanczyk Y, Ogura Y, Hayashi T, Urbanczyk H.
Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida.
Int J Syst Evol Microbiol. 66(8):3214-3218, 2016.

Garcia BG, Ooka T, Gotoh Y, Vieira MA, Yamamoto D, Ogura Y, Girao DM, Sampaio SC, Melo AB, Irino K, Hayashi T, Gomes TA.
Genetic relatedness and virulence properties of enteropathogenic Escherichia coli strains of serotype O119:H6 expressing localized adherence or localized and aggregative adherence-like patterns on HeLa cells.
Int J Med Microbiol. 306(3):152-164, 2016.

Iwase T, Ogura Y, Hayashi T, Mizunoe Y.
Complete Genome Sequence of Klebsiella pneumoniae YH43.
Genome Announc. 4(2):e00242-16, 2016.

Kusumoto M, Hikoda Y, Fujii Y, Murata M, Miyoshi H, Ogura Y, Gotoh Y, Iwata T, Hayashi T, Akiba M.
Emergence of a Multidrug-Resistant Shiga Toxin-Producing Enterotoxigenic Escherichia coli Lineage in Diseased Swine in Japan.
J Clin Microbiol. 54(4):1074-1081, 2016.

Ushida K, Tsuchida S, Ogura Y, Hayashi T, Sawada A, Hanya G.
Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese Macaques in Yakushima Island.
Genome Announc. 4(1):e01694-15, 2016.

Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M.
The genomic basis of parasitism in the Strongyloides clade of nematodes.
Nat Genet. 48(3):299-307, 2016.

Naito M, Ogura Y, Itoh T, Shoji M, Okamoto M, Hayashi T, Nakayama K.
The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat.
DNA Res. 23(1):11-9, 2016.

Ooka T, Ogura Y, Katsura K, Seto K, Kobayashi H, Kawano K, Tokuoka E, Furukawa M, Harada S, Yoshino S, Seto J, Ikeda T, Yamaguchi K, Murase K, Gotoh Y, Imuta N, Nishi J, Gomes TA, Beutin L, Hayashi T.
Defining the Genome Features of Escherichia albertii., an Emerging Enteropathogen Closely Related to Escherichia coli.
Genome Biol Evol. 7(12):3170-3179, 2015.

Ogura Y, Mondal SI, Islam MR, Mako T, Arisawa K, Katsura K, Ooka T, Gotoh Y, Murase K, Ohnishi M, Hayashi T.
The Shiga toxin 2 production level in enterohemorrhagic Escherichia coli O157:H7 is correlated with the subtypes of toxin-encoding phage.
Sci Rep. 5:16663, 2015.

Ozeki Y, Igarashi M, Doe M, Tamaru A, Kinoshita N, Ogura Y, Iwamoto T, Sawa R, Umekita M, Enany S, Nishiuchi Y, Osada-Oka M, Hayashi T, Niki M, Tateishi Y, Hatano M, Matsumoto S.
A New Screen for Tuberculosis Drug Candidates Utilizing a Luciferase-Expressing Recombinant Mycobacterium bovis Bacillus Calmette-Gueren.
PLoS One. 10(11):e0141658, 2015.

Tsuchida S, Nezuo M, Tsukahara M, Ogura Y, Hayashi T, Ushida K.
Draft Genome Sequence of Lactobacillus gorillae Strain KZ01T, Isolated from a Western Lowland Gorilla.
Genome Announc. 3(5):e01196-15, 2015.

Yamauchi K, Kondo S, Hamamoto M, Takahashi Y, Ogura Y, Hayashi T, Nishida H.
Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata.
Genome Announc. 3(3):e00220-15, 2015.

Urbanczyk Y, Ogura Y, Hayashi T, Urbanczyk H.
Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization.
Syst Appl Microbiol. 38(5):300-304, 2015.

Tani A, Ogura Y, Hayashi T, Kimbara K.
Complete Genome Sequence of Methylobacterium aquaticum Strain 22A, Isolated from Racomitrium japonicum Moss.
Genome Announc. 3(2):e00266-15, 2015.

Shimizu W, Kouda S, Ogura Y, Kayama S, Kobayashi K, Shigemoto N, Shimada N, Yano R, Hisatsune J, Kato F, Hayashi T, Sueda T, Ohge H, and Sugai M.
Persistence and epidemic propagation of a Pseudomonas aeruginosa sequence type 235 clone harboring an IS26 composite transposon carrying the blaIMP-1 integron in Hiroshima, Japan, 2005 to 2012.
Antimicrob Agents Chemother. 59(5):2678-2687, 2015.

Okada K, Abe H, Ike F, Ogura Y, Hayashi T, Fukui-Miyazaki A, Nakamura K, Shinzawa N, Horiguchi Y.
Polymorphisms influencing expression of dermonecrotic toxin in Bordetella bronchiseptica..
PLoS One. 10(2):e011660, 2015.

Kojima H, Ogura Y, Yamamoto N, Togashi T, Mori H, Watanabe T, Nemoto F, Kurokawa K., Hayashi T, Fukui M.
Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence.
ISME J. 9(5):1166-76, 2015.

Urbanczyk H, Ogura Y, Hayashi T.
Contrasting inter- and intraspecies recombination patterns in the ‘Harveyi clade’ Vibrio collected over large spatial and temporal scales.
Genome Biol Evol. 7(1):71-80, 2014.


Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K, Ohnishi M, Hayashi T, Thomson NR.
A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster.
DNA Res. 22(1):101-7, 2014.

Tanaka R, Hino A, Tsai IJ, Palomares-Rius JE, Yoshida A, Ogura Y, Hayashi T, Maruyama H, Kikuchi T.
Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics.
PLoS One. 9(10):e110769, 2014.

Iyoda S, Manning SD, Seto K, Kimata K, Isobe J, Etoh Y, Ichihara S, Migita Y, Ogata K, Honda M, Kubota T, Kawano K, Matsumoto K, Kudaka J, Asai N, Yabata J, Tominaga K, Terajima J, Morita-Ishihara T, Izumiya H, Ogura Y, Saitoh T, Iguchi A, Kobayashi H, Hara-Kudo Y, Ohnishi M, EHEC Working Group in Japan.
Phylogenetic clades 6 and 8 of enterohemorrhagic Escherichia coli O157:H7 with particular stx subtypes are more frequently found in isolates from hemolytic uremic syndrome patients than from asymptomatic carriers.
Open Forum Infect Dis. 1(2):ofu061, 2014.

Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J, Sebaihia M, Coulthurst SJ, Gotoh N, Thomson NR, Ewbank JJ, Hayashi T.
Genome evolution and plasticity of Serratia marcescens, an important multidrug resistant nosocomial pathogen.
Genome Biol Evol. 6(8):2096-2110, 2014.

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Okuno M, Yabana M, Ogura Y, Nagayasu E, Maruyama H, Hayashi T, Kohara Y, Fujiyama A, Itoh T.
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
Genome Res. 24(8):1384-1395, 2014.

Okada K, Ogura Y, Hayashi T, Abe A, Kuwae A, Horiguchi Y, Abe H.
Complete genome sequence of Bordetella bronchiseptica. S798, an isolate from a pig with atrophic rhinitis.
Genome Announc. 2(3):e00436-14, 2014.

Yoshizawa S, Kumagai Y, Kim H, Ogura Y, Hayashi T, Iwasaki W, DeLong EF, Kogure K.
Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria.
Proc Natl Acad Sci U S A. 111(18):6732-6737, 2014.

Nonaka L, Maruyama F, Onishi Y, Kobayashi T, Ogura Y, Hayashi T, Suzuki S, Masuda M.
Various pAQU plasmids possibly contribute to disseminate tetracycline resistance gene tet(M) among marine bacterial community.
Front Microbiol. 5:152, 2014.

Ohtsubo Y, Kishida K, Sato T, Tabata M, Kawasumi T, Ogura Y, Hayashi T, Tsuda M, Nagata Y. Complete genome sequence of Pseudomonas sp. strain TKP isolated from a γ- hexachlorocyclohexane- degrading mixed culture.
Genome Announc. 2(1):e01241-13, 2014.

Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura Y, Hayashi T, Kurokawa K, Ohnishi M, Sekine Y.
A novel small regulatory RNA enhances cell motility in enterohemorrhagic Escherichia coli.
J Gen Appl Microbiol. 60(1):44-50, 2014.

Kusumoto M, Fukamizu D, Ogura Y, Yoshida E, Yamamoto F, Iwata T, Ooka T, Akiba M, Hayashi T.
The lineage-specific distribution of IS-excision enhancer in enterotoxigenic Escherichia coli isolated from swine.
Appl Environ Microbiol. 80(4):1394-1402, 2014.

Ohtsubo Y, Sato T, Kishida K, Tabata M, Ogura Y, Hayashi T, Tsuda M, Nagata Y.
Complete genome sequence of Pseudomonas aeruginosa MTB-1, isolated from a microbial community enriched by the technical formulation of hexachlorocyclohexane.
Genome Announc. 2(1):e01130-13, 2014.

Sakaguchi Y, Hosomi K, Uchiyama J, Ogura Y, Umeda K, Sakaguchi M, Kohda T, Mukamoto M, Misawa N, Matsuzaki S, Hayashi T, Kozaki S.
Draft genome sequence of Clostridium botulinum type B strain Osaka05, isolated from an infant patient with botulism in Japan.
Genome Announc. 2(1):e01010-13, 2014.

Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR, Mino S, Nakagawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R, Thompson FL, Gomez-Gil B, Christen R, Maruyama F, Kurokawa K, Hayashi T.
Front Microbiol. 4:414, 2013.

Urbanczyk H, Urbanczyk Y, Hayashi T, Ogura Y.
Diversification of two lineages of symbiotic Photobacterium.
PLoS One. 8(12):e82917, 2013.

Tateishi Y, Tamaru A, Ogura Y, Niki M, Wada T, Yamamoto T, Hirata K, Hayashi T, Matsumoto S. Whole-genome sequence of the potentially hyper-transmissible multi-drug resistant mycobacterium tuberculosis Beijing strain, OM-V02_005.
Genome Announc. 1(4):e00608-13, 2013.

Kawada-Matsuo M, Oogai Y, Zendo T, Nagao J, Shibata Y, Yamashita Y, Ogura Y, Hayashi T, Sonomoto K, Komatsuzawa H.
Involvement of the novel two-component NsrRS and LcrRS systems in distinct resistance pathways against nisin A and nukacin ISK-1 in Streptococcus mutans.
Appl Environ Microbiol. 79(15):4751-4755, 2013.

Urbanczyk H, Ogura Y, Hayashi T.
Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences.
Int J Syst Evol Microbiol. 63(Pt 7):2742-2751, 2013.

Ooka T, Tokuoka E, Fukuhara M, Nagamura T, Ogura Y, Aisawa K, Harada S, Hayashi T.
Human gastroenteritis outbreak associated with Escherichia albertii., Japan.
Emerg Infect Dis. 19(1): 144-146, 2013.

Nagayasu E, Ogura Y, Itoh T, Yoshida A, Chakraborty G, Hayashi T, Maruyama H.
Transcriptomic analysis of four developmental stages of Strongyloides venezuelensis.
Parasitol Int. 62(1):57-65, 2013.

Minegishi K, Aikawa C, Furukawa A, Watanabe T, Nakano T, Ogura Y, Ohtsubo Y, Kurokawa K, Hayashi T, Maruyama F, Nakagawa I, Eishi Y.
Complete genome sequence of a Propionibacterium acnes isolate from a sarcoidosis patient.
Genome Announc. 1(1):e00016-12, 2013.

Tateishi Y, Kitada S, Miki K, Maekura R, Ogura Y, Ozeki Y, Nishiuchi Y, Niki M, Hayashi T, Hirata K, Kobayashi K, Matsumoto S.
Whole-genome sequence of a hypervirulent clinical strain Mycobacterium intracellulare M.i.198.
J Bacteriol. 194(22): 6336, 2012.

Yokota A, Fukiya S, Ooka T, Ogura Y, Hayashi T, Ishizuka S.
Is bile acid a determinant of the gut microbiota on a high-fat diet?
Gut Microbes. 3(5):455-459, 2012.

Goto T, Ogura Y, Hirakawa H, Tomida J, Morita Y, Akaike T, Hayashi T, Kawamura Y.
Complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia.
J Bacteriol. 194(14):3744-3745, 2012.

Kakizaki E, Ogura Y, Kozawa S, Nishida S, Uchiyama T, Hayashi T, Yukawa N.
Detection of diverse aquatic microbes in blood and organs of drowning victims: First metagenomic approach using high-throughput 454-pyrosequencing.
Forensic Sci Int. 220(1-3): 135-146, 2012.

Islam MR, Ogura Y, Asdulghani M, Ooka T, Murase K, Gotoh Y, Hayashi T.
A sensitive and simple plaque formation method for the Stx2 phage of Escherichia coli O157:H7, which does not form plaques in the standard plating procedure.
Plasmid. 67(3):227-235, 2012.

Murase M, Ooka T, Iguchi A, Ogura Y, Nakayama K, Asadulghani M, Islam MR, Hiyoshi H, Kodama T, Beutin L, Hayashi T.
Hemolysin E- and enterohemolysin-derived hemolytic activity of O55/O157 strains and other Escherichia coli lineages.
Microbiology. 158(Pt 3):746-758, 2012.

Ooka T, Seto K, Kawano K, Kobayashi H, Etoh Y, Ichihara S, Kaneko A, Isobe J, Yamaguchi K, Horikawa K, Gomes TAT, Linden A, Bardiau M, Mainil J, Beutin L, Ogura Y, Hayashi T.
Clinical significance of Escherichia albertii..
Emerg Infect Dis. 18(3):488-492, 2012.

Islam KB, Fukiya S, Hagio M, Fujii N, Ishizuka S, Ooka T, Ogura Y, Hayashi T, Yokota A.
Bile acid is a host factor that regulates the composition of the cecal microbiota in rats.
Gastroenterology. 141(5):1773-81. 2011.

Iguchi A, Shirai H, Seto K, Ooka T, Ogura Y, Hayashi T, Osawa K, Osawa R.
Wide distribution of O157-antigen biosynthesis gene clusters 1 in Escherichia coli.
PLoS One. 6(8):e23250, 2011.

Kuwahara T, Ogura Y, Oshima K, Kurokawa K, Ooka T, Hirakawa H, Itoh T, Nakayama-Imaohji H, Ichimura M, Itoh K, Ishifune C, Maekawa Y, Yasutomo K, Hattori M, Hayashi T.
The lifestyle of the segmented filamentous bacterium: a nonculturable gut-associated immunostimulating microbe inferred by whole-genome sequencing.
DNA Res. 18(4): 291-303, 2011.

Naito M, Sato K, Shoji M, Yukitake H, Ogura Y, Hayashi T, Nakayama K.
Characterisation of the Porphyromonas gingivalis conjugative transposon CTnPg1: determination of the integration site and the genes essential for conjugal transfer.
Microbiology. 157(Pt 7):2022-2032, 2011.

Mainil JG, Bardiau M, Ooka T, Ogura Y, Murase K, Etoh Y, Ichihara S, Horikawa K, Buvens G, Pierard D, Itoh T, Hayashi T.
IS621-based multiplex PCR printing method of O26 enterohaemorrhagic and enteropathogenic Escherichia coli isolated from humans and cattle.
J Appl Microbiol. 111(3):773-786, 2011.

Ogawa Y, Ooka T, Shi F, Ogura Y, Nakayama K, Hayashi T, Shimoji Y.
The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of Firmicutes and the organism's intracellular adaptations.
J Bacteriol. 193(12):2959-2971, 2011.

Urbanczyk H, Ogura Y, Hendry TA, Gould AL, Kiwaki N, Atkinson JT, Hayashi T., Dunlap PV.
Genome sequence of Photobacterium mandapamensis strain svers.1.1, the bioluminescent symbiont of the cardinal fish Siphamia versicolor.
J Bacteriol. 193(12):3144-3145, 2011.

Kusumoto M, Ooka T, Nishiya Y, Ogura Y, Saito T, Sekine Y, Iwata T, Akiba M, Hayashi T.
IS-excision enhancer removes transposable elements from bacterial genomes and induces various genomic deletions.
Nat Commun. 2:152, 2011.

Nakayama K, Kurokawa K, Fukuhara M, Urakami H, Yamamoto S, Yamazaki K, Ogura Y, Ooka T., Hayashi T.
Genome Comparison and Phylogenetic Analysis of Orientia tsutsugamushi Strains.
DNA Res. 17(5):281-291, 2010.

Toh H, Oshima K, Toyoda A, Ogura Y, Ooka T, Sasamoto H, Park SH, Iyoda S, Kurokawa K, Morita H, Itoh K, Taylor TD, Hayashi T, Hattori M.
Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2.
J Bacteriol. 192(4):1165-1166, 2010.

Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, Tobe T, Hattori M, Hayashi T.
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli.
Proc Natl Acad Sci U S A. 106(42):17939-17944, 2009.

Ooka T, Terajima J, Kusumoto M, Iguchi A, Kurokawa K, Ogura Y, Asadulghani M, Nakayama K, Murase K, Ohnishi M, Iyoda S, Watanabe H, Hayashi T.
Development of a multiplex PCR-based rapid typing method 1 for enterohemorrhagic Escherichia coli O157 strains.
J Clin Microbiol. 47(9):2888-2894, 2009.

Yoshii N, Ogura Y, Hayashi T, Ajiro T, Sameshima T, Nakazawa M, Kusumoto M, Iwata T, Akiba M.
Pulsed-field gel electrophoresis profile changes resulting from spontaneous chromosomal deletions in enterohemorrhagic Escherichia coli O157:H7 during passage in cattle.
Appl Environ Microbiol. 75(17):5719-5726, 2009.

Ooka T, Ogura Y, Asadulghani M, Ohnishi M, Nakayama K, Terajima J, Watanabe H, Hayashi T.
Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes.
Genome Res. 19(10):1809-1816, 2009.

Leopold SR, Magrini V, Holt NJ, Shaikh N, Mardis ER, Cagno J, Ogura Y, Iguchi A, Hayashi T, Mellmann A, Karch H, Besser TE, Sawyer SA, Whittam TS, Tarr PI.
A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis.
Proc Natl Acad Sci U S A. 106(21):8713-8718, 2009.

Asadulghani M, Ogura Y, Ooka T, Itoh T, Sawaguchi A, Iguchi A, Nakayama K, Hayashi T.
The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants.
PLoS Pathog. 5(5):e1000408, 2009.

Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P, Kenny B, Quail MA, Thurston S, Dougan G, Hayashi T, Parkhill J, Frankel G.
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69.
J Bacteriol. 191(1):347-354, 2009.

Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T, Itoh K, Hattori M.
Complete Genome Sequence and Comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.
DNA Res. 15(6):375-386, 2008.

Ogura Y, Abe H, Katsura K, Kurokawa K, Asadulghani M, Iguchi A, Ooka T, Nakayama K, Yamashita A, Hattori M, Tobe T, Hayashi T.
Systematic identification and sequence analysis of the genomic islands of the enteropathogenic Escherichia coli strain B171-8 by the combined use of Whole Genome PCR Scanning and fosmid mapping.
J Bacteriol. 190(21):6948-6960, 2008.

Nakayama K, Yamashita A, Kurokawa K, Morimoto T, Ogawa M, Fukuhara M, Urakami H, Ohnishi M, Uchiyama I, Ogura Y, Ooka T, Oshima K, Tamura A, Hattori M, Hayashi T.
The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution.
DNA Res. 15(4):185-199, 2008.

Abe H, Miyahara A, Oshima T, Tashiro K, Ogura Y, Kuhara S, Ogasawara N, Hayashi T, Tobe T.
Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli.
DNA Res. 15(1):25-38, 2008.

Iguchi A, Ooka T, Ogura Y, Asadulghani, Nakayama K, Frankel G, Hayashi T.
Genomic comparison of the O-antigen biosynthesis gene clusters of Escherichia coli O55 strains belonging to three distinct lineages.
Microbiology. 154(Pt 2):559-570, 2008.

Loukiadis E, Nobe R, Herold S, Tramuta C, Ogura Y, Ooka T, Morabito S, Kerouredan M, Brugere H, Schmidt H, Hayashi T, Oswald E.
Distribution, functional expression, and genetic organization of Cif, a phage-encoded type III-secreted effector from enteropathogenic and enterohemorrhagic Escherichia coli.
J Bacteriol. 190(1):275-285, 2008.

Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M.
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.
DNA Res. 14(4):169-181, 2007.

Ishikawa S, Ogura Y, Yoshimura M, Okumura H, Cho E, Kawai Y, Kurokawa K, Oshima T, Ogasawara N.
Distribution of stable DnaA-binding sites on the Bacillus Subtilis genome detected using a modified ChIP-chip method.
DNA Res. 14(4):155-168, 2007.

Ogura Y, Ooka T, Asadulghani, Terajima J, Nougayrede JP, Kurokawa K, Tashiro K, Tobe T, Nakayama K, Kuhara S, Oswald E, Watanabe H, Hayashi T.
Extensive genomic diversity and selective conservation of virulence-determinants in enterohaemorrhagic Escherichia coli strains of O157 and non-O157 serotypes.
Genome Biol. 8(7):R138, 2007.

Whale A, Hernandes RT, Ooka T, Krause G, Schuller S, Garmendia J, Crowther L, Vieira MA, Ogura Y, Phillips, AD, Beutin L, Gomes TA, Hayashi T, and Frankel G.
TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.
Microbiology. 153(Pt 6):1743-1755, 2007.

Ooka T, Vieira MA, Ogura Y, Beutin L, Ragione RL, van Diemen PM, Stevens MP, Aktan I, Cawthraw S, Best A, Hernandes RT, Krause G, Gomes TAT, Hayashi T, and Frankel G.
Characterization of tccP2 carried by atypical enteropathogenic Escherichia coli.
FEMS Microbiol Lett. 271(1):126-135, 2007.

Ogura Y, Ooka T, Whale A, Garmendia J, Beutin L, Tennant S, Krause G, Morabito S, Chinen I, Tobe T, Abe H, Tozzoli R, Caprioli A, Rivas M, Browne RR, Hayashi T, and Frankel G.
TccP2 of O157:H7 and Non-O157 Enterohemorrhagic Escherichia coli (EHEC): Challenging the Dogma of EHEC-Induced Actin Polymerization.
Infect Immun. 75(2):604-612, 2007.

Ogura Y, Kurokawa K, Ooka T, Tashiro K, Tobe T, Ohnishi M, Nakayama K, Morimoto T, Terajima J, Watanabe H, Kuhara S, and Hayashi T.
Complexity of the genomic diversity of enterohaemorrhagic Escherichia coli O157 revealed by the combinational use of the O157 Sakai oligo DNA microarray and the Whole Genome PCR Scanning.
DNA Res. 13(1):3-14, 2006.

Nakanishi N, Abe H, Ogura Y, Hayashi T, Tashiro K, Kuhara S, Sugimoto N, Tobe T.
ppGpp with DksA controls gene expression in the LEE pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes.
Mol Microbiol. 61(1):194-205, 2006.

Hayashi M, Ogura Y, Harry EJ, Ogasawara N, Moriya S.
Bacillus Subtilis YabA is involved in determining the timing and synchrony of replication initiation.
FEMS Microbiol Lett. 247(1):73-79, 2005.

Ogura Y, Ogasawara N, Harry EJ, Moriya S.
Increasing the ratio of Soj to Spo0J promotes replication initiation in Bacillus subtilis.
J Bacteriol. 185(21):6316-6324, 2003.

Ohnishi M, Terajima J, Kurokawa K, Nakayama K, Murata T, Tamura K, Ogura Y, Watanabe H, Hayashi T.
Genomic diversity of Escherichia coli O157 revealed by whole genome PCR Scanning.
Proc Natl Acad Sci U S A. 99(26):17043-17048, 2002.

Ogura Y, Imai Y, Ogasawara N, Moriya S.
Autoregulation of the dnaA-dnaN operon and effects of DnaA protein levels on replication initiation in Bacillus subtilis.
J Bacteriol. 183(13):3833-3841, 2001.



総説
小椋義俊
「病原菌ゲノムの多様性解析 -新興病原体出現の新知見」
実験医学 39(3): 171-177 2021

小椋義俊、中島遥子、林哲也
「現在のメタゲノム解析からは見えてこない細菌ゲノムの菌株間多様性とそのメカニズム-大腸菌を例として」 
生体の科学 68 (2):102-107, 2017.

小椋義俊
「菌種・サブタイプ横断的な大規模比較ゲノム解析-進化,多様化,パンゲノム-」
  化学療法の領域 33 (7)1381-1391. 2017.

小椋義俊、林哲也
「腸管出血性大腸菌における病原性のゲノム進化」
感染・炎症・免疫 42:182-195, 2012.

小椋義俊、大岡唯祐、林哲也
「腸管出血性大腸菌O111の進化と病原性」
神経内科 76(2):155-163, 2012.

小椋義俊
「腸管出血性大腸菌と腸管病原性大腸菌のゲノム解読と病原性進化メカニズムの解明」
日本細菌学雑誌 66(2):175-186, 2011.

小椋義俊、大岡唯祐、林哲也
「ゲノム解析から見えてきた腸管出血性大腸菌の毒素及び病原因子の新知見」
化学療法の領域 25(5):767-777, 2009.

大岡唯祐、小椋義俊、林哲也
「大腸菌O157のゲノム研究とその応用」
臨床微生物迅速診断研究会誌(JARMAM) 16(2):179-181, 2005.

大岡唯祐、小椋義俊、林哲也
「腸管出血性大腸菌のゲノムの特徴」
化学療法の領域 20(9):1328-1333, 2004.

小椋義俊、林哲也
「腸管出血性大腸菌のゲノム解析」
ゲノム医学 4(2):219-224, 2004.



著書
小椋義俊, 林哲也
「細菌ゲノム」新規ゲノム配列決定編
細胞工学別冊 次世代シークエンサー 目的別アドバンストメソッド, 菅野純夫, 鈴木穣 監修, 秀潤社, pp120-129, 2012, 全252頁.

小椋義俊, 林哲也
「病原菌と常在菌の境界」(第6章腸内共生系の破綻と疾病)
腸内共生系のバイオサイエンス, 財団法人日本ビフィズス菌センター編, 丸善 出版, 東京, pp207-219, 2011, 全292頁

Hayashi T., Ooka T., Ogura Y. and Asadulghani
「Genomic view on the evolution of enterohemorrhagic Escherichia coli.」
Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press. Washington, D.C. 全622頁, 2007.