氏名

ハットリ マサヒラ

服部 正平

職名

教授(任期付)

所属理工学術院

(大学院先進理工学研究科)

連絡先

URL等

研究者番号
70175537

本属以外の学内所属

学内研究所等

規範科学総合研究所

研究所員 2015年-2015年

理工学術院総合研究所(理工学研究所)

兼任研究員 2018年-

論文

A Histone Methyltransferase ESET Is Critical for T Cell Development

Takikita, Shoichi;Muro, Ryunosuke;Takai, Toshiyuki;Otsubo, Takeshi;Kawamura, Yuki I.;Dohi, Taeko;Oda, Hiroyo;Kitajima, Masayuki;Oshima, Kenshiro;Hattori, Masahira;Endo, Takaho A.;Toyoda, Tetsuro;Weis, John;Shinkai, Yoichi;Suzuki, Harumi

JOURNAL OF IMMUNOLOGY197(6)p.2269 - 22792016年-2016年

DOIWoS

詳細

ISSN:0022-1767

Fecal microbiota transplantation for patients with steroid-resistant acute graft-versus-host disease of the gut

Kakihana, Kazuhiko;Fujioka, Yuki;Suda, Wataru;Najima, Yuho;Kuwata, Go;Sasajima, Satoshi;Mimura, Iyo;Morita, Hidetoshi;Sugiyama, Daisuke;Nishikawa, Hiroyoshi;Hattori, Masahira;Hino, Yutaro;Ikegawa, Shuntaro;Yamamoto, Keita;Toya, Takashi;Doki, Noriko;Koizumi, Koichi;Honda, Kenya;Ohashi, Kazuteru

BLOOD128(16)p.2083 - 20882016年-2016年

DOIWoS

詳細

ISSN:0006-4971

Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

Kikuchi, Mami;Ueno, Mariko;Itoh, Yoshiharu;Suda, Wataru;Hattori, Masahira

NEPHRON135(1)p.51 - 602017年-2017年

DOIWoS

詳細

ISSN:1660-8151

好熱性細菌BP-863の経口給与が犬の腸内細菌叢と脂肪蓄積に与える影響について

枡岡 久志;宮本 浩邦;須田 瓦;宇田川 元章;井藤 俊行;岩田 菖子;大野 博司;服部 正平;児玉 浩明

ペット栄養学会誌19(0)p.suppl_30 - suppl_312016年-2016年

CiNii

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概要:近年、プロバイオティクスやプレバイオティクスへの関心が高まっているが、ペッ ト業界では犬の腸内細菌叢や代謝に与える影響についての研究は限られている。本研究では、畜産分野で利用研究が進んでいる Bacillus thermoamylovoraus の近縁種である好熱性細菌 Bacillus hisashii N11T(国際寄託番号BP-863)の経口投与試験を実施し、血中成分、内臓脂肪の変化、 並びに腸内細菌叢の生理的な変化について検討した。
 腸内細菌叢の解析の結果、投与後に Firmicutes門の構成比が減少し、Bacteroides門の構成比が増加していた。また、Firmicutes門の中でも特に Clostridium属Cluster XIに属する種が減少していた。この時、CT画像の解析の結果、脂肪領域の減少が確認され、併せて血中の脂肪代謝に関連する分子の変化が確認された。

好熱性細菌 Bacillus hisashii を経口給与した犬の糞中の代謝物の網羅的解析

枡岡 久志;井藤 俊行;宮本 浩邦;中西 裕美子;須田 亙;宇田川 元章;松浦 真紀子;服部 正平;大野 博司;児玉 浩明

ペット栄養学会誌20(0)p.suppl_39 - suppl_402017年-2017年

CiNii

詳細

概要:昨年度、畜産分野で利用研究が進んでいる Bacillus thermoamylovoraus の近縁種である好熱性細菌 Bacillus hisashii N11T(国際寄託番号BP-863)の経口投与試験を実施し、血中成分、内臓脂肪の変化、並びに腸内細菌叢の生理的な変化について報告した。腸内細菌叢の解析の結果、投与後に Firmicutes 門の構成比が減少し、Bacteroides 門の構成比が増加していた。また、Firmicutes 門の中でも特に Clostridium 属Cluster XIに属する種が減少していた。この時、CT画像の解析の結果、脂肪領域の減少が確認され、併せて血中の脂肪代謝に関連する分子の変化が確認された。本年度は、これらの影響をもたらす要因を探索することを目的として糞中の代謝物の挙動を解析した。

Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3709, Which Harbors a Phycoerythrin-Rich Phycobilisome.

Hirose Yuu;Katayama Mitsunori;Ohtsubo Yoshiyuki;Misawa Naomi;Iioka Erica;Suda Wataru;Oshima Kenshiro;Hanaoka Mitsumasa;Tanaka Kan;Eki Toshihiko;Ikeuchi Masahiko;Kikuchi Yo;Ishida Makoto;Hattori Masahira

Genome announcements3(2)2015年-2015年

PubMedDOI

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概要::The cyanobacterium Geminocystis sp. strain NIES-3709 accumulates a larger amount of phycoerythrin than the related NIES-3708 strain does. Here, we determined the complete genome sequence of the NIES-3709 strain. Our genome data suggest that the different copy number of rod linker genes for phycoerythrin leads to the different phycoerythrin contents between the two strains.

Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3708, Which Performs Type II Complementary Chromatic Acclimation.

Hirose Yuu;Katayama Mitsunori;Ohtsubo Yoshiyuki;Misawa Naomi;Iioka Erica;Suda Wataru;Oshima Kenshiro;Hanaoka Mitsumasa;Tanaka Kan;Eki Toshihiko;Ikeuchi Masahiko;Kikuchi Yo;Ishida Makoto;Hattori Masahira

Genome announcements3(3)2015年-2015年

PubMedDOI

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概要::To explore the variation of the light-regulated genes during complementary chromatic acclimation (CCA), we determined the complete genome sequence of the cyanobacterium Geminocystis sp. strain NIES-3708. Within the light-regulated operon for CCA, we found genes for phycoerythrin but not phycocyanin, suggesting that this cyanobacterium modulates phycoerythrin composition only (type II CCA).

Interferon-γ constrains cytokine production of group 2 innate lymphoid cells

Kudo, Fujimi; Ikutani, Masashi; Seki, Yoichi; Otsubo, Takeshi; Kawamura, Yuki I.; Dohi, Taeko; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Nakae, Susumu; Nakae, Susumu; Takatsu, Kiyoshi; Takatsu, Kiyoshi; Takaki, Satoshi

Immunology147(1)p.21 - 292016年01月-2016年01月 

DOIScopus

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ISSN:00192805

概要:© 2016 John Wiley & Sons Ltd.Group 2 innate lymphoid cells (ILC2s) produce a significant amount of interleukin-5 (IL-5), which supports eosinophil responses in various tissues; they also produce IL-13, which induces mucus production and contributes to tissue repair or fibrosis. The ILC2s are activated by alarmins, such as IL-33 released from epithelia, macrophages and natural killer T (NKT) cells in response to infection and allergen exposure, leading to epithelial injury. We examined gene expression in lung ILC2s and found that ILC2s expressed Ifngr1, the receptor for interferon-γ (IFN-γ). Interferon-γ severely inhibited IL-5 and IL-13 production by lung and kidney ILC2s. To evaluate the effects in vivo, we used α-galactosylceramide (α-GalCer) to induce NKT cells to produce IL-33 and IFN-γ. Intraperitoneal injection of α-GalCer in mice induced NKT cell activation resulting in IL-5 and IL-13 production by ILC2s. Administration of anti-IFN-γ together with α-GalCer significantly enhanced the production of IL-5 and IL-13 by ILC2s in lung and kidney. Conversely, cytokine production from ILC2s was markedly suppressed after injection of exogenous IL-33 in Il33-/- mice pre-treated with α-GalCer. Hence, IFN-γ induced or already present in tissues can impact downstream pleiotropic functions mediated by ILC2s, such as inflammation and tissue repair.

Polymicrobial Amniotic Fluid Infection with Mycoplasma/Ureaplasma and Other Bacteria Induces Severe Intra-Amniotic Inflammation Associated with Poor Perinatal Prognosis in Preterm Labor

Yoneda, Noriko; Yoneda, Satoshi; Niimi, Hideki; Ueno, Tomohiro; Hayashi, Shirou; Ito, Mika; Shiozaki, Arihiro; Urushiyama, Daichi; Urushiyama, Daichi; Hata, Kenichiro; Suda, Wataru; Hattori, Masahira; Hattori, Masahira; Kigawa, Mika; Kitajima, Isao; Saito, Shigeru

American Journal of Reproductive Immunology75(2)p.112 - 1252016年01月-2016年01月 

DOIScopus

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ISSN:10467408

概要:© 2016 John Wiley & Sons A/S.Problem: To study the relationship between perinatal prognosis in cases of preterm labor (PTL) and polymicrobial infection in amniotic fluid (AF) and intra-amniotic (IA) inflammation using a highly sensitive and reliable PCR-based method. Method of Study: To detect prokaryotes using a nested PCR-based method, eukaryote-made thermostable DNA polymerase without bacterial DNA contamination was used in combination with bacterial universal primers. We collected AF aseptically from 118 PTL cases and 50 term subjects. Results: The prevalence of microorganisms was 33% (39/118) by PCR and only 7.6% (9/118) by culture. PTL caused by a combination of positive Mycoplasma/Ureaplasma and other bacteria had significantly higher AF IL-8 levels and a significantly shorter amniocentesis-to-delivery interval. Conclusions: Our newly established PCR method is useful for detecting IA microorganisms. Polymicrobial infection with Mycoplasma/Ureaplasma and other bacteria induces severe IA inflammation associated with poor perinatal prognosis in PTL.

First microbiota assessments of children's paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis

Sawabe, Toko; Suda, Wataru; Suda, Wataru; Ohshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Sawabe, Tomoo

Journal of Infection and Public Health9(3)p.362 - 3652016年05月-2016年05月 

DOIScopus

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ISSN:18760341

概要:© 2015 King Saud Bin Abdulaziz University for Health Sciences.Insufficient chloric sterilization of children's paddling pool waters increases the risk of diarrheal illness. Therefore, we investigated the microbiota changes after children use pools. First, we applied 16S rRNA gene-based metagenome analysis to understand the dynamics of microbiota in pool water, especially with respect to the bio-contamination by potential pathogens. Proteobacteria were major taxa detected in every pool water sample after children spent time in the pool. In more detail, Gammaproteobacteria comprised the dominant class, which was followed by Betaproteobacteria. Five phyla, Bacteroidetes, Firmicutes, Actinobacteria and Deinococcus-Thermus phyla were minor groups. The pool water microbiota are likely to be a consortium of intestinal and skin microbiota from humans. Interestingly, the ratio of Gammaproteobacteria and Betaproteobacteria differed according to the age of the children who used the pool, which means the pool water was additionally contaminated by soil microbiota as a result of the children's behavior. Furthermore, potential pathogens, such as Campylobacter spp., Comamonas testosteroni and Burkholderia pseudomallei, were also found. Considering the standard plate counts, the abundances of these human pathogens are unlikely to be a sufficiently infectious dose. We suggest the importance of sanitary measures in paddling pool waters to reduce bio-contamination from both humans and the environment.

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps

Sawabe, Tomoo; Yamazaki, Yohei; Meirelles, Pedro Milet; Mino, Sayaka; Suda, Wataru; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Thompson, Fabiano L.; Sakai, Yuichi; Sawabe, Toko

Scientific Reports62016年02月-2016年02月 

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概要:Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan

Gao, Feng; Al-saari, Nurhidayu; Rohul Amin, A. K M; Sato, Kazumichi; Mino, Sayaka; Suda, Wataru; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Ohkuma, Moriya; Hargreaves, Paulo Iiboshi; Meirelles, Pedro Milet; Thompson, Fabiano L.; Thompson, Cristiane; Gomez-Gil, Bruno; Sawabe, Toko; Sawabe, Tomoo

Systematic and Applied Microbiology39(5)p.330 - 3352016年07月-2016年07月 

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ISSN:07232020

概要:© 2016 Elsevier GmbHFive novel strains showing non-motile, alginolytic, halophilic and fermentative features were isolated from seawater samples off Okinawa in coral reef areas. These strains were characterized by an advanced polyphasic taxonomy including genome based taxonomy using multilocus sequence analysis (MLSA) and in silico DNA–DNA similarity (in silico DDH). Phylogenetic analyses on the basis of 16S rRNA gene sequences revealed that the isolates could be assigned to the genus Vibrio, however they were not allocated into any distinct cluster with known Vibrionaceae species. MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the vibrios formed an outskirt branch of Halioticoli clade. The experimental DNA–DNA hybridization data revealed that the five strains were in the range of being defined as conspecific but separate from nine Halioticoli clade species. The G + C contents of the Vibrio ishigakensis strains were 47.3–49.1 mol%. Both Amino Acid Identity and Average Nucleotide Identity of the strain C1T against Vibrio ezurae HDS1-1T, Vibrio gallicus HT2-1T, Vibrio halioticoli IAM 14596T, Vibrio neonatus HDD3-1T and Vibrio superstes G3-29T showed less than 95% similarity. The genome-based taxonomic approach by means of in silico DDH values also supports the V. ishigakensis strains being distinct from the other known Halioticoli clade species. Sixteen traits (growth temperature range, DNase and lipase production, indole production, and assimilation of 10 carbon compounds) distinguished these strains from Halioticoli clade species. The names V. ishigakensis sp. nov. is proposed for the species of Halioticoli clade, with C1T as the type strain (JCM 19231T = LMG 28703T).

A histone methyltransferase ESET is critical for T cell development

Takikita, Shoichi; Takikita, Shoichi; Muro, Ryunosuke; Takai, Toshiyuki; Otsubo, Takeshi; Kawamura, Yuki I.; Dohi, Taeko; Oda, Hiroyo; Kitajima, Masayuki; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Endo, Takaho A.; Toyoda, Tetsuro; Weis, John; Weis, John; Weis, John; Shinkai, Yoichi; Suzuki, Harumi

Journal of Immunology197(6)p.2269 - 22792016年09月-2016年09月 

DOIScopus

詳細

ISSN:00221767

概要:Copyright © 2016 by The American Association of Immunologists, Inc.ESET/SETDB1, one of the major histone methyltransferases, catalyzes histone 3 lysine 9 (H3K9) trimethylation. ESET is critical for suppressing expression of retroviral elements in embryonic stem cells; however, its role in the immune system is not known.We found that thymocyte-specific deletion of ESET caused impaired T cell development, with CD8 lineage cells being most severely affected. Increased apoptosis of CD8 single-positive cells was observed, and TCR-induced ERK activation was severely inhibited in ESET2/2 thymocytes. Genome-wide comprehensive analysis of mRNA expression and H3K9 trimethylation revealed that ESET regulates expression of numerous genes in thymocytes. Among them, FcgRIIB, whose signaling can inhibit ERK activation, was strongly and ectopically expressed in ESET2/2 thymocytes. Indeed, genetic depletion of FcgRIIB in ESET2/2 thymocytes rescued impaired ERK activation and partially restored defective positive selection in ESET2/2 mice. Therefore, impaired T cell development in ESET2/2 mice is partly due to the aberrant expression of FcgRIIB. Collectively, to our knowledge, we identify ESET as the first trimethylated H3K9 histone methyltransferase playing a crucial role in T cell development.

Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

Kikuchi, Mami; Ueno, Mariko; Itoh, Yoshiharu; Suda, Wataru; Suda, Wataru; Hattori, Masahira; Hattori, Masahira

Nephron135(1)p.51 - 602017年01月-2017年01月 

PubMedDOIScopus

詳細

ISSN:16608151

概要:© 2016 S. Karger AG, Basel.Background: 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. Methods: We analyzed UT production and the composition of gut microbiota in CKD rats and cecectomized rats. AST-120, a spherical carbon adsorbent, was administrated to evaluate how the precursors of UT affect gut microbiota. Serum and urine levels of UTs were quantified by liquid chromatography/electrospray ionization-tandem mass spectrometry. Gut microbiota were analyzed using 454-pyrosequencing of the 16S rRNA gene. Operational taxonomic unit (OTU) clustering and UniFrac analysis were performed to compare gut microbiota among the groups. Results: Serum and urine levels of indoxyl sulfate and phenyl sulfate were higher in CKD versus control rats (p < 0.05). AST-120 administration decreased UT production (p < 0.01) and changed overall gut microbiota composition in CKD rats. UT urinary excretion and gut microbiota composition changed in cecectomized rats, with the relative abundance of Clostridia- and Bacteroidia-affiliated species being significantly reduced (p < 0.01). We identified candidate indole- and phenol-producing intestinal microbiota, 3 Clostridia, and 2 Bacteroidia. These OTUs have a tryptophanase/tyrosine phenol-lyase gene in the closest sequenced genome out of the OTUs declined following cecectomy. Conclusion: Our data suggest that UT production is correlated with a subset of indigenous gut microbiota. However, UT may be induced by other non-symbiotic microbiota that are influenced by factors other than microbiota populations. The relationship between specific microbiota and UTs in patients requires further clarification.

Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn’s disease in the Ryukyu Islands

Nakagome, Shigeki; Nakagome, Shigeki; Nakagome, Shigeki; Nakagome, Shigeki; Chinen, Hiroshi; Iraha, Atsushi; Hokama, Akira; Takeyama, Yasuaki; Sakisaka, Shotaro; Matsui, Toshiyuki; Kidd, Judith R.; Kidd, Kenneth K.; Said, Heba S.; Said, Heba S.; Said, Heba S.; Suda, Wataru; Morita, Hidetoshi; Morita, Hidetoshi; Hattori, Masahira; Hattori, Masahira; Hanihara, Tsunehiko; Kimura, Ryosuke; Ishida, Hajime; Fujita, Jiro; Kinjo, Fukunori; Mano, Shuhei; Mano, Shuhei; Mano, Shuhei; Oota, Hiroki

Human Genetics136(4)p.387 - 3972017年04月-2017年04月 

PubMedDOIScopus

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ISSN:03406717

概要:© 2017, Springer-Verlag Berlin Heidelberg. Crohn’s disease (CD) involves chronic inflammation in the gastrointestinal tract due to dysregulation of the host immune response to the gut microbiome. Even though the host-microbiome interactions are likely contributors to the development of CD, a few studies have detected genetic variants that change bacterial compositions and increase CD risk. We focus on one of the well-replicated susceptible genes, tumor necrosis factor superfamily member 15 (TNFSF15), and apply statistical analyses for personal profiles of genotypes and salivary microbiota collected from CD cases and controls in the Ryukyu Islands, southernmost islands of the Japanese archipelago. Our association test confirmed the susceptibility of TNFSF15 in the Ryukyu Islands. We found that the recessive model was supported to fit the observed genotype frequency of risk alleles slightly better than the additive model, defining the genetic effect on CD if a pair of the chromosomes in an individual consists of all risk alleles. The combined analysis of haplotypes and salivary microbiome from a small set of samples showed a significant association of the genetic effect with the increase of Prevotella, which led to a significant increase of CD risk. However, the genetic effect on CD disappeared if the abundance of Prevotella was low, suggesting the genetic contribution to CD is conditionally ind ependent given a fixed amount of Prevotella. Although our statistical power is limited due to the small sample size, these results support an idea that the genetic susceptibility of TNFSF15 to CD may be confounded, in part, by the increase of Prevotella.

Single fecal microbiota transplantation failed to change intestinal microbiota and had limited effectiveness against ulcerative colitis in Japanese patients

Mizuno, Shinta; Nanki, Kosaku; Matsuoka, Katsuyoshi; Saigusa, Keiichiro; Ono, Keiko; Arai, Mari; Sugimoto, Shinya; Kiyohara, Hiroki; Nakashima, Moeko; Takeshita, Kozue; Takeshita, Kozue; Naganuma, Makoto; Suda, Wataru; Suda, Wataru; Hattori, Masahira; Hattori, Masahira; Kanai, Takanori

Intestinal Research15(1)p.68 - 742017年01月-2017年01月 

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ISSN:15989100

概要:© 2017. Korean Association for the Study of Intestinal Diseases. All rights reserved.Background/Aims: Recent developments in analytical techniques including next-generation sequencing have clarified the correlation between intestinal microbiota and inflammatory bowel disease. Fecal microbiota transplantation (FMT) for patients with ulcerative colitis (UC) is proposed as a potential approach to resolving their dysbiosis; however, its safety and efficacy have not been confirmed. This single-arm, open-label, non-randomized study aimed to evaluate the safety and efficacy of FMT for Japanese patients with UC as the first registered clinical trial in Japan. Methods: We enrolled 10 patients with active UC despite medical therapy. The donors were the patients' relatives and were carefully screened for infectious diseases. Fecal material was administered via colonoscopy, and the primary endpoint was the presence or absence of serious adverse events related to FMT. The secondary endpoint was a change in partial Mayo score at 12 weeks post-FMT. Scores ≤2 were considered a clinical response. Fecal samples were collected to follow changes in gut microbiota, while extracted complementary DNA were analyzed by a next-generation sequencer. We obtained written informed consent from all patients and donors. This study was approved by our Institutional Review Board and is registered in the University hospital Medical Information Network (UMIN) Clinical Trials Registry (UMIN 000012814). Results: Five patients with moderate disease and five with severe disease were enrolled. No severe adverse effects were observed. One patient achieved clinical response; however, none of the patients' microbiota diversity recovered to the donor levels. Conclusions: The use of single FMT for UC was safe; however, we failed to show its clinical efficacy and potential to change the intestinal microbiota.

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation

Aoki, Ryo; Aoki, Ryo; Kamikado, Kohei; Suda, Wataru; Suda, Wataru; Takii, Hiroshi; Mikami, Yumiko; Suganuma, Natsuki; Hattori, Masahira; Hattori, Masahira; Koga, Yasuhiro

Scientific Reports72017年03月-2017年03月 

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概要:© 2017 The Author(s). The gut microbiota is an important contributor to the worldwide prevalence of metabolic syndrome (MS), which includes obesity and diabetes. The anti-MS effects exerted by Bifidobacterium animalis ssp. lactis GCL2505 (BlaG), a highly proliferative Bifidobacterium strain in the gut, and B. longum ssp. longum JCM1217 T (BloJ) were comparatively examined. BlaG treatment reduced visceral fat accumulation and improved glucose tolerance, whereas BloJ had no effect on these parameters. Gut microbial analysis revealed that BlaG exerted stronger effects on the overall bacterial structure of the gut microbiota than BloJ, including enrichment of the genus Bifidobacterium. The levels of acetate and glucagon-like peptide-1 were increased by BlaG treatment in both the gut and plasma, but not by BloJ treatment. Correlation analysis suggested that the elevation of gut acetate levels by BlaG treatment plays a pivotal role in the BlaG-induced anti-MS effects. These findings indicated that BlaG, a highly viable and proliferative probiotic, improves metabolic disorders by modulating gut microbiota, which results in the elevation of SCFAs, especially acetate.

Draft genome sequencing of the highly halotolerant and allopolyploid yeast Zygosaccharomyces rouxii NBRC 1876

Sato, Atsushi; Sato, Atsushi; Matsushima, Kenichiro; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Koyama, Yasuji; Koyama, Yasuji

Genome Announcements5(7)2017年01月-2017年01月 

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概要:© 2017 Sato et al.The highly halotolerant and allopolyploid yeast Zygosaccharomyces rouxii is industrially used for the food production in high concentrations of salt, such as brewing soy sauce and miso paste. Here, we report the draft genome sequence of Z. rouxii NBRC 1876 isolated from miso paste.

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure

Kamo, Takehiro; Akazawa, Hiroshi; Suda, Wataru; Suda, Wataru; Saga-Kamo, Akiko; Shimizu, Yu; Yagi, Hiroki; Liu, Qing; Nomura, Seitaro; Naito, Atsuhiko T.; Takeda, Norifumi; Harada, Mutsuo; Toko, Haruhiro; Kumagai, Hidetoshi; Kumagai, Hidetoshi; Ikeda, Yuichi; Takimoto, Eiki; Suzuki, Jun Ichi; Honda, Kenya; Honda, Kenya; Morita, Hidetoshi; Hattori, Masahira; Hattori, Masahira; Komuro, Issei

PLoS ONE12(3)2017年03月-2017年03月 

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概要:Copyright © 2017 Kamo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Emerging evidence has suggested a potential impact of gut microbiota on the pathophysiology of heart failure (HF). However, it is still unknown whether HF is associated with dysbiosis in gut microbiota. We investigated the composition of gut microbiota in patients with HF to elucidate whether gut microbial dysbiosis is associated with HF. We performed 16S ribosomal RNA gene sequencing of fecal samples obtained from 12 HF patients and 12 agematched healthy control (HC) subjects, and analyzed the differences in gut microbiota. We further compared the composition of gut microbiota of 12 HF patients younger than 60 years of age with that of 10 HF patients 60 years of age or older. The composition of gut microbial communities of HF patients was distinct from that of HC subjects in both unweighted and weighted UniFrac analyses. Eubacterium rectale and Dorea longicatena were less abundant in the gut microbiota of HF patients than in that of HC subjects. Compared to younger HF patients, older HF patients had diminished proportions of Bacteroidetes and larger quantities of Proteobacteria. The genus Faecalibacterium was depleted, while Lactobacillus was enriched in the gut microbiota of older HF patients. These results suggest that patients with HF harbor significantly altered gut microbiota, which varies further according to age. New concept of heart-gut axis has a great potential for breakthroughs in the development of novel diagnostic and therapeutic approach for HF.

Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis

Iwasawa, Kentaro; Iwasawa, Kentaro; Suda, Wataru; Suda, Wataru; Tsunoda, Tomoyuki; Oikawa-Kawamoto, Manari; Oikawa-Kawamoto, Manari; Umetsu, Shuichiro; Inui, Ayano; Fujisawa, Tomoo; Morita, Hidetoshi; Sogo, Tsuyoshi; Hattori, Masahira; Hattori, Masahira

Gut66(7)p.1344 - 13462017年07月-2017年07月 

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ISSN:00175749

Bifidobacterium -Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome

Mizuno, Shinta; Masaoka, Tatsuhiro; Naganuma, Makoto; Kishimoto, Taishiro; Kitazawa, Momoko; Kurokawa, Shunya; Nakashima, Moeko; Takeshita, Kozue; Takeshita, Kozue; Suda, Wataru; Suda, Wataru; Mimura, Masaru; Hattori, Masahira; Hattori, Masahira; Kanai, Takanori

Digestion96(1)p.29 - 382017年08月-2017年08月 

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ISSN:00122823

概要:© 2017 The Author(s) Published by S. Karger AG, Basel. Background/Aims: Dysbiosis is associated with various systemic disorders including irritable bowel syndrome (IBS). Fecal microbiota transplantation (FMT) might restore intestinal microbial balance. The study aimed to determine the safety and efficacy of FMT in IBS patients, as well as also positive predictors for FMT. Methods: This was a single-arm, open-label study. Eligible patients were diagnosed based on Rome III Diagnostic Criteria. Fecal materials were administered to the patient via colonoscopy. The primary end point was a change in the Bristol stool form scale at 4 weeks after FMT. Recovery to types 3-4 was considered a clinical response. The secondary end point was a change in intestinal microbiota and psychological status using the Hamilton Rating Scale. Results: Ten patients were enrolled. Six patients achieved a clinical response. The diversity of patients 4 weeks after FMT increased significantly compared with patients before FMT, and that of responding patients was significantly higher than non-responder patients. The abundance of Bifidobacterium in effective donors was significantly higher than in ineffective donors and patients. Psychological status of all patients was significantly improved after FMT. Conclusions: FMT for patients with IBS is safe, and relatively effective. Bifidobacterium-rich fecal donor may be a positive predictor for successful FMT. Key Summary: (1) Dysbiosis is associated with various gastrointestinal disorders including IBS. (2) FMT has potential to restore intestinal microbial balance. (3) We showed that FMT improved stool form and psychological status of IBS patients. (4) Bifidobacterium-rich donor efficiently induced symbiosis in IBS patients.

Circadian oscillations of microbial and functional composition in the human salivary microbiome

Takayasu, Lena; Suda, Wataru; Suda, Wataru; Takanashi, Kageyasu; Iioka, Erica; Kurokawa, Rina; Shindo, Chie; Hattori, Yasue; Yamashita, Naoko; Nishijima, Suguru; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira

DNA Research24(3)p.261 - 2702017年06月-2017年06月 

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ISSN:13402838

概要:© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. The human microbiomes across the body evidently interact with various signals in response to biogeographical physiological conditions. To understand such interactions in detail, we investigated how the salivary microbiome in the oral cavity would be regulated by host-related signals. Here, we show that the microbial abundance and gene participating in keeping the human salivary microbiome exhibit global circadian rhythm. Analysis of the 16S rRNA sequences of salivary microbial samples of six healthy adults collected at 4-h intervals for three days revealed that the microbial genera accounting for 68.4-89.6% of the total abundance were observed to significantly oscillate with the periodicity of -1/424 h. These oscillation patterns showed high variations amongst individuals, and the extent of circadian variations in individuals was generally lower than that of interindividual variations. Of the microbial categories oscillated, those classified by aerobic/anaerobic growth and Gram staining, Firmicutes including Streptococcus and Gemella, and Bacteroidetes including Prevotella showed high association with the circadian oscillation. The circadian oscillation was completely abolished by incubating the saliva in vitro, suggesting that host's physiological changes mostly contributed to the microbial oscillation. Further metagenomic analysis showed that circadian oscillation enriched the functions of environmental responses such as various transporters and two-component regulatory systems in the evening, and those of metabolisms such as the biosynthesis of vitamins and fatty acids in the morning.

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Tanaka, Mami; Endo, Shoko; Kotake, Fumihito; Al-Saari, Nurhidayu; Amin, A. K.M.Rohul; Feng, Gao; Mino, Sayaka; Doi, Hidetaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Suda, Wataru; Suda, Wataru; Hattori, Masahira; Hattori, Masahira; Yumoto, Isao; Sawabe, Toko; Sawabe, Tomoo; Araki, Toshiyoshi

PLoS ONE12(6)2017年06月-2017年06月 

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概要:© 2017 Tanaka et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were nonmotile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation

Doki, Noriko; Suyama, Masahiro; Suyama, Masahiro; Sasajima, Satoshi; Ota, Junko; Igarashi, Aiko; Mimura, Iyo; Morita, Hidetoshi; Fujioka, Yuki; Fujioka, Yuki; Sugiyama, Daisuke; Nishikawa, Hiroyoshi; Nishikawa, Hiroyoshi; Shimazu, Yutaka; Suda, Wataru; Suda, Wataru; Takeshita, Kozue; Atarashi, Koji; Hattori, Masahira; Hattori, Masahira; Sato, Eiichi; Watakabe-Inamoto, Kyoko; Yoshioka, Kosuke; Najima, Yuho; Kobayashi, Takeshi; Kakihana, Kazuhiko; Takahashi, Naoto; Sakamaki, Hisashi; Honda, Kenya; Honda, Kenya; Ohashi, Kazuteru

Annals of Hematology96(9)p.1517 - 15232017年09月-2017年09月 

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ISSN:09395555

概要:© 2017, Springer-Verlag GmbH Germany. Post-transplant microbial diversity in the gastrointestinal tract is closely associated with clinical outcomes following allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about the impact of the fecal microbiota before allo-HSCT. We analyzed fecal samples approximately 2 weeks before conditioning among 107 allo-HSCT recipients between 2013 and 2015. Microbial analysis was performed using 16S rRNA gene sequencing. Operational taxonomic unit-based microbial diversity was estimated by calculating the Shannon index. Patients were classified into three groups based on the diversity index: low ( < 2), intermediate (2, 3), and high ( > 3) diversity (18 (16.8%), 48 (44.9%), and 41 (38.3%) patients, respectively). There were no significant differences in the 20-month overall survival, cumulative incidence of relapse, and non-relapse mortality among three groups. The cumulative incidence of grade II to IV acute graft-versus-host disease (aGVHD) was similar among the three groups (low 55.6%; intermediate 35.4%; high 48.8%, p = 0.339, at day 100). Furthermore, we found no differences in the cumulative incidence of grade II to IV acute gastrointestinal GVHD among the three groups (low 38.9%; intermediate 21.3%; high 24.4%, p = 0.778, at day 100). Regarding the composition of microbiota before allo-HSCT, aGVHD patients showed a significantly higher abundance of phylum Firmicutes (p  <  0.01) and a lower tendency for Bacteroidetes (p = 0.106) than non-aGVHD patients. Maintenance of Bacteroidetes throughout allo-HSCT may be a strategy to prevent aGVHD.

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes

Takayasu, Lena; Suda, Wataru; Suda, Wataru; Watanabe, Eiichiro; Fukuda, Shinji; Fukuda, Shinji; Takanashi, Kageyasu; Ohno, Hiroshi; Takayasu, Misako; Takayasu, Hideki; Hattori, Masahira; Hattori, Masahira

PLoS ONE12(8)2017年08月-2017年08月 

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概要:© 2017 Takayasu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The gut microbiome is highly variable among individuals, largely due to differences in host lifestyle and physiology. However, little is known about the underlying processes or rules that shape the complex microbial community. In this paper, we show that the cumulative relative abundance distribution (CRAD) of microbial species can be approximated by a power law function, and found that the power exponent of CRADs generated from 16S rRNA gene and metagenomic data for normal gut microbiomes of humans and mice was similar consistently with *0.9. A similarly robust power exponent was observed in CRADs of gut microbiomes during dietary interventions and several diseases. However, the power exponent was found to be *0.6 in CRADs from gut microbiomes characterized by lower species richness, such as those of human infants and the small intestine of mice. In addition, the CRAD of gut microbiomes of mice treated with antibiotics differed slightly from those of infants and the small intestines of mice. Based on these observations, in addition to data on the spatial distribution of microbes in the digestive tract, we developed a 3-dimensional mathematical model of microbial proliferation that reproduced the experimentally observed CRAD patterns. Our model indicated that the CRAD may be determined by the ratio of emerging to pre-existing species during non-uniform spatially competitive proliferation, independent of species composition.

Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice

Hayashi, Atsushi; Hayashi, Atsushi; Mikami, Yohei; Miyamoto, Kentaro; Miyamoto, Kentaro; Kamada, Nobuhiko; Sato, Toshiro; Mizuno, Shinta; Naganuma, Makoto; Teratani, Toshiaki; Aoki, Ryo; Aoki, Ryo; Fukuda, Shinji; Suda, Wataru; Suda, Wataru; Hattori, Masahira; Hattori, Masahira; Amagai, Masayuki; Amagai, Masayuki; Ohyama, Manabu; Ohyama, Manabu; Kanai, Takanori; Kanai, Takanori

Cell Reports20(7)p.1513 - 15242017年08月-2017年08月 

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概要:© 2017 Metabolism by the gut microbiota affects host physiology beyond the gastrointestinal tract. Here, we find that antibiotic-induced dysbiosis, in particular, overgrowth of Lactobacillus murinus (L. murinus), impaired gut metabolic function and led to the development of alopecia. While deprivation of dietary biotin per se did not affect skin physiology, its simultaneous treatment with vancomycin resulted in hair loss in specific pathogen-free (SPF) mice. Vancomycin treatment induced the accumulation of L. murinus in the gut, which consumes residual biotin and depletes available biotin in the gut. Consistently, L. murinus induced alopecia when monocolonized in germ-free mice fed a biotin-deficient diet. Supplementation of biotin can reverse established alopecia symptoms in the SPF condition, indicating that L. murinus plays a central role in the induction of hair loss via a biotin-dependent manner. Collectively, our results indicate that luminal metabolic alterations associated with gut dysbiosis and dietary modifications can compromise skin physiology.

Aging-related changes in the diversity of women's skin microbiomes associated with oral bacteria

Shibagaki, Nakako; Suda, Wataru; Suda, Wataru; Clavaud, Cecile; Bastien, Philippe; Takayasu, Lena; Iioka, Erica; Kurokawa, Rina; Yamashita, Naoko; Hattori, Yasue; Shindo, Chie; Breton, Lionel; Hattori, Masahira; Hattori, Masahira

Scientific Reports7(1)2017年12月-2017年12月 

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概要:© 2017 The Author(s). Skin aging is associated with changes in cutaneous physiology including interactions with a skin microbial community. A striking alteration and diversification in the skin microbiome with aging was observed between two different age groups of 37 healthy Japanese women, i.e. younger adults of 21-37 years old and older adults of 60-76 years old, using bacterial 16S rRNA gene sequencing. The analyses revealed that the alpha diversity/species richness was significantly higher in the older than the younger group for the cheek and forehead microbiomes, while the beta diversity in the overall structure significantly differed particularly for the forearm and scalp microbiomes between the two age groups. Taxonomic profiling showed a striking reduction in the relative abundance of the majority skin genus Propionibacterium in the cheek, forearm and forehead microbiomes of the older adults, and identified 38 species including many oral bacteria that significantly differentiated the two age groups with a skin site dependency. Furthermore, we found chronological age-related and unrelated skin clinical parameters that correlate with the observed changes in the skin microbiome diversity. Thus, our data suggested that the diversification of skin microbiomes in adult women was largely affected by chronological and physiological skin aging in association with oral bacteria.

Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita

Yamazaki, Tomokazu; Ichihara, Kensuke; Suzuki, Ryogo; Oshima, Kenshiro; Miyamura, Shinichi; Kuwano, Kazuyoshi; Toyoda, Atsushi; Suzuki, Yutaka; Sugano, Sumio; Hattori, Masahira; Hattori, Masahira; Kawano, Shigeyuki

Scientific Reports7(1)2017年12月-2017年12月 

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概要:© 2017 The Author(s). The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt - and mt + strains identified highly rearranged MT loci of 1.0 and 1.5 Mb in size and containing 46 and 67 genes, respectively, including 23 gametologs. Molecular evolutionary analyses suggested that the MT loci diverged over a prolonged period in the individual mating types after their establishment in an ancestor. A gene encoding an RWP-RK domain-containing protein was found in the mt - MT locus but was not an ortholog of the chlorophycean mating type determination gene MID. Taken together, our results suggest that the genomic structure and its evolutionary history in the U. partita MT locus are similar to those on other UV chromosomes and that the MT locus genes are quite different from those of Chlorophyceae.

Gallbladder-derived surfactant protein D regulates gut commensal bacteria for maintaining intestinal homeostasis

Sarashina-Kida, Hana; Sarashina-Kida, Hana; Negishi, Hideo; Nishio, Junko; Suda, Wataru; Suda, Wataru; Suda, Wataru; Nakajima, Yuki; Yasui-Kato, Mika; Iwaisako, Keiko; Kang, Sujin; Kang, Sujin; Endo, Nobuyasu; Yanai, Hideyuki; Yanai, Hideyuki; Asagiri, Masataka; Asagiri, Masataka; Kida, Hiroshi; Hattori, Masahira; Hattori, Masahira; Hattori, Masahira; Kumanogoh, Atsushi; Taniguchi, Tadatsugu; Taniguchi, Tadatsugu

Proceedings of the National Academy of Sciences of the United States of America114(38)p.10178 - 101832017年09月-2017年09月 

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ISSN:00278424

概要:© 2017, National Academy of Sciences. All rights reserved. The commensal microbiota within the gastrointestinal tract is essential in maintaining homeostasis. Indeed, dysregulation in the repertoire of microbiota can result in the development of intestinal immune–inflammatory diseases. Further, this immune regulation by gut microbiota is important systemically, impacting health and disease of organ systems beyond the local environment of the gut. What has not been explored is how distant organs might in turn shape the microbiota via microbe-targeted molecules. Here, we provide evidence that surfactant protein D (SP-D) synthesized in the gallbladder and delivered into intestinal lumen binds selectively to species of gut commensal bacteria. SP-D–deficient mice manifest intestinal dysbiosis and show a susceptibility to dextran sulfate sodium-induced colitis. Further, fecal transfer from SP-D–deficient mice to wild-type, germ-free mice conveyed colitis susceptibility. Interestingly, colitis caused a notable increase in Sftpd gene expression in the gallbladder, but not in the lung, via the activity of glucocorticoids produced in the liver. These findings describe a unique mechanism of interorgan regulation of intestinal immune homeostasis by SP-D with potential clinical implications such as cholecystectomy.

Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome

Urushiyama, Daichi; Urushiyama, Daichi; Suda, Wataru; Suda, Wataru; Ohnishi, Eriko; Araki, Ryota; Kiyoshima, Chihiro; Kurakazu, Masamitsu; Sanui, Ayako; Yotsumoto, Fusanori; Murata, Masaharu; Nabeshima, Kazuki; Yasunaga, Shin'ichiro; Saito, Shigeru; Nomiyama, Makoto; Hattori, Masahira; Hattori, Masahira; Miyamoto, Shingo; Hata, Kenichiro

Scientific Reports7(1)2017年12月-2017年12月 

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概要:© 2017 The Author(s). Chorioamnionitis (CAM), an inflammation of the foetal membranes due to infection, is associated with preterm birth and poor perinatal prognosis. The present study aimed to determine whether CAM can be diagnosed prior to delivery based on the bacterial composition of the amniotic fluid (AF). AF samples from 79 patients were classified according to placental inflammation: Stage III (n = 32), CAM; Stage II (n = 27), chorionitis; Stage 0-I (n = 20), sub-chorionitis or no neutrophil infiltration; and normal AF in early pregnancy (n = 18). Absolute quantification and sequencing of 16S rDNA showed that in Stage III, the 16S rDNA copy number was significantly higher and the α-diversity index lower than those in the other groups. In principal coordinate analysis, Stage III formed a separate cluster from Stage 0-I, normal AF, and blank. Forty samples were classified as positive for microbiomic CAM (miCAM) defined by the presence of 11 bacterial species that were found to be significantly associated with CAM and some parameters of perinatal prognosis. The diagnostic accuracy for CAM according to miCAM was: sensitivity, approximately 94%, and specificity, 79-87%. Our findings indicate the possibility of predicting CAM prior to delivery based on the AF microbiome profile.

Small genome symbiont underlies cuticle hardness in beetles

Anbutsu, Hisashi; Anbutsu, Hisashi; Moriyama, Minoru; Nikoh, Naruo; Hosokawa, Takahiro; Hosokawa, Takahiro; Futahashi, Ryo; Tanahashi, Masahiko; Meng, Xian Ying; Kuriwada, Takashi; Kuriwada, Takashi; Mori, Naoki; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Fujie, Manabu; Satoh, Noriyuki; Maeda, Taro; Shigenobu, Shuji; Koga, Ryuichi; Fukatsu, Takema; Fukatsu, Takema; Fukatsu, Takema

Proceedings of the National Academy of Sciences of the United States of America114(40)p.E8382 - E83912017年10月-2017年10月 

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ISSN:00278424

概要:© 2017, National Academy of Sciences. All rights reserved. Beetles, representing the majority of the insect species diversity, are characterized by thick and hard cuticle, which plays important roles for their environmental adaptation and underpins their inordinate diversity and prosperity. Here, we report a bacterial endosymbiont extremely specialized for sustaining beetle’s cuticle formation. Many weevils are associated with a γ-proteobacterial endosymbiont lineage Nardonella, whose evolutionary origin is estimated as older than 100 million years, but its functional aspect has been elusive. Sequencing of Nardonella genomes from diverse weevils unveiled drastic size reduction to 0.2 Mb, in which minimal complete gene sets for bacterial replication, transcription, and translation were present but almost all of the other metabolic pathway genes were missing. Notably, the only metabolic pathway retained in the Nardonella genomes was the tyrosine synthesis pathway, identifying tyrosine provisioning as Nardonella’s sole biological role. Weevils are armored with hard cuticle, tyrosine is the principal precursor for cuticle formation, and experimental suppression of Nardonella resulted in emergence of reddish and soft weevils with low tyrosine titer, confirming the importance of Nardonella-mediated tyrosine production for host’s cuticle formation and hardening. Notably, Nardonella’s tyrosine synthesis pathway was incomplete, lacking the final step transaminase gene. RNA sequencing identified host’s aminotransferase genes up-regulated in the bacteriome. RNA interference targeting the aminotransferase genes induced reddish and soft weevils with low tyrosine titer, verifying host’s final step regulation of the tyrosine synthesis pathway. Our finding highlights an impressively intimate and focused aspect of the host–symbiont metabolic integrity via streamlined evolution for a single biological function of ecological relevance.

Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues

Hashimoto, Shinichi; Hashimoto, Shinichi; Tabuchi, Yuta; Yurino, Hideaki; Yurino, Hideaki; Hirohashi, Yoshihiko; Hirohashi, Yoshihiko; Deshimaru, Shungo; Asano, Takuya; Mariya, Tasuku; Oshima, Kenshiro; Takamura, Yuzuru; Ukita, Yoshiaki; Ametani, Akio; Kondo, Naoto; Monma, Norikazu; Takeda, Tadayuki; Misu, Sadahiko; Okayama, Toshitugu; Ikeo, Kazuho; Saito, Tsuyoshi; Kaneko, Shuich; Suzuki, Yutaka; Hattori, Masahira; Hattori, Masahira; Matsushima, Kouji; Torigoe, Toshihiko; Torigoe, Toshihiko

Scientific Reports7(1)2017年12月-2017年12月 

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概要:© 2017 The Author(s). Single cell transcriptome analysis of a cancer tissue can provide objective assessment of subtype population or the activation of each of various microenvironment component cells. In this study, we applied our newly developed technique of single cell analysis to the myometrial infiltration side (M-side) and the endometrial side (E-side) of a human endometrioid adenocarcinoma with squamous differentiation tissues. We also analyzed spherogenic cultures derived from the same tissue to identify putative regulators of stemness in vivo. Cancer cells in the E-side were highly malignant compared with those in the M-side. Many cells on the E-side were positive for spheroid-specific tumorigenesis-related markers including SOX2. In addition, there were higher numbers of epithelial-to-mesenchymal transition (EMT) cells in the E-side compared with the M-side. This study identified a site containing cells with high malignant potential such as EMT and cancer stem-like cells in cancer tissues. Finally, we demonstrate that established endometrioid adenocarcinoma subtype classifiers were variably expressed across individual cells within a tumor. Thus, such intratumoral heterogeneity may be related to prognostic implications.

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

Atarashi, Koji; Atarashi, Koji; Suda, Wataru; Suda, Wataru; Suda, Wataru; Luo, Chengwei; Luo, Chengwei; Kawaguchi, Takaaki; Kawaguchi, Takaaki; Motoo, Iori; Narushima, Seiko; Kiguchi, Yuya; Yasuma, Keiko; Watanabe, Eiichiro; Tanoue, Takeshi; Tanoue, Takeshi; Thaiss, Christoph A.; Sato, Mayuko; Toyooka, Kiminori; Said, Heba S.; Said, Heba S.; Yamagami, Hirokazu; Rice, Scott A.; Gevers, Dirk; Johnson, Ryan C.; Segre, Julia A.; Chen, Kong; Kolls, Jay K.; Elinav, Eran; Morita, Hidetoshi; Xavier, Ramnik J.; Xavier, Ramnik J.; Hattori, Masahira; Hattori, Masahira; Honda, Kenya; Honda, Kenya

Science358(6361)p.359 - 3652017年10月-2017年10月 

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ISSN:00368075

概要:Intestinal colonization by bacteria of oral origin has been correlated with several negative health outcomes, including inflammatory bowel disease. However, a causal role of oral bacteria ectopically colonizing the intestine remains unclear. Using gnotobiotic techniques, we show that strains of Klebsiella spp. isolated from the salivary microbiota are strong inducers of T helper 1 (TH1) cells when they colonize in the gut. These Klebsiella strains are resistant to multiple antibiotics, tend to colonize when the intestinal microbiota is dysbiotic, and elicit a severe gut inflammation in the context of a genetically susceptible host. Our findings suggest that the oral cavity may serve as a reservoir for potential intestinal pathobionts that can exacerbate intestinal disease.

Towards standards for human fecal sample processing in metagenomic studies

Costea, Paul I.; Zeller, Georg; Sunagawa, Shinichi; Sunagawa, Shinichi; Pelletier, Eric; Pelletier, Eric; Pelletier, Eric; Alberti, Adriana; Levenez, Florence; Tramontano, Melanie; Driessen, Marja; Hercog, Rajna; Jung, Ferris Elias; Kultima, Jens Roat; Hayward, Matthew R.; Coelho, Luis Pedro; Allen-Vercoe, Emma; Bertrand, Laurie; Blaut, Michael; Brown, Jillian R.M.; Carton, Thomas; Cools-Portier, Stéphanie; Daigneault, Michelle; Derrien, Muriel; Druesne, Anne; De Vos, Willem M.; De Vos, Willem M.; Finlay, B. Brett; Flint, Harry J.; Guarner, Francisco; Hattori, Masahira; Hattori, Masahira; Heilig, Hans; Luna, Ruth Ann; Van Hylckama Vlieg, Johan; Junick, Jana; Klymiuk, Ingeborg; Langella, Philippe; Le Chatelier, Emmanuelle; Mai, Volker; Manichanh, Chaysavanh; Martin, Jennifer C.; Mery, Clémentine; Morita, Hidetoshi; O'toole, Paul W.; Orvain, Céline; Patil, Kiran Raosaheb; Penders, John; Persson, Søren; Pons, Nicolas; Popova, Milena; Salonen, Anne; Saulnier, Delphine; Scott, Karen P.; Singh, Bhagirath; Slezak, Kathleen; Veiga, Patrick; Versalovic, James; Zhao, Liping; Zoetendal, Erwin G.; Ehrlich, S. Dusko; Ehrlich, S. Dusko; Dore, Joel; Bork, Peer; Bork, Peer; Bork, Peer; Bork, Peer

Nature Biotechnology35(11)p.1069 - 10762017年11月-2017年11月 

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ISSN:10870156

概要:Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.

Corrigendum to “Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan” [Syst. Appl. Microbiol. 39 (5) (2016) 330–335](S0723202016300030)(10.1016/j.syapm.2016.04.002)

Gao, Feng; Al-saari, Nurhidayu; Rohul Amin, A. K.M.; Sato, Kazumichi; Mino, Sayaka; Suda, Wataru; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Ohkuma, Moriya; Hargreaves, Paulo Iiboshi; Meirelles, Pedro Milet; Thompson, Fabiano L.; Thompson, Cristiane; Gomez-Gil, Bruno; Sawabe, Toko; Sawabe, Tomoo

Systematic and Applied Microbiology40(8)2017年12月-2017年12月 

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ISSN:07232020

概要:© 2017 On page 34, strain number was missing in the description of V. ishigakensis. Corrected description is follows; Description of Vibrio ishigakensis sp. nov Vibrio ishigakensis, (i.shi.gak.en'sis. N.L. masc. adj. ishigakensis, from Ishigaki Island, referring to the first isolation site of these strains in Ishigaki coral reef area, Okinawa, Japan.) Gram-negative, facultatively anaerobic, non-motile rods isolated from seawater collected from coral reef near Ishigaki Island. Colonies on ZoBell 2216E agar medium are beige, circular, and smooth and convex with entire edge. Sodium ion is essential for growth. Growth occurs at NaCl concentrations of 1.0–3.0% and pH5–10. No growth observed at NaCl > 5.0% or pH > 10. The bacterium is a mesophilic and neutrophilic chemoorganotroph which grows at temperatures between 20 and 40 °C with an optimum growth temperature of 30 °C. The bacteria are positive for production of alginase, lipase and DNase, and is able to assimilate D-glucose, D-mannitol, maltose, D-mannose, sucrose, D-galactose, cellobiose, trehalose, D-fructose, N-acetylglucosamine and D-glucosamine. The bacteria are positive for oxidase, catalase. The bacteria show negative for gas production from glucose, indole production, lysine decarboxylase, arginine dihydrolase and ornithine decarboxylase, and is incapable of assimilating D-gluconate, D-sorbitol, melibiose, lactose, D-glucuronate, putrescine, γ-aminobutyrate, pyruvate, L-tyrosine, propionate, meso-erythritol, D-xylose, L-arabinose, DL-malate and citrate. The G + C content of DNA is 47.3–49.1 mol%. The type strain is JCM 19231 T = LMG 28703 T = C1 T .

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice

Nakamoto, Nobuhiro; Amiya, Takeru; Amiya, Takeru; Aoki, Ryo; Aoki, Ryo; Taniki, Nobuhito; Koda, Yuzo; Koda, Yuzo; Miyamoto, Kentaro; Miyamoto, Kentaro; Teratani, Toshiaki; Suzuki, Takahiro; Chiba, Sayako; Chu, Po Sung; Hayashi, Atsushi; Hayashi, Atsushi; Yamaguchi, Akihiro; Shiba, Shunsuke; Miyake, Rei; Katayama, Tadashi; Suda, Wataru; Suda, Wataru; Mikami, Yohei; Kamada, Nobuhiko; Ebinuma, Hirotoshi; Saito, Hidetsugu; Hattori, Masahira; Hattori, Masahira; Kanai, Takanori

Cell Reports21(5)p.1215 - 12262017年10月-2017年10月 

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概要:© 2017 The Authors Gut-derived microbial antigens trigger the innate immune system during acute liver injury. During recovery, regulatory immunity plays a role in suppressing inflammation; however, the precise mechanism underlying this process remains obscure. Here, we find that recruitment of immune-regulatory classical dendritic cells (cDCs) is crucial for liver tolerance in concanavalin A-induced acute liver injury. Acute liver injury resulted in enrichment of commensal Lactobacillus in the gut. Notably, Lactobacillus activated IL-22 production by gut innate lymphoid cells and raised systemic IL-22 levels. Gut-derived IL-22 enhanced mucosal barrier function and promoted the recruitment of regulatory cDCs to the liver. These cDCs produced IL-10 and TGF-β through TLR9 activation, preventing further liver inflammation. Collectively, our results indicate that beneficial gut microbes influence tolerogenic immune responses in the liver. Therefore, modulation of the gut microbiota might be a potential option to regulate liver tolerance. Nakamoto et.al. find that Lactobacillus accumulates in the gut and activates IL-22 production by innate lymphoid cells during acute liver injury. Gut-derived IL-22 contributes to liver tolerance via induction of regulatory DCs.

Lactobacillus kosoi sp. nov., a fructophilic species isolated from kôso, a Japanese sugar-vegetable fermented beverage

Chiou, Tai Ying; Suda, Wataru; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Matsuzaki, Chiaki; Yamamoto, Kenji; Takahashi, Tomoya

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiologyp.1 - 82018年01月-2018年01月 

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ISSN:00036072

概要:© 2018 Springer International Publishing AG, part of Springer Nature A novel Gram-positive, fructophilic, catalase negative, and rod-shaped strain, designated strain 10H T was isolated from kôso, a Japanese sugar-vegetable fermented beverage obtained from a food processing factory in Saku City, Nagano Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed strain 10H T to belong to the genus Lactobacillus, with closely related type strains being Lactobacillus kunkeei YH-15 T (95.5% sequence similarity), Lactobacillus ozensis Mizu2-1 T (95.4% sequence similarity), and Lactobacillus apinorum Fhon13N T (95.3% sequence similarity). The isolate was found to grow at 18–39 °C (optimum 27 °C), pH 4.0–7.0 (optimum pH 6.5) and in the presence of 0–2% NaCl (optimum 0% NaCl). The G + C content of its genomic DNA was determined to be 30.5 mol%. The major fatty acid (≥ 10%) components identified included C 16:0 , C 19:0 cyclo ω7c, C 19:0 cyclo ω9c, and C 18:1 ω9c. The polar lipids were identified as lysophosphatidylethanolamine, phosphatidylethanolamine and glycolipids. The predominant isoprenoid quinones ( > 10%) were identified as MK-7, MK-8, MK-9 and MK-10. The amino acid composition of the cell wall was detected as comprising Asp, Glu, Ala, and Lys but the strain lacks meso-diaminopimelic acid. As with other fructophilic lactic acid bacteria, such as L. kunkeei and L. apinorum, strain 10H T was found to prefer d-fructose to d-glucose as a growth substrate. On the basis of these genetic and phenotypic results, the isolate is concluded to represent a novel species, for which the name Lactobacillus kosoi is proposed. The type strain is 10H T (= NBRC 113063 T = BCRC 81100 T ).

Fecal microbiota transplantation for recurrent Clostridium difficile infection in a patient with ulcerative colitis

Nanki, Kosaku; Mizuno, Shinta; Matsuoka, Katsuyoshi; Ono, Keiko; Sugimoto, Shinya; Kiyohara, Hiroki; Arai, Mari; Nakashima, Moeko; Takeshita, Kozue; Saigusa, Keiichiro; Senoh, Mitsutoshi; Fukuda, Tadashi; Naganuma, Makoto; Kato, Haru; Suda, Wataru; Hattori, Masahira; Kanai, Takanori

Intestinal Research16(1)p.142 - 1462018年01月-2018年01月 

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ISSN:15989100

概要:© 2018. Korean Association for the Study of Intestinal Diseases. Fecal microbiota transplantation (FMT) has been reported as a safe and effective therapy in patients with refractory and recurrent Clostridium difficile infection (CDI). FMT has also been reported as a promising therapy in patients with ulcerative colitis (UC). Both, CDI and UC, are believed to be caused by dysbiosis, such as altered compositions or decreased diversity of the intestinal microbiota. This report describes a patient with UC in remission with a second recurrent episode of CDI, who was treated with FMT. A single FMT performed via colonoscopy completely resolved the patient's diarrhea and eradicated C. difficile bacteriologically without any severe complications. Molecular biological analysis of the patient's fecal microbiota showed that FMT could dramatically change the altered composition of intestinal microbiota and restore its diversity. Despite the restoration of the intestinal microbiota, FMT could not prevent a relapse of UC in this patient. However, it improved the intestinal symptoms of CDI and could prevent further recurrences of CDI.

Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia

Kumagai, Yohei; Kumagai, Yohei; Yoshizawa, Susumu; Yoshizawa, Susumu; Nakajima, Yu; Nakajima, Yu; Watanabe, Mai; Fukunaga, Tsukasa; Ogura, Yoshitoshi; Hayashi, Tetsuya; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Ikeuchi, Masahiko; Kogure, Kazuhiro; Kogure, Kazuhiro; DeLong, Edward F.; Iwasaki, Wataru; Iwasaki, Wataru; Iwasaki, Wataru

ISME Journalp.1 - 152018年02月-2018年02月 

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ISSN:17517362

概要:© 2018 The Author(s) Proteorhodopsin (PR) is a light-driven proton pump that is found in diverse bacteria and archaea species, and is widespread in marine microbial ecosystems. To date, many studies have suggested the advantage of PR for microorganisms in sunlit environments. The ecophysiological significance of PR is still not fully understood however, including the drivers of PR gene gain, retention, and loss in different marine microbial species. To explore this question we sequenced 21 marine Flavobacteriia genomes of polyphyletic origin, which encompassed both PR-possessing as well as PR-lacking strains. Here, we show that the possession or alternatively the lack of PR genes reflects one of two fundamental adaptive strategies in marine bacteria. Specifically, while PR-possessing bacteria utilize light energy (“solar-panel strategy”), PR-lacking bacteria exclusively possess UV-screening pigment synthesis genes to avoid UV damage and would adapt to microaerobic environment (“parasol strategy”), which also helps explain why PR-possessing bacteria have smaller genomes than those of PR-lacking bacteria. Collectively, our results highlight the different strategies of dealing with light, DNA repair, and oxygen availability that relate to the presence or absence of PR phototrophy.

Efficacy of Indigo Naturalis in a Multicenter Randomized Controlled Trial of Patients With Ulcerative Colitis

Naganuma, Makoto; Sugimoto, Shinya; Mitsuyama, Keiichi; Kobayashi, Taku; Yoshimura, Naoki; Ohi, Hidehisa; Tanaka, Shinji; Andoh, Akira; Ohmiya, Naoki; Saigusa, Keiichiro; Yamamoto, Takayuki; Morohoshi, Yuichi; Ichikawa, Hitoshi; Matsuoka, Katsuyoshi; Hisamatsu, Tadakazu; Watanabe, Kenji; Watanabe, Kenji; Mizuno, Shinta; Suda, Wataru; Suda, Wataru; Hattori, Masahira; Hattori, Masahira; Fukuda, Shinji; Hirayama, Akiyoshi; Abe, Takayuki; Watanabe, Mamoru; Hibi, Toshifumi; Suzuki, Yasuo; Kanai, Takanori; Naganuma, Makoto; Sugimoto, Shinya; Mizuno, Shinta; Nakazato, Yoshihiro; Fukuda, Tomohiro; Teratani, Toshiaki; Ogata, Haruhiko; Iwao, Yasushi; Kanai, Takanori; Yamasaki, Hiroshi; Mitsuyama, Keiichi; Kobayashi, Taku; Toyonaga, Takahiko; Nakano, Masaru; Hibi, Toshifumi; Yoshimura, Naoki; Sameshima, Yoichi; Ohi, Hidehisa; Hayashi, Ryohei; Ueno, Yoshitaka; Tanaka, Shinji; Bamba, Shigeki; Andoh, Akira; Matsuoka, Katsuyoshi; Watanabe, Mamoru; Saigusa, Keiichiro; Nakazawa, Atsushi; Morohoshi, Yuichi; Koike, Yuji; Imai, Jin; Ichikawa, Hitoshi; Shimoyama, Takahiro; Yamamoto, Takayuki; Takeuchi, Ken; Suzuki, Yasuo; Nagasaka, Mitsuo; Ohmiya, Naoki; Kitano, Atsuo; Ashizuka, Shinya; Inatsu, Haruhiko; Onodera, Kei; Nakase, Hiroshi; Kitamura, Kazuya; Ikeya, Kentaro; Hanai, Hiroyuki; Watanabe, Chikako; Hokari, Ryota; Hirai, Fumihito; Naito, Yuji; Hoshi, Namiko; Kinjo, Fukunori; Ishiguro, Yo; Sasaki, Makoto; Matsumoto, Takayuki; Watanabe, Kenji; Hisamatsu, Tadakazu; Sano, Fumiya; Roberts, Rachel; Abe, Takayuki; Suda, Wataru; Hattori, Masahira; Fukuda, Shinji; Hirayama, Akiyoshi

Gastroenterology154(4)p.935 - 9472018年03月-2018年03月 

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ISSN:00165085

概要:© 2018 AGA Institute Background & Aims: Indigo naturalis (IN) is a traditional Chinese medicine that contains ligands for the aryl hydrocarbon receptor and promotes regeneration of the mucosa by inducing production of interleukin 22. IN might induce mucosal healing in patients with ulcerative colitis (UC). We performed a randomized controlled trial to investigate the safety and efficacy of IN in patients with UC. Methods: We performed a multicenter, double-blind trial evaluating the safety of 86 patients in Japan with active UC (Mayo scores of 6 or more), enrolled from March 30 through December 27, 2016. Patients were randomly assigned to groups and given a daily dose of 0.5, 1.0, or 2.0 g IN or placebo (1:1:1:1 ratio) for 8 weeks. The primary endpoint was the rate of clinical response at week 8, defined as a 3-point decrease in the Mayo score and a decrease of at least 30% from baseline, with a decrease of at least 1 point for the rectal bleeding subscore or absolute rectal bleeding score of 0–1. The main secondary endpoint was the rate of clinical remission at week 8, defined as a Mayo score or ≤2 and no subscores with a value > 1. Mucosal healing was also assessed at week 8. Results: The trial was terminated because of an external reason: a report of pulmonary arterial hypertension in a patient who used self-purchased IN for 6 months. In the intent-to-treat analysis, we observed a significant, dose-dependent linear trend in proportions of patients with clinical responses (13.6% with a clinical response to placebo; 69.6% to 0.5 g IN; 75.0% to 1.0 g IN; and 81.0% to 2.0 g IN) (Cochran-Armitage trend test P < .0001 compared with placebo). Proportions of patients in clinical remission at week 8 were significantly higher in the 1.0 g IN group (55.0%, P =.0004) and the 2.0 g IN group (38.1%, (P =.0093) than in the placebo group (4.5%). Proportions of patients with mucosal healing were 13.6% in the placebo group, 56.5% in the 0.5 g IN group, 60.0% in the 1.0 g IN group, and 47.6% in the 2.0 g IN group (P =.0278 compared with placebo). Although mild liver dysfunction was observed in 10 patients who received IN, no serious adverse events were observed. Conclusions: In a randomized, placebo-controlled trial, we found 8 weeks of IN (0.5–2.0 g per day) to be effective in inducing a clinical response in patients with UC. However, IN should not yet be used because of the potential for adverse effects, including pulmonary arterial hypertension. Clinical Trials Registry no: UMIN000021439 (http://www.umin.ac.jp/ctr/).

Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae.

Al-Saari Nurhidayu;Gao Feng;Rohul Amin A K M;Sato Kazumichi;Sato Keisuke;Mino Sayaka;Suda Wataru;Oshima Kenshiro;Hattori Masahira;Ohkuma Moriya;Meirelles Pedro M;Thompson Fabiano L;Thompson Cristiane;Filho Gilberto M A;Gomez-Gil Bruno;Sawabe Toko;Sawabe Tomoo

PloS one10(8)2015年-2015年

PubMedDOI

詳細

ISSN:1932-6203

概要::Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity) and V. agarivorans CECT 5085T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085T, V. hangzhouensis JCM 15146T V. maritimus LMG 25439T, and V. variabilis LMG 25438T). In silico DDH data also supported the genomic relationship. The strains C7T also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1T, V. brasiliensis LMG 20546T, V. orientalis ATCC 33934T, and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058T and V. astriarenae C7T are members of the newest clade of Vibrionaceae named Agarivorans.

Advanced microbial taxonomy combined with genome-based-approaches reveals that vibrio astriarenae sp. Nov., an agarolytic marine bacterium, forms a new clade in Vibrionaceae

Al-Saari, Nurhidayu; Gao, Feng; Rohul, Amin A K M; Sato, Kazumichi; Sato, Keisuke; Mino, Sayaka; Suda, Wataru; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Ohkuma, Moriya; Meirelles, Pedro M.; Thompson, Fabiano L.; Thompson, Cristiane; Filho, Gilberto M A; Gomez-Gil, Bruno; Sawabe, Toko; Sawabe, Tomoo

PLoS ONE10(8)2015年08月-2015年08月 

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概要:© 2015 Al-saari et al. Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. Nov. C7T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity) and V. agarivorans CECT 5085T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085T, V. hangzhouensis JCM 15146T V. maritimus LMG 25439T, and V. variabilis LMG 25438T). In silico DDH data also supported the genomic relationship. The strains C7T also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1T, V. brasiliensis LMG 20546T, V. orientalis ATCC 33934T, and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. Nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058T and V. astriarenae C7T are members of the newest clade of Vibrionaceae named Agarivorans.

Unique pioneer microbial communities exposed to volcanic sulfur dioxide

Fujimura, Reiko; Fujimura, Reiko; Kim, Seok Won; Kim, Seok Won; Sato, Yoshinori; Oshima, Kenshiro; Hattori, Masahira; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

Scientific Reports62016年01月-2016年01月 

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概要:© 2016, Nature Publishing Group. All rights reserved.Newly exposed volcanic substrates contain negligible amounts of organic materials. Heterotrophic organisms in newly formed ecosystems require bioavailable carbon and nitrogen that are provided from CO2 and N2 fixation by pioneer microbes. However, the knowledge of initial ecosystem developmental mechanisms, especially the association between microbial succession and environmental change, is still limited. This study reports the unique process of microbial succession in fresh basaltic ash, which was affected by long-term exposure to volcanic sulfur dioxide (SO2). Here we compared the microbial ecosystems among deposits affected by SO2 exposure at different levels. The results of metagenomic analysis suggested the importance of autotrophic iron-oxidizing bacteria, particularly those involved in CO2 and N2 fixation, in the heavily SO2 affected site. Changes in the chemical properties of the deposits after the decline of the SO2 impact led to an apparent decrease in the iron-oxidizer abundance and a possible shift in the microbial community structure. Furthermore, the community structure of the deposits that had experienced lower SO2 gas levels showed higher similarity with that of the control forest soil. Our results implied that the effect of SO2 exposure exerted a selective pressure on the pioneer community structure by changing the surrounding environment of the microbes.

The gut microbiome of healthy Japanese and its microbial and functional uniqueness

Nishijima, Suguru; Suda, Wataru; Suda, Wataru; Oshima, Kenshiro; Kim, Seok Won; Hirose, Yuu; Morita, Hidetoshi; Hattori, Masahira; Hattori, Masahira

DNA Research23(2)p.125 - 1332016年04月-2016年04月 

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ISSN:13402838

概要:© The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibiting a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by comparing the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regarding the microbial functions, those of carbohydrate metabolism were overrepresented with a concurrent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and enrichment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes.

Fecal microbiota transplantation for patients with steroid-resistant acute graft-versus-host disease of the gut

Kakihana, Kazuhiko; Fujioka, Yuki; Fujioka, Yuki; Suda, Wataru; Najima, Yuho; Kuwata, Go; Sasajima, Satoshi; Mimura, Iyo; Morita, Hidetoshi; Sugiyama, Daisuke; Nishikawa, Hiroyoshi; Hattori, Masahira; Hattori, Masahira; Hino, Yutaro; Ikegawa, Shuntaro; Yamamoto, Keita; Toya, Takashi; Doki, Noriko; Koizumi, Koichi; Honda, Kenya; Honda, Kenya; Honda, Kenya; Ohashi, Kazuteru

Blood128(16)p.2083 - 20882016年10月-2016年10月 

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ISSN:00064971

概要:© 2016 by The American Society of Hematology.Increasing evidence indicates that the gut microbiota is closely associated with ACute graft-versus-host disease (aGVHD) in stem cell transplantation (SCT). Fecal microbiota transplantation (FMT) could represent an alternative treatment option for aGVHD. However, FMT for SCT patients carries a potential risk of infection by infused microbiota because of the severely immuno suppressed status. We there for econducte dapilot study to evaluate the safety of FMT in SCT. A total of 4 patients with steroid-resistant (n 53) or steroid-dependent gut aGVHD (n 51) received FMT. No severe adverse events attributed to FMT were observed. All patients responded to FMT, with 3 complete responses and 1 partial response. Temporal dynamics of microbiota seemed to be linked to the gut condition of patients and peripheral effector regulatory T cells also increased during response to FMT. FMT was safely performed in our patients and might offer a novel therapeutic option for aGVHD.

外部研究資金

科学研究費採択状況

研究種別:

免疫性神経疾患を修飾する新たな内分泌性制御因子と環境因子のクロストーク

2018年-0月-2023年-0月

配分額:¥43810000

研究種別:

神経性やせ症の病態解明と新パラダイムの創出:腸内細菌による体重・行動特性の制御

2016年-0月-2019年-0月

配分額:¥17160000

研究種別:

Molecular mechanisms for IgA-mediated regulations of host-microbiota symbiosis

2016年-0月-2019年-0月

配分額:¥43810000

研究種別:

心不全における腸内細菌叢の機能的役割の解明

2014年-0月-2016年-0月

配分額:¥3640000

研究種別:

不耕起栽培畑地土壌の物質循環系メタゲノム解析

2014年-0月-2017年-0月

配分額:¥16250000

研究種別:

ヒト唾液中に存在する腸内常在性細菌種の特定とその特徴解明

2013年-0月-2014年-0月

配分額:¥4030000

研究種別:

アジア人種の食と腸内フローラと健康に関する調査研究

2013年-0月-2016年-0月

配分額:¥17680000

研究種別:

水田メタゲノミクス:持続的生産を支える土壌-根圏微生物とその機能の全貌解明

2013年-0月-2016年-0月

配分額:¥47580000

研究種別:

歯周病細菌性因子の解明を目指したプラーク由来臨床株の分離とそのゲノム解析

2012年-0月-2015年-0月

配分額:¥5330000

研究種別:

多発性硬化症と腸内細菌・腸管免疫の関連に関する研究

2012年-0月-2016年-0月

配分額:¥146120000

研究種別:

腸内フローラを用いた動物個体識別法の開発

2011年-0月-2013年-0月

配分額:¥3900000

研究種別:

比較メタゲノミクスによる土壌微生物性解析の基盤構築

2010年-0月-2013年-0月

配分額:¥46670000

研究種別:

ゲノム科学の総合的推進に向けた大規模ゲノム情報生産・高度情報解析支援

2010年-0月-2015年-0月

研究種別:

口腔・歯周病フローラのメタゲノム解析

配分額:¥48360000

研究種別:

歯根膜トランスクリプトーム解析によるオーダーメード歯周組織再生療法の新展開

配分額:¥16180000

研究種別:

Theileria orientalisゲノム完全解読と機能分子の比較解析

配分額:¥48750000

研究種別:

微生物ゲノムシーケンシング体制の活用による微生物システム解明への基盤構築

配分額:¥516300000

研究種別:

生命のシステム的理解に向けたゲノム研究推進のための総合的基盤構築

配分額:¥108600000

研究種別:

ダウン症候群原因遺伝子の同定とその発症機構のゲノム科学的研究

配分額:¥7000000

研究種別:

ダウン症候群原因遺伝子の同定とその発症機構のゲノム科学的研究

研究種別:

乳児期における腸内細菌叢の構成、新たなバイオマーカーとアレルギー疾患の発症の解明

2016年-0月-2019年-0月

配分額:¥4680000

学内研究制度

特定課題研究

メタゲノム情報を用いたヒト唾液常在菌叢の概日リズムに関する研究

2015年度

研究成果概要:健康な成人被験者より唾液を4時間ごとに3日間採取し、各唾液から調製した細菌叢から唾液細菌叢DNAを調製した。このDNAから細菌の16SリボソームRNA(16S rRNA)遺伝子をPCR増幅し、増幅したDNAを次世代シークエンサーに...健康な成人被験者より唾液を4時間ごとに3日間採取し、各唾液から調製した細菌叢から唾液細菌叢DNAを調製した。このDNAから細菌の16SリボソームRNA(16S rRNA)遺伝子をPCR増幅し、増幅したDNAを次世代シークエンサーにより配列決定を行った。得られた16SrRNA遺伝子の配列データより各サンプルの門及び属レベルでの菌種組成を求め、その変動をUniFrac-主座標及び距離や自己相関係数等の情報・統計手法を用いて評価した。その結果、解析した被験者において、唾液細菌叢が約24時間で自己相関係数が最大になること等を見いだし、概日リズムを有することを明らかにした。

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