Updated on 2026/03/27

写真a

 
HONGOH Yuichi
 
Organization
School of Life Science and Technology Professor
Title
Professor
Homepage
http://www.hongoh.bio.titech.ac.jp/
External link

Degree

  • Doctor of Sciences ( Graduate School of Sciences, University of Tokyo )

Research Interests

  • Entomology

  • Microbiology

  • Molecular Ecology

  • Symbiology

  • 分子進化

  • 微生物生態

  • 難培養性微生物

  • Environmental Genomics

  • 昆虫

  • 環境ゲノム

  • 共生

  • 分子生態学

Research Areas

  • Life Science / Biodiversity and systematics

  • Life Science / Molecular biology

  • Life Science / Genome biology

  • Life Science / Ecology and environment

  • Life Science / Evolutionary biology

Education

  • The University of Tokyo   Graduate School of Science   Department of Biological Sciences

    1996.4 - 2000.3

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    Country： Japan

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  • University of Tokyo   Graduate School of Sciences   Depratment of Biological Sciences

    - 2000

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  • The University of Tokyo   Graduate School of Science   Department of Biological Sciences

    1993.4 - 1996.3

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  • The University of Tokyo   Faculty of Science

    1989.4 - 1993.3

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    Country： Japan

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  • 私立武蔵高校

    1985.4 - 1988.3

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Research History

  • Institute of Science Tokyo   School of Life Science and Technology   Professor

    2024.10

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    Country：Japan

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  • Tokyo Institute of Technology   School of Life Science and Technology   Professor

    2014.11 - 2024.9

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    Country：Japan

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  • Tokyo Institute of Technology   Graduate School of Bioscience and Technology   Associate Professor

    2009 - 2014

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  • RIKEN   Research Associate

    2007 - 2009

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  • RIKEN   Special Postdoctoral Fellow

    2004 - 2007

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  • JST   ICORP   Research Scientist

    2000 - 2004

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  • JSPS   Special Doctoral Fellow

    1997 - 1999

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Professional Memberships

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Committee Memberships

  • 日本共生生物学会   理事  

    2024.1   

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  • 日本微生物生態学会   評議員  

    2022.1   

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    Committee type：Academic society

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  • 日本ゲノム微生物学会   評議員  

    2020   

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    Committee type：Academic society

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  • 国際微生物生態学会   The ISME Journal Editorial Board  

    2017 - 2021.9   

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    Committee type：Academic society

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  • 日本微生物生態学会   評議員  

    2017 - 2020   

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    Committee type：Academic society

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  • 日本微生物生態学会   評議員  

    2011 - 2014   

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    Committee type：Academic society

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  • 日本農芸化学会   代議員  

    2010 - 2011   

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Papers

  • Reclassification of the genus Dysgonomonas and description of Dysgonomonas reticulitermitis sp. nov. and Viscerimonas tarda gen. nov., sp. nov. from the gut of the subterranean termite Reticulitermes speratus Reviewed

    K. Takahashi, A. Hisatom, K. Mori, M. Yuki, S. Noda, Y. Hongoh, M. Ohkuma, M. Sakamoto

    Int. J. Syst. Evol. Microbiol.   76 ( 1 )   2026.1

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    Language：English  

    DOI： 10.1099/ijsem.0.007031

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  • Field dynamics of the root endosphere microbiome assembly in paddy rice cultivated under no fertilizer input Reviewed International journal

    Asahi Adachi, John Jewish Dominguez, Yuniar Devi Utami, Masako Fuji, Sumire Kirita, Shunsuke Imai, Takumi Murakami, Yuichi Hongoh, Rina Shinjo, Takehiro Kamiya, Toru Fujiwara, Kiwamu Minamisawa, Naoaki Ono, Shigehiko Kanaya, Yusuke Saijo

    Plant And Cell Physiology   pcaf045   2025.6

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    Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

    Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared with a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars—Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.

    DOI： 10.1093/pcp/pcaf045

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  • Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont

    Jieyang Fu, Yiting Liu, Takuya Yoshioka, Katsura Igai, Takako Mabuchi, Kumiko Kihara, Takumi Murakami, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh

    The ISME Journal   19 ( 1 )   2025.1

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    Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

    Mixotricha paradoxa is a large cellulolytic flagellate present in the hindgut of the termite Mastotermes darwiniensis. This parabasalid flagellate is unique in its reliance on ectosymbiotic spirochetes for motility. We analyzed the transcriptome of M. paradoxa and the genomes of the ectosymbiotic spirochete Propulsinema mixotrichae (“Treponematales”), the rod-shaped ectosymbiont Synergitannerella mixotrichae (Bacteroidales), and the endosymbiont Endomicrobiellum mixotrichae (Endomicrobiales), all of which are obligately associated with M. paradoxa and were taxonomically described in this study. Mixotricha paradoxa highly expressed genes for diverse glycoside hydrolases (GHs) and likely ferments sugars to H2, CO2, acetate, ethanol, and glycerol. Similar to the case for parasitic parabasalids such as Trichomonas vaginalis, transcripts for biosynthesis of nucleotides and many amino acids were not detected in our analyses of M. paradoxa. Propulsinema mixotrichae possesses genes encoding proteins for the assembly of flagella and for those in pathways associated with chemotaxis and dinitrogen fixation. Such genes are absent in S. mixotrichae, which instead possesses numerous genes encoding glycoside hydrolase enzymes, which are largely complementary to the glycoside hydrolase repertoire of M. paradoxa. Endomicrobiellum mixotrichae appears to provide nucleotides and nine amino acids to its host, which in turn likely supplies three amino acids, including tryptophan, to E. mixotrichae. Because bacterial cells, in addition to wood particles, were observed in food vacuoles of M. paradoxa, these ecto- and endosymbionts may be digested by the flagellate host. Overall, the distinct roles of each symbiont highlight the efficient functional division of labor that has evolved in this holobiont.

    DOI： 10.1093/ismejo/wraf178

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    Other Link： https://academic.oup.com/ismej/article-pdf/19/1/wraf178/64088606/wraf178.pdf

  • Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus Reviewed International journal

    Masayuki Kaneko, Tatsuki Omori, Katsura Igai, Takako Mabuchi, Miho Sakai-Tazawa, Arisa Nishihara, Kumiko Kihara, Tsuyoshi Yoshimura, Moriya Ohkuma, Yuichi Hongoh

    ISME Communications   4 ( 1 )   ycae09   2024.7

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

    Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts’ fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here “Candidatus Methanobrevibacter cononymphae”, is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, “Ca. Methanobrevibacter cononymphae” is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of “Ca. Methanobrevibacter cononymphae” showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.

    DOI： 10.1093/ismeco/ycae097

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    Other Link： https://academic.oup.com/ismecommun/article-pdf/4/1/ycae097/58684733/ycae097.pdf

  • Transmission dynamics of symbiotic protist communities in the termite gut: association with host adult eclosion and dispersal Reviewed International journal

    Tatsuya Inagaki, Katsura Igai, Kazuki Takahashi, Yuichi Hongoh

    Royal Society Open Science   11 ( 5 )   231527   2024.5

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    Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Royal Society  

    The fidelity of vertical transmission is a critical factor in maintaining mutualistic associations with microorganisms. The obligate mutualism between termites and intestinal protist communities has been maintained for over 130 million years, suggesting the faithful transmission of diverse protist species across host generations. Although a severe bottleneck can occur when alates disperse with gut protists, how protist communities are maintained during this process remains largely unknown. In this study, we examined the dynamics of intestinal protist communities during adult eclosion and alate dispersal in the termite Reticulitermes speratus . We found that the protist community structure in last-instar nymphs differed significantly from that in workers and persisted intact during adult eclosion, whereas all protists disappeared from the gut during moults between worker stages. The number of protists in nymphs and alates was substantially lower than in workers, whereas the proportion of protist species exhibiting low abundance in workers was higher in nymphs and alates. Using a simulation-based approach, we demonstrate that such changes in the protist community composition of nymphs and alates improve the transmission efficiency of whole protist species communities. This study thus provides novel insights into how termites have maintained mutualistic relationships with diverse gut microbiota for generations.

    DOI： 10.1098/rsos.231527

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    Other Link： https://royalsocietypublishing.org/doi/full-xml/10.1098/rsos.231527

  • Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade Reviewed International journal

    Kazuki Takahashi, Hirokazu Kuwahara, Yutaro Horikawa, Kazuki Izawa, Daiki Kato, Tatsuya Inagaki, Masahiro Yuki, Moriya Ohkuma, Yuichi Hongoh

    The ISME Journal   17 ( 11 )   1895 - 1906   2023.8

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

    The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0–1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.

    DOI： 10.1038/s41396-023-01502-0

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    Other Link： https://www.nature.com/articles/s41396-023-01502-0

  • Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system Reviewed International coauthorship International journal

    Jaclyn Thompson, Casey Barr, Lydia Babcock-Adams, Lina Bird, Eugenio La Cava, Arkadiy Garber, Yuichi Hongoh, Mark Liu, Kenneth H. Nealson, Akihiro Okamoto, Daniel Repeta, Shino Suzuki, Clarissa Tacto, Michelle Tashjian, Nancy Merino

    Frontiers in Microbiology   14   e1179857   2023.7

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

    The terrestrial serpentinite-hosted ecosystem known as “The Cedars” is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < −550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars (‘Paeni-Cedars’), Alishewanella sp. BS5-314 (‘Ali-BS5-314’), and Anaerobacillus sp. CMMVII (‘Anaero-CMMVII’). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7–10 (minimum pH tested was 7), temperatures 20–40°C, and 0–3% NaCl concentration. The addition of 10–20 mM CaCl2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10–12 and temperatures 10–40°C, with limited growth observed 1–5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9–12, with the addition of 0.01–1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.

    DOI： 10.3389/fmicb.2023.1179857

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  • Agarose gel microcapsules enable easy-to-prepare, picolitre-scale, single-cell genomics, yielding high-coverage genome sequences Reviewed International journal

    Hiroyoshi Aoki, Yuki Masahiro, Michiru Shimizu, Yuichi Hongoh, Moriya Ohkuma, Yutaka Yamagata

    Scientific Reports   12 ( 1 )   2022.10

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    DOI： 10.1038/s41598-022-20923-z

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    Other Link： https://www.nature.com/articles/s41598-022-20923-z

  • Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses Reviewed

    Yukihiro Kinjo, Thomas Bourguignon, Yuichi Hongoh, Nathan Lo, Gaku Tokuda, Moriya Ohkuma

    Microbiology Spectrum   2022.9

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    Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

    The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as “collaborative pathways”. To date, collaborative pathways have only been reported from sap-feeding insects.

    DOI： 10.1128/spectrum.02779-22

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  • Improving the nutritional value and bioactivity of soybean meal in solid-state fermentation using Bacillus strains newly isolated from the gut of the termite Termes propinquus. Reviewed International journal

    Maneeploy Nualkul, Bundit Yuangsoi, Yuichi Hongoh, Akinori Yamada, Pinsurang Deevong

    FEMS Microbiology Letters   369 ( 1 )   2022.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    The present study aimed to isolate and characterize proteolytic Bacillus spp. from termite guts to test the possibility of application for improving the nutritional value and bioactivity of fermented soybean meal (FSBM). Aerobic endospore-forming bacteria were isolated from the gut of the termite Termes propinquus. Ten isolates with high levels of soy milk degradation were selected and tested for extracellular enzyme production. Among them, two isolates, Tp-5 and Tp-7, exhibited all tested hydrolytic enzyme activities (cellulase, xylanase, pectinase, amylase, protease, lipase and phytase), weak alpha hemolytic and also antagonistic activities against fish pathogenic species of Aeromonas and Streptococcus. Both phylogenetic and biochemical analyses indicated that they were closely related to Bacillus amyloliquefaciens. During solid-state fermentation of SBM, Tp-5 and Tp-7 exhibited the highest protease activity (1127.2 and 1552.4 U g-1, respectively) at 36 h, and the resulting FSBMs showed a significant increase in crude protein content and free radical-scavenging ability (P < 0.05), as well as an improvement in the composition of amino acids, metabolites and other nutrients, while indigestible materials such as fiber, lignin and hemicellulose were decreased. The potential strains, especially Tp-7, improved the nutritional value of FSBM by their strong hydrolytic and antioxidant activities, together with reducing antinutritional components.

    DOI： 10.1093/femsle/fnac044

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  • Fine‐scale genetic diversity and putative ecotypes of oxymonad protists coinhabiting the hindgut of Reticulitermes speratus Reviewed

    Katsura Igai, Osamu Kitade, Jieyang Fu, Kazumi Omata, Takahiro Yonezawa, Moriya Ohkuma, Yuichi Hongoh

    Molecular Ecology   31 ( 4 )   1317 - 1331   2022.2

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1111/mec.16309

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    Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.16309

  • Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes. Reviewed International journal

    Thomas Bourguignon, Yukihiro Kinjo, Paula Villa-Martín, Nicholas V Coleman, Qian Tang, Daej A Arab, Zongqing Wang, Gaku Tokuda, Yuichi Hongoh, Moriya Ohkuma, Simon Y W Ho, Simone Pigolotti, Nathan Lo

    Current Biology : CB   30 ( 19 )   3848 - 3855   2020.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (Ne) is thought to play an important role in shaping genome size [1-3]-a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the existence of reduced genomes in marine and terrestrial prokaryote species with large Ne indicate that genome reduction is influenced by multiple processes [3]. One candidate process is enhanced mutation rate, which can increase adaptive capacity but can also promote gene loss. To investigate evolutionary forces associated with prokaryotic genome reduction, we performed molecular evolutionary and phylogenomic analyses of nine lineages from five bacterial and archaeal phyla. We found that gene-loss rate strongly correlated with synonymous substitution rate (a proxy for mutation rate) in seven of the nine lineages. However, gene-loss rate showed weak or no correlation with the ratio of nonsynonymous/synonymous substitution rate (dN/dS). These results indicate that genome reduction is largely associated with increased mutation rate, while the association between gene loss and changes in Ne is less well defined. Lineages with relatively high dS and dN, as well as smaller genomes, lacked multiple DNA repair genes, providing a proximate cause for increased mutation rates. Our findings suggest that similar mechanisms drive genome reduction in both intracellular and free-living prokaryotes, with implications for developing a comprehensive theory of prokaryote genome size evolution.

    DOI： 10.1016/j.cub.2020.07.034

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  • Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut. Reviewed International journal

    Mariko Takeuchi, Hirokazu Kuwahara, Takumi Murakami, Kazuki Takahashi, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Moriya Ohkuma, Yuichi Hongoh

    The ISME Journal   14 ( 9 )   2288 - 2301   2020.9

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    Several Trichonympha protist species in the termite gut have independently acquired Desulfovibrio ectosymbionts in apparently different stages of symbiosis. Here, we obtained the near-complete genome sequence of Desulfovibrio phylotype ZnDsv-02, which attaches to the surface of Trichonympha collaris cells, and compared it with a previously obtained genome sequence of 'Candidatus Desulfovibrio trichonymphae' phylotype Rs-N31, which is almost completely embedded in the cytoplasm of Trichonympha agilis. Single-nucleotide polymorphism analysis indicated that although Rs-N31 is almost clonal, the ZnDsv-02 population on a single host cell is heterogeneous. Despite these differences, the genome of ZnDsv-02 has been reduced to 1.6 Mb, which is comparable to that of Rs-N31 (1.4 Mb), but unlike other known ectosymbionts of protists with a genome similar in size to their free-living relatives. Except for the presence of a lactate utilization pathway, cell-adhesion components and anti-phage defense systems in ZnDsv-02, the overall gene-loss pattern between the two genomes is very similar, including the loss of genes responsive to environmental changes. Our study suggests that genome reduction can occur in ectosymbionts, even when they can be transmitted horizontally and obtain genes via lateral transfer, and that the symbiont genome size depends heavily on their role in the symbiotic system.

    DOI： 10.1038/s41396-020-0688-1

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  • Single-cell genomics of novel Actinobacteria With the Wood–Ljungdahl pathway discovered in a serpentinizing system Reviewed

    Nancy Merino, Mikihiko Kawai, Eric S. Boyd, Daniel R. Colman, Shawn E. McGlynn, Kenneth H. Nealson, Ken Kurokawa, Yuichi Hongoh

    Frontiers in Microbiology   11   e1031   2020.6

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

    DOI： 10.3389/fmicb.2020.01031

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  • Native Architecture of the Centriole Proximal Region Reveals Features Underlying Its 9-Fold Radial Symmetry. International journal

    Paul Guichard, Virginie Hachet, Norbert Majubu, Aitana Neves, Davide Demurtas, Natacha Olieric, Isabelle Fluckiger, Akinori Yamada, Kumiko Kihara, Yuichiro Nishida, Shigeharu Moriya, Michel O Steinmetz, Yuichi Hongoh, Pierre Gönczy

    Current Biology : CB   30 ( 11 )   2204 - 2204   2020.6

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  • Ectosymbiotic bacterial microbiota densely colonize the surface of thelastomatid nematodes in the gut of the wood-feeding cockroach Panesthia angustipennis. Reviewed

    Murakami T, Onouchi S, Igai K, Ohkuma M, Hongoh Y

    FEMS Microbiology Ecology   95 ( 2 )   fiy238   2019.2

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/femsec/fiy238

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  • Genome analyses of uncultured TG2/ZB3 bacteria in ‘Margulisbacteria’ specifically attached to ectosymbiotic spirochetes of protists in the termite gut. Reviewed

    Utami Y.D, Kuwahara H, Igai K, Murakami T, Sugaya K, Morikawa T, Nagura Y, Yuki M, Deevong P, Inoue T, Kihara K, Lo N, Yamada A, Ohkuma M, Hongoh Y

    The ISME Journal   13 ( 2 )   455 - 467   2019

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    DOI： 10.1038/s41396-018-0297-4

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    Other Link： http://www.nature.com/articles/s41396-018-0297-4.pdf

  • The relationship between microbial community structures and environmental parameters revealed by metagenomic analysis of hot spring water in the Kirishima area, Japan. Reviewed

    Nishiyama E, Higashi K, Mori H, Suda K, Nakamura H, Omori S, Maruyama S, Hongoh Y, Kurokawa K

    Frontiers in Bioengineering and Biotechnology   6   e202   2018.12

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  • Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community Reviewed International journal

    Murakami T, Segawa T, Takeuchi N, Sepulveda G.B, Labarca P, Kohshima S, Hongoh Y

    Environmental Microbiology   20 ( 11 )   4170 - 4183   2018.11

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    Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

    The glacier stonefly Andiperla willinki is the largest metazoan inhabiting the Patagonian glaciers. In this study, we analysed the gut microbiome of the aquatic nymphs by 16S rRNA gene amplicon and metagenomic sequencing. The bacterial gut community was consistently dominated by taxa typical of animal digestive tracts, such as Dysgonomonadaceae and Lachnospiraceae, as well as those generally indigenous to glacier environments, such as Polaromonas. Interestingly, the dominant Polaromonas phylotypes detected in the stonefly gut were almost never detected in the glacier surface habitat. Fluorescence in situ hybridization analysis revealed that the bacterial lineages typical of animal guts colonized the gut wall in a co-aggregated form, while Polaromonas cells were not included in the aggregates. Draft genomes of several dominant bacterial lineages were reconstructed from metagenomic datasets and indicated that the predominant Dysgonomonadaceae bacterium is capable of degrading various polysaccharides derived from host-ingested food, such as algae, and that other dominant bacterial lineages ferment saccharides liberated by the polysaccharide degradation. Our results suggest that the gut bacteria-host association in the glacier stonefly contributes to host nutrition as well as material cycles in the glacier environment.

    DOI： 10.1111/1462-2920.14420

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  • Parallel and gradual genome erosion in the Blattabacterium endosymbionts of Mastotermes darwiniensis and Cryptocercus wood roaches Reviewed

    Yukihiro Kinjo, Thomas Bourguignon, Kwei Jun Tong, Hirokazu Kuwahara, Sang Jin Lim, Kwang Bae Yoon, Shuji Shigenobu, Yung Chul Park, Christine A. Nalepa, Yuichi Hongoh, Moriya Ohkuma, Nathan Lo, Gaku Tokuda

    Genome Biology and Evolution   10 ( 6 )   1622 - 1630   2018.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/gbe/evy110

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  • Phylogenetic diversity and single-cell genome analysis of “Melainabacteria”, a non-photosynthetic cyanobacterial group, in the termite gut Reviewed

    Yuniar Devi Utami, Hirokazu Kuwahara, Takumi Murakami, Takahiro Morikawa, Kaito Sugaya, Kumiko Kihara, Masahiro Yuki, Nathan Lo, Pinsurang Deevong, Sasitorn Hasin, Warin Boonriam, Tetsushi Inoue, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh

    Microbes and Environments   33 ( 1 )   50 - 57   2018

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    DOI： 10.1264/jsme2.ME17137

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  • Draft genome sequence of Lactococcus sp. strain Rs-Y01, isolated from the gut of the lower termite Reticulitermes speratus Reviewed International journal

    Yuki, M, Sakamoto, M, Kuwahara, H, Hongoh, Y, Ohkuma, M

    Genome Announcments   5 ( 38 )   e00999-17   2017.9

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    DOI： 10.1128/genomeA.00999-17

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  • Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites Reviewed

    Kazuki Izawa, Hirokazu Kuwahara, Kaito Sugaya, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh

    Environmental Microbiology Reports   9 ( 4 )   411 - 418   2017.8

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    DOI： 10.1111/1758-2229.12549

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  • Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem

    Arisa Tsuboi, Misao Itouga, Yuichi Hongoh, Shigeharu Moriya

    BioRxiv   2017.7

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    DOI： 10.1101/159293

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  • Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut Reviewed

    Ajeng K. Pramono, Hirokazu Kuwahara, Takehiko Itoh, Atsushi Toyoda, Akinori Yamada, Yuichi Hongoh

    Microbes and Environments   32 ( 2 )   112 - 117   2017.6

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    DOI： 10.1264/jsme2.ME16175

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  • Genome of 'Ca. Desulfovibrio trichonymphae', an H-2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut Reviewed

    Hirokazu Kuwahara, Masahiro Yuki, Kazuki Izawa, Moriya Ohkuma, Yuichi Hongoh

    ISME JOURNAL   11 ( 3 )   766 - 776   2017.3

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    DOI： 10.1038/ismej.2016.143

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  • Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites Reviewed

    Takahiro Yonezawa, Takahiro Segawa, Hiroshi Mori, Paula F. Campos, Yuichi Hongoh, Hideki Endo, Ayumi Akiyoshi, Naoki Kohno, Shin Nishida, Jiaqi Wu, Haofei Jin, Jun Adachi, Hirohisa Kishino, Ken Kurokawa, Yoshifumi Nogi, Hideyuki Tanabe, Harutaka Mukoyama, Kunio Yoshida, Armand Rasoamiaramanana, Satoshi Yamagishi, Yoshihiro Hayashi, Akira Yoshida, Hiroko Koike, Fumihito Akishinonomiya, Eske Willerslev, Masami Hasegawa

    Current Biology   27 ( 1 )   68 - 77   2017.1

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    DOI： 10.1016/j.cub.2016.10.029

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  • Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages Reviewed

    Takumi Murakami, Takahiro Segawa, Roman Dial, Nozomu Takeuchi, Shiro Kohshima, Yuichi Hongoh

    Microbes and Environments   32 ( 1 )   32 - 39   2017

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    DOI： 10.1264/jsme2.ME16158

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  • Comparison of Intracellular "Ca. Endomicrobium Trichonymphae" Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA Reviewed

    Kazuki Izawa, Hirokazu Kuwahara, Kumiko Kihara, Masahiro Yuki, Nathan Lo, Takehiko Itoh, Moriya Ohkuma, Yuichi Hongoh

    GENOME BIOLOGY AND EVOLUTION   8 ( 10 )   3099 - 3107   2016.10

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    DOI： 10.1093/gbe/evw227

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  • Nitrogen fixation and nifH diversity in human gut microbiota Reviewed

    Katsura Igai, Manabu Itakura, Suguru Nishijima, Hirohito Tsurumaru, Wataru Suda, Takumi Tsutaya, Eriko Tomitsuka, Kiyoshi Tadokoro, Jun Baba, Shingo Odani, Kazumi Natsuhara, Ayako Morita, Minoru Yoneda, Andrew R. Greenhill, Paul F. Horwood, Jun-ichi Inoue, Moriya Ohkuma, Yuichi Hongoh, Taro Yamamoto, Peter M. Siba, Masahira Hattori, Kiwamu Minamisawa, Masahiro Umezaki

    Scientific Reports   6   e31932   2016.8

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    DOI： 10.1038/srep31942

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  • Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont Reviewed

    Hao Zheng, Carsten Dietrich, Yuichi Hongoh, Andreas Brune

    Molecular Biology and Evolution   33 ( 3 )   721 - 725   2016.3

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    DOI： 10.1093/molbev/msv264

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  • Trapping and isolation of single prokaryotic cells in a micro-chamber array using dielectrophoresis Reviewed

    K. Mogi, C. Shirataki, K. Kihara, H. Kuwahara, Y. Hongoh, T. Yamamoto

    RSC ADVANCES   6 ( 114 )   113000 - 113006   2016

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    DOI： 10.1039/c6ra21229h

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  • Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose Reviewed

    Masahiro Yuki, Hirokazu Kuwahara, Masaki Shintani, Kazuki Izawa, Tomoyuki Sato, David Starns, Yuichi Hongoh, Moriya Ohkuma

    ENVIRONMENTAL MICROBIOLOGY   17 ( 12 )   4942 - 4953   2015.12

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    DOI： 10.1111/1462-2920.12945

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  • Acetogenesis from H-2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist Reviewed

    Moriya Ohkuma, Satoko Noda, Satoshi Hattori, Toshiya Iida, Masahiro Yuki, David Starns, Jun-ichi Inoue, Alistair C. Darby, Yuichi Hongoh

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   112 ( 33 )   10224 - 10230   2015.8

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    DOI： 10.1073/pnas.1423979112

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  • Census of bacterial microbiota associated with the glacier ice worm Mesenchytraeus solifugus Reviewed

    Takumi Murakami, Takahiro Segawa, Dylan Bodington, Roman Dial, Nozomu Takeuchi, Shiro Kohshima, Yuichi Hongoh

    FEMS MICROBIOLOGY ECOLOGY   91 ( 3 )   fiv003   2015.3

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    DOI： 10.1093/femsec/fiv003

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  • Two Different Rickettsial Bacteria Invading Volvox carteri Reviewed

    Kaoru Kawafune, Yuichi Hongoh, Takashi Hamaji, Tomoaki Sakamoto, Tetsuya Kurata, Shunsuke Hirooka, Shin-ya Miyagishima, Hisayoshi Nozaki

    PLOS ONE   10 ( 2 )   e0116192   2015.2

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    DOI： 10.1371/journal.pone.0116192

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  • Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. Reviewed International journal

    Ajeng K Pramono, Mitsuo Sakamoto, Takao Iino, Yuichi Hongoh, Moriya Ohkuma

    International journal of systematic and evolutionary microbiology   65 ( Pt 2 )   681 - 5   2015.2

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    A facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, strain N-10(T), was isolated from the gut of the termite Reticulitermes speratus. Strain N-10(T) was closely related to Dysgonomonas gadei JCM 16698(T) according to 16S rRNA gene sequence similarity analysis (98 %) and DNA-DNA relatedness value (≤61.3 %). The optimum growth temperature of strain N-10(T) was 30 °C, which was distinct from that (37 °C) of known species of the genus Dysgonomonas. Growth of strain N-10(T) was inhibited on medium containing 5 or 20 % bile, unlike other species of the genus Dysgonomonas. In addition, acid production in the API 20A system and enzymic reactions in the Rapid ID 32A system of strain N-10(T) differed from those of other species of the genus Dysgonomonas. Based on these characteristics, strain N-10(T) represents a novel species of the genus Dysgonomonas, for which the name Dysgonomonas termitidis sp. nov. is proposed. The type strain is N-10(T) ( = JCM 30204(T) = CCUG 66188(T)).

    DOI： 10.1099/ijs.0.070391-0

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  • Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes. Reviewed

    Jun-ichi Inoue, Kenshiro Oshima, Wataru Suda, Mitsuo Sakamoto, Takao Iino, Satoko Noda, Yuichi Hongoh, Masahira Hattori, Moriya Ohkuma

    Microbes and Environments   30 ( 1 )   44 - 50   2015

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    Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093(T) and Geofilum rubicundum JCM 15548(T). In addition to these and previously reported 'Candidatus Azobacteroides pseudotrichonymphae' and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.

    DOI： 10.1264/jsme2.ME14142

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  • The nitrogen cycle in cryoconites: naturally occurring nitrification-denitrification granules on a glacier Reviewed

    Takahiro Segawa, Satoshi Ishii, Nobuhito Ohte, Ayumi Akiyoshi, Akinori Yamada, Fumito Maruyama, Zhongqin Li, Yuichi Hongoh, Nozomu Takeuchi

    ENVIRONMENTAL MICROBIOLOGY   16 ( 10 )   3250 - 3262   2014.10

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    DOI： 10.1111/1462-2920.12543

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  • Reply to comment on "Origin of methane in serpentinite-hosted hydrothermal systems: The CH4-H-2-H2O hydrogen isotope systematics of the Hakuba Happo hot spring" by Suda et al. [Earth Planet. Sci. Lett. 386 (2014) 112-125] Reviewed

    Konomi Suda, Yuichiro Ueno, Motoko Yoshizaki, Hitomi Nakamura, Ken Kurokawa, Eri Nishiyama, Koji Yoshino, Yuichi Hongoh, Kenichi Kawachi, Soichi Omori, Keita Yamada, Naohiro Yoshida, Shigenori Maruyama

    EARTH AND PLANETARY SCIENCE LETTERS   401   376 - 377   2014.9

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    DOI： 10.1016/j.epsl.2014.06.005

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  • Who digests the lignocellulose? Reviewed

    Yuichi Hongoh

    ENVIRONMENTAL MICROBIOLOGY   16 ( 9 )   2644 - 2645   2014.9

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    DOI： 10.1111/1462-2920.12449

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  • Aphid gene of bacterial origin encodes a protein transported to an obligate endosymbiont Reviewed

    Atsushi Nakabachi, Kinji Ishida, Yuichi Hongoh, Moriya Ohkuma, Shin-ya Miyagishima

    CURRENT BIOLOGY   24 ( 14 )   R640 - R641   2014.7

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    DOI： 10.1016/j.cub.2014.06.038

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  • Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod. Reviewed

    Kudo T, Kawauchi A, Nakahara T, Zhang X, Taniyama S, Takatani T, Arakawa O, Oshima K, Suda W, Kitamura K, Iida T, Iino T, Inoue T, Hongoh Y, Hattori M, Ohkuma M

    Genome announcements   2 ( 3 )   2014.6

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    DOI： 10.1128/genomeA.00623-14

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  • Draft Genome Sequences of Geomicrobium sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples. Reviewed

    Kudo T, Nakahara T, Zhang X, Taniyama S, Arakawa O, Murase S, Nakata H, Oshima K, Suda W, Kitamura K, Iida T, Oshida Y, Inoue T, Hongoh Y, Hattori M, Ohkuma M

    Genome announcements   2 ( 3 )   2014.6

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    DOI： 10.1128/genomeA.00622-14

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  • Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut Reviewed

    Tomoyuki Sato, Hirokazu Kuwahara, Kazuma Fujita, Satoko Noda, Kumiko Kihara, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh

    The ISME JOURNAL   8 ( 5 )   1008 - 1019   2014.5

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    DOI： 10.1038/ismej.2013.222

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  • Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms. Reviewed

    Kudo T, Kidera A, Kida M, Kawauchi A, Shimizu R, Nakahara T, Zhang X, Yamada A, Amano M, Hamada Y, Taniyama S, Arakawa O, Yoshida A, Oshima K, Suda W, Kuwahara H, Nogi Y, Kitamura K, Yuki M, Iida T, Moriya S, Inoue T, Hongoh Y, Hattori M, Ohkuma M

    Genome announcements   2 ( 2 )   2014.4

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    DOI： 10.1128/genomeA.00280-14

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  • Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047. Reviewed

    Kudo T, Sakamoto K, Akinaga M, Kawauchi A, Nakahara T, Zhang X, Yamada A, Oshima K, Suda W, Kuwahara H, Nakamura N, Nogi Y, Kitamura K, Yuki M, Iida T, Moriya S, Inoue T, Hongoh Y, Hattori M, Ohkuma M

    Genome announcements   2 ( 2 )   2014.3

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    DOI： 10.1128/genomeA.00211-14

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  • Molecular diversity of endosymbiotic Nephroselmis (Nephroselmidophyceae) in Hatena arenicola (Katablepharidophycota) Reviewed

    Haruyo Yamaguchi, Takeshi Nakayama, Yuichi Hongoh, Masanobu Kawachi, Isao Inouye

    JOURNAL OF PLANT RESEARCH   127 ( 2 )   241 - 247   2014.3

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    DOI： 10.1007/s10265-013-0591-1

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  • A rickettsial endosymbiont inhabiting the cytoplasm of Volvox carteri (Volvocales, Chlorophyceae) Reviewed

    Kaoru Kawafune, Yuichi Hongoh, Hisayoshi Nozaki

    PHYCOLOGIA   53 ( 1 )   95 - 99   2014.1

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    DOI： 10.2216/13-193.1

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  • Origin of methane in serpentinite-hosted hydrothermal systems: The CH4-H-2-H2O hydrogen isotope systematics of the Hakuba Happo hot spring Reviewed

    Konomi Suda, Yuichiro Ueno, Motoko Yoshizaki, Hitomi Nakamura, Ken Kurokawa, Eri Nishiyama, Koji Yoshino, Yuichi Hongoh, Kenichi Kawachi, Soichi Omori, Keita Yamada, Naohiro Yoshida, Shigenori Maruyama

    EARTH AND PLANETARY SCIENCE LETTERS   386   112 - 125   2014.1

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    DOI： 10.1016/j.epsl.2013.11.001

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  • Horizontal Gene Acquisition of Liberibacter Plant Pathogens from a Bacteriome-Confined Endosymbiont of Their Psyllid Vector Reviewed

    Atsushi Nakabachi, Naruo Nikoh, Kenshiro Oshima, Hiromitsu Inoue, Moriya Ohkuma, Yuichi Hongoh, Shin-ya Miyagishima, Masahira Hattori, Takema Fukatsu

    PLOS ONE   8 ( 12 )   e82612   2013.12

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    DOI： 10.1371/journal.pone.0082612

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  • Native architecture of the centriole proximal region reveals features underlying its 9-fold radial symmetry Reviewed

    Paul Guichard, Virginie Hachet, Norbert Majubu, Aitana Neves, Davide Demurtas, Natacha Olieric, Isabelle Fluckiger, Akinori Yamada, Kumiko Kihara, Yuichiro Nishida, Shigeharu Moriya, Michel O. Steinmetz, Yuichi Hongoh, Pierre Gönczy

    Current Biology   23 ( 17 )   1620 - 1628   2013.9

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    DOI： 10.1016/j.cub.2013.06.061

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  • Defensive Bacteriome Symbiont with a Drastically Reduced Genome Reviewed

    Atsushi Nakabachi, Reiko Ueoka, Kenshiro Oshima, Roberta Teta, Alfonso Mangoni, Mihaela Gurgui, Neil J. Oldham, Gerhild van Echten-Deckert, Keiko Okamura, Kohei Yamamoto, Hiromitsu Inoue, Moriya Ohkuma, Yuichi Hongoh, Shin-ya Miyagishima, Masahira Hattori, Joern Piel, Takema Fukatsu

    CURRENT BIOLOGY   23 ( 15 )   1478 - 1484   2013.8

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    DOI： 10.1016/j.cub.2013.06.027

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  • Comprehensive phylogenetic diversity of [FeFe]-hydrogenase genes in termite gut microbiota Reviewed

    Hao Zheng, Dylan Bodington, Chong Zhang, Kazuhiko Miyanaga, Yasunori Tanji, Yuichi Hongoh, Xin-Hui Xing

    Microbes and Environments   28 ( 4 )   491 - 494   2013

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    DOI： 10.1264/jsme2.ME13082

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  • Sporomusa intestinalis sp nov., a homoacetogenic bacterium isolated from the gut of a higher termite, Termes comis (Termitinae) Reviewed

    Satoshi Hattori, Yuichi Hongoh, Takashi Itoh, Pinsurang Deevong, Savitr Trakulnaleamsai, Napavarn Noparatnaraporn, Toshiaki Kudo, Moriya Ohkuma

    JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY   59 ( 4 )   321 - 324   2013

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    DOI： 10.2323/jgam.59.321

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  • Functional genome analysis of unculturable microbial species as genetic resources

    Hongoh Yuichi

    Nyusankin Kenkyu Shudan Kaishi   24 ( 3 )   167 - 173   2013

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    Language：Japanese   Publisher：Japan Society for Lactic Acid Bacteria  

    The majority of microorganisms on Earth are unculturable and their functions are almost unknown. Whereas metagenomics has enabled us to comprehensively capture genome fragments in an unculturable microbial community, the functions of individual members of the microbiota remain unidentified. Recently, an innovative technology, whole genome amplification, has emerged, and now one can obtain the complete genome of an uncultured bacterial species from a small number of cells. Furthermore, even from a single bacterial cell, one can reconstruct a draft genome by single cell genomics. In this review, I introduce the methodology to analyze the genome of uncultured microbes, using termite gut bacterial community as an example. I also outline the current status of single cell genomics and describe perspectives for exploiting unculturable microbes as genetic resources.

    DOI： 10.4109/jslab.24.167

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  • Molecular Identification of Rickettsial Endosymbionts in the Non-Phagotrophic Volvocalean Green Algae Reviewed

    Kaoru Kawafune, Yuichi Hongoh, Takashi Hamaji, Hisayoshi Nozaki

    PLOS ONE   7 ( 2 )   e31749   2012.2

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    DOI： 10.1371/journal.pone.0031749

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  • Whole-genome sequencing of unculturable bacterium using whole-genomeamplification. Reviewed

    Hongoh, Y, Toyoda, A

    Methods Mol Biol.   733   25 - 33   2011

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    国立遺伝学研究所以外の共著者あり

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  • Functional analysis of uncultured bacterial species by acquiring their complete genome sequences

    Hongoh Yuichi

    Soil Microorganisms   64 ( 2 )   77 - 80   2010

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    DOI： 10.18946/jssm.64.2_77

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    Other Link： http://agriknowledge.affrc.go.jp/RN/2010800101

  • Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites Reviewed

    Satoko Noda, Yuichi Hongoh, Tomoyuki Sato, Moriya Ohkuma

    BMC EVOLUTIONARY BIOLOGY   9   e158   2009.7

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    DOI： 10.1186/1471-2148-9-158

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  • 動物と窒素固定細菌の共生は成立するか? : シロアリ腸内での共進化・共生機構からみえてきたもの

    大熊 盛也, 本郷 裕一

    化学と生物   47 ( 5 )   307 - 309   2009.5

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    DOI： 10.1271/kagakutoseibutsu.47.307

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    Other Link： https://jlc.jst.go.jp/DN/JALC/00331091791?from=CiNii

  • Candidatus Desulfovibrio trichonymphae, a novel intracellular symbiont of the flagellate Trichonympha agilis in termite gut Reviewed

    Tomoyuki Sato, Yuichi Hongoh, Satoko Noda, Satoshi Hattori, Sadaharu Ui, Moriya Ohkuma

    ENVIRONMENTAL MICROBIOLOGY   11 ( 4 )   1007 - 1015   2009.4

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    DOI： 10.1111/j.1462-2920.2008.01827.x

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  • Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and the cockroach Cryptocercus Reviewed

    Moriya Ohkuma, Satoko Noda, Yuichi Hongoh, Christine A. Nalepa, Tetsushi Inoue

    PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES   276 ( 1655 )   239 - 245   2009.1

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    DOI： 10.1098/rspb.2008.1094

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  • ゲノムから解き明かす難培養性細菌の機能 : 数百細胞からの未培養細菌のゲノム完全長の取得

    本郷 裕一, 大熊 盛也

    化学と生物   46 ( 11 )   742 - 743   2008.11

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    DOI： 10.1271/kagakutoseibutsu.46.742

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  • Genome of an Endosymbiont Coupling N(2) Fixation to Cellulolysis Within Protist Cells in Termite Gut Reviewed

    Yuichi Hongoh, Vineet K. Sharma, Tulika Prakash, Satoko Noda, Hidehiro Toh, Todd D. Taylor, Toshiaki Kudo, Yoshiyuki Sakaki, Atsushi Toyoda, Masahira Hattori, Moriya Ohkuma

    SCIENCE   322 ( 5904 )   1108 - 1109   2008.11

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    DOI： 10.1126/science.1165578

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  • Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell Reviewed

    Yuichi Hongoh, Vineet K. Sharma, Tulika Prakash, Satoko Noda, Todd D. Taylor, Toshiaki Kudo, Yoshiyuki Sakaki, Atsushi Toyoda, Masahira Hattori, Moriya Ohkuma

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   105 ( 14 )   5555 - 5560   2008.4

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    DOI： 10.1073/pnas.0801389105

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  • Identification of endosymbiotic methanogen and ectosymbiotic spirochetes of gut protists of the termite Coptotermes formosanus Reviewed

    Jun-Ichi Inoue, Satoko Noda, Yuichi Hongoh, Sadaharu Ui, Moriya Ohkuma

    MICROBES AND ENVIRONMENTS   23 ( 1 )   94 - 97   2008

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    DOI： 10.1264/jsme2.23.94

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  • Candidatus Symbiothrix dinenymphae: bristle-like Bacteroidales ectosymbionts of termite gut protists Reviewed

    Yuichi Hongoh, Tomoyuki Sato, Satoko Noda, Sadaharu Ui, Toshiaki Kudo, Moriya Ohkuma

    ENVIRONMENTAL MICROBIOLOGY   9 ( 10 )   2631 - 2635   2007.10

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    DOI： 10.1111/j.1462-2920.2007.01365.x

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  • The motility symbiont of the termite gut flagellate Caduceia versatilis is a member of the "Synergistes" group Reviewed

    Yuichi Hongoh, Tomoyuki Sato, Michael F. Dolan, Satoko Noda, Sadaharu Ui, Toshiaki Kudo, Moriya Ohkuma

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY   73 ( 19 )   6270 - 6276   2007.10

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    DOI： 10.1128/AEM.00750-07

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  • Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites Reviewed

    A. Yamada, T. Inoue, S. Noda, Y. Hongoh, M. Ohkuma

    MOLECULAR ECOLOGY   16 ( 18 )   3768 - 3777   2007.9

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    DOI： 10.1111/j.1365-294X.2007.03326.x

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  • The candidate phylum 'Termite Group 1' of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists Reviewed

    Moriya Ohkuma, Tomoyuki Sato, Satoko Noda, Sadaharu Ui, Toshiaki Kudo, Yuichi Hongoh

    FEMS MICROBIOLOGY ECOLOGY   60 ( 3 )   467 - 476   2007.6

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    DOI： 10.1111/j.1574-6941.2007.00311.x

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  • Cospeciation in the triplex symbiosis of termite gut protists (Pseudotrichonympha spp.), their hosts, and their bacterial endosymbionts Reviewed

    S. Noda, O. Kitade, T. Inoue, M. Kawai, M. Kanuka, K. Hiroshima, Y. Hongoh, R. Constantino, V. Uys, J. Zhong, T. Kudo, M. Ohkuma

    Molecular Ecology   16 ( 6 )   1257 - 1266   2007.3

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    DOI： 10.1111/j.1365-294X.2006.03219.x

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  • Phylogenetic diversity, localization, and cell morphologies of members of the candidate phylum TG3 and a subphylum in the phylum Fibrobacteres, recently discovered bacterial groups dominant in termite guts Reviewed

    Yuichi Hongoh, Pinsurang Deevong, Satoshi Hattori, Tetsushi Inoue, Satoko Noda, Napavarn Noparatnaraporn, Toshiaki Kudo, Moriya Ohkuma

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY   72 ( 10 )   6780 - 6788   2006.10

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    DOI： 10.1128/AEM.00891-06

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  • Intracolony variation of bacterial gut microbiota among castes and ages in the fungus-growing termite Macrotermes gilvus Reviewed

    Y Hongoh, L Ekpornprasit, T Inoue, S Moriya, S Trakulnaleamsai, M Ohkuma, N Noparatnaraporn, T Kudo

    MOLECULAR ECOLOGY   15 ( 2 )   505 - 516   2006.2

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    DOI： 10.1111/j.1365-294X.2005.02795.x

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  • Effect of Temporal Sample Preservation on the Molecular Study of a Complex Microbial Community in the Gut of the Termite Microcerotermes sp Reviewed

    Pinsurang Deevong, Yuichi Hongoh, Tetsushi Inoue, Savitr Trakulnaleamsai, Toshiaki Kudo, Napavarn Noparatnaraporn, Moriya Ohkuma

    Microbes and Environments   21 ( 2 )   78 - 85   2006

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    DOI： 10.1264/jsme2.21.78

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  • Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host Reviewed

    Y Hongoh, P Deevong, T Inoue, S Moriya, S Trakulnaleamsai, M Ohkuma, C Vongkaluang, N Noparatnaraporn, T Kudol

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY   71 ( 11 )   6590 - 6599   2005.11

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    DOI： 10.1128/AEM.71.11.6590-6599.2005

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  • Spatial distribution of bacterial phylotypes in the gut of the termite Reticulitermes speratus and the bacterial community colonizing the gut epithelium Reviewed

    H Nakajima, Y Hongoh, R Usami, T Kudo, M Ohkuma

    FEMS MICROBIOLOGY ECOLOGY   54 ( 2 )   247 - 255   2005.10

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    DOI： 10.1016/j.femsec.2005.03.010

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  • Comparison of bacterial communities in the alkaline gut segment among various species of higher termites Reviewed

    T Thongaram, Y Hongoh, S Kosono, M Ohkuma, S Trakulnaleamsai, N Noparatnaraporn, T Kudo

    EXTREMOPHILES   9 ( 3 )   229 - 238   2005.6

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    DOI： 10.1007/s00792-005-0440-9

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  • Plasticity and specificity of termite nest structure (Isoptera) Reviewed

    T Inoue, Y Hongoh, C Klangkaew, Y Takematsu, C Vongkaluang, N Noparatnaraporn, M Ohkuma, T Kudo

    SOCIOBIOLOGY   45 ( 3 )   671 - 678   2005

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  • Phylogenetic diversity of bacterial symbionts in the guts of wood-feeding termites (in Thai) Reviewed

    S Trakulnaleamsai, Y Hongoh, P Deevong, N Noparatnaraporn

    PROCEEDINGS OF 42ND KASETSART UNIVERSITY ANNUAL CONFERENCE   35 - 42   2004

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  • Erratum to molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae) (vol 44, pg 231, 2003) Reviewed

    Y Hongoh, M Ohkuma, T Kudo

    FEMS MICROBIOLOGY ECOLOGY   45 ( 3 )   317 - 317   2003.8

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    DOI： 10.1016/S0168-6496(03)00026-6

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  • Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae) Reviewed

    Y Hongoh, M Ohkuma, T Kudo

    FEMS MICROBIOLOGY ECOLOGY   44 ( 2 )   231 - 242   2003.5

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    DOI： 10.1016/S0168-6496(03)00026-6

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  • Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment Reviewed

    Y Hongoh, H Yuzawa, M Ohkuma, T Kudo

    FEMS MICROBIOLOGY LETTERS   221 ( 2 )   299 - 304   2003.4

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    DOI： 10.1016/S0378-1097(03)00218-0

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  • Phylogenetic position and in situ identification of ectosymbiotic spirochetes on protists in the termite gut Reviewed

    S Noda, M Ohkuma, A Yamada, Y Hongoh, T Kudo

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY   69 ( 1 )   625 - 633   2003.1

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    DOI： 10.1128/AEM.69.1.625-633.2003

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  • Gut of Higher Termites as a Niche for Alkaliphiles as Shown by Culture-Based and Culture-Independent Studies Reviewed

    Taksawan Thongaram, Saori Kosono, Moriya Ohkuma, Yuichi Hongoh, Makio Kitada, Toko Yoshinaka, Savitr Trakulnaleamsai, Napavarn Noparatnaraporn, Toshiaki Kudo

    Microbes and Environments   18 ( 3 )   152 - 159   2003

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    DOI： 10.1264/jsme2.18.152

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  • Diverse bacteria related to the bacteroides subgroup of the CFB phylum within the gut symbiotic communities of various termites Reviewed

    M Ohkuma, S Noda, Y Hongoh, T Kudo

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   66 ( 1 )   78 - 84   2002.1

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    DOI： 10.1271/bbb.66.78

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  • Evolutionary studies on uricases of fungal endosymbionts of aphids and planthoppers Reviewed

    Y Hongoh, H Ishikawa

    JOURNAL OF MOLECULAR EVOLUTION   51 ( 3 )   265 - 277   2000.9

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  • Cloning, sequence analysis and expression in Escherichia coli of the gene encoding a uricase from the yeast-like symbiont of the brown planthopper, Nilaparvata lugens Reviewed

    Y Hongoh, T Sasaki, H Ishikawa

    INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY   30 ( 2 )   173 - 182   2000.2

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    DOI： 10.1016/S0965-1748(99)00116-2

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  • Uric acid as a nitrogen resource for the brown planthopper, Nilaparvata lugens: Studies with synthetic diets and aposymbiotic insects Reviewed

    Y Hongoh, H Ishikawa

    ZOOLOGICAL SCIENCE   14 ( 4 )   581 - 586   1997.8

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  • CHANGES OF MYCETOCYTE SYMBIOSIS IN RESPONSE TO FLYING BEHAVIOR OF ALATIFORM APHID (ACYRTHOSIPHON-PISUM) Reviewed

    Y HONGOH, H ISHIKAWA

    ZOOLOGICAL SCIENCE   11 ( 5 )   731 - 735   1994.10

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MISC

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Presentations

  • Identification and characterization of ‘softenin’, a candidate protein softening the catch connective tissue International conference

    Masaki Tamori, Yasuhiro Takehana, Akira Yamada, Atsuhiro Sakuma, Shunsuke Taki, Katsura Igai, Masato Nikaido, Kohei Hamamoto, Yuichi Hongoh

    The 17th International Echinoderm Conference  2024.7 

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  • 氷河微生物群集「クリオコナイト」の形成過程をメタゲノムデータから解き明かす

    村上匠, 瀬川高弘, 森宙史, 本郷裕一, 竹内望

    第18回日本ゲノム微生物学会年会  2024.3 

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    Event date： 2024.3

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  • Genomics of uncultivable bacteria deciphers multilayered symbiotic system in the termite gut International conference

    Yuichi Hongoh

    2018 World Life Science Conference  2018.10 

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  • Multi-layered symbiotic system in the termite gut" Invited International conference

    Yuichi Hongoh

    The 46th Naito Conference  2018.10 

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  • Genomics to decipher the multi-layered symbiotic system in the termite gut Invited International conference

    Yuichi Hongoh

    TokyoTech International Symposium: The Nucleic Acid World - Interfaces between Biology and Chemistry  2014.1 

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  • Evolution of nitrogen-fixing endosymbionts of termite-gut protists Invited International conference

    Yuichi Hongoh

    International Union for the Study of Social Insects (IUSSI2014): Ecology and evolution of digestive symbioses intermites  2014.7 

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  • Evolution and functions of multilayered symbiosis in termite guts Invited International conference

    Yuichi Hongoh

    International Symposium: Matryoshka-type Evolution of Eukaryotic Cells  2013.7 

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  • Nitrogen-fixing symbionts of cellulolytic protists in termite guts Invited International conference

    Yuichi Hongoh

    18th International Congress on Nitrogen Fixation (ICNF18)  2013.10 

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  • Single-cell genomics deciphers the termite gut ecosystem Invited International conference

    Yuichi Hongoh

    第91回日本細菌学会総会国際シンポジウム：Frontiers in Bacterial Genomics  2018.3 

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  • Genomics of uncultivable bacteria deciphers multilayered symbiotic system in the termite gut Invited International conference

    Yuichi Hongoh

    Max Planck Institute（Marburg) Workshop: International Workshop on Insect Gut Microbiology  2018.8 

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  • Diversity and functions of the ecto- and endosymbionts of cellulolytic protists in the gut of termites Invited International conference

    Yuichi Hongoh

    Annual Conference 2015 of the Association for General and Applied Microbiology (VAAM2015)  2015.3 

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  • Single cell genomics deciphers the complex symbiotic system in the termite gut microbiota Invited International conference

    Yuichi Hongoh

    The 11th International Workshop on Advanced Genomics (IWAG11)  2015.5 

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  • Genome analysis of symbiotic microorganisms in termite guts Invited International conference

    Yuichi Hongoh

    International Symposium on Digestive systems in Termites -from Fundamentals to Applications to Biomass Utilization-  2011.10 

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  • Evolution and functions of the multilayered symbiosis in termite guts Invited International conference

    Yuichi Hongoh

    14th International Symposium on Microbial Ecology (ISME14)  2012.8 

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  • Genome analysis of unculturable microbial symbionts in the termite gut Invited International conference

    Yuichi Hongoh

    International Union of Microbiological Societies (IUMS) 2011Congress  2011.9 

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  • Genomics of single bacterial species in termite gut Invited International conference

    Yuichi Hongoh

    109th General Meeting of American Society for Microbiology (ASM)  2009.5 

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  • Complete genome sequences from uncultivable bacterial species in a complex microbial community Invited International conference

    Yuichi Hongoh

    Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB)  2010.3 

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  • Termites, protists, and bacteria: a multi-layered symbiosis for thriving on lignocellulose Invited International conference

    Yuichi Hongoh

    国際生物学賞記念シンポジウム: Biology of Symbiosis  2010.12 

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  • Genomes of symbiotic bacterial species in termite gut Invited International conference

    Yuichi Hongoh

    Okazaki Biology Conference (OBC-7)  2010.1 

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  • Diversity and functional analysis of uncultivable microorganisms in environments Invited International conference

    Yuichi Hongoh

    2nd Regional Conference on Biotechnology: R & D on Food Biotechnology  2010.2 

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  • ゲノムから読み解くシロアリ腸内多重共生システム Invited

    本郷裕一

    東京工業大学生命理工学院・東京医科歯科大学難治疾患研究所 教員交流シンポジウム  2024.9 

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  • Diverse and complex cellular symbioses between cellulolytic protists and prokaryotes in the termite gut Invited International conference

    Yuichi Hongoh

    International Congress of Entomology 2024  2024.8 

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  • 様々な時空間条件から検証する氷河シアノバクテリアの多様性

    村上匠, 瀬川高弘, 大沼友貴彦, 河合繁, 広瀬侑, 竹内望, 本郷裕一

    日本微生物生態学会第37回大会  2024.10 

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  • メタゲノムデータから紐解く氷河微生物生態系のダイナミクス

    村上匠, 瀬川高弘, 大沼友貴彦, 薄羽珠ノ介, 河合繁, 広瀬侑, 竹内望, 本郷裕一

    メタゲノムデータから紐解く氷河微生物生態系のダイナミクス  2025.3 

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Awards

  • 日本ゲノム微生物学会奨励賞

    2009  

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  • The Japan Bioscience, Biotechnology and Agrochemistry Society Award for the Encouragement of Young Scientists

    2009  

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  • 日本農学進歩賞

    2009  

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    Country：Japan

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  • 日本農芸化学会奨励賞

    2009  

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    Country：Japan

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  • The young scientist award from the Society of Genome Microbiolgy, Japan

    2009  

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  • 東工大挑戦的研究賞

    2009  

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    Country：Japan

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  • 優秀ポスター賞（日本微生物生態学会）

    2008  

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    Country：Japan

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  • The Excellent Poster Award (IWAG-7, Tokyo)

    2007  

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  • カセサート大学優秀研究賞

    2005  

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  • Best Poster Award (ICCC-10, Tsukuba)

    2004  

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Research Projects

  • 無脊椎動物腸内原生生物の系統的・機能的多様性と共生進化過程の解明

    Grant number：24KK0142  2024.9 - 2029.3

    日本学術振興会  科学研究費助成事業  国際共同研究加速基金(海外連携研究)

    本郷 裕一

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    Grant amount：\20800000 （ Direct Cost: \16000000 、 Indirect Cost：\4800000 ）

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  • シロアリ腸内原生生物の比較ゲノム解析による多種共存機構の解明

    Grant number：23K27244  2023.4 - 2026.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    本郷 裕一

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    Grant amount：\18850000 （ Direct Cost: \14500000 、 Indirect Cost：\4350000 ）

    本研究課題は、生態系における役割（生態的地位、ニッチ）が類似すると見られる生物種同士の共存機構、つまり多種共存機構の分子的基盤を明らかにすることを大きな目的としている。例えばシロアリにおいて、その高効率な木質消化を腸内原生生物叢が担うことはよく知られているが、そこでは、同属の木質分解性原生生物が10-20種類も一つの腸内に共存する場合がある。なぜ系統的に近縁かつ同様に木質を餌としていると見られる原生生物の多種がそのように共存できるのか、未知である。また、そもそもシロアリ腸内原生生物は人工培養不能であるため、これまで木質消化を含むその詳細な生理・生態は不明であった。そこで、シロアリ腸内共生原生生物のゲノム解読による基本代謝系等の解明も目的としている。
    2023年度は、まず材料とする原生生物属について、1細胞ずつ顕微鏡下で採取し、1細胞ゲノム・転写産物配列取得のための処理を、数細胞について行なった。1細胞解析はサンプルごとの品質差が大きいため、予備的は配列取得を行い、良好なサンプルの選抜と取得条件の最適化を実施してきた（継続中）。また、これらの配列には、原生生物に絶対あるいは日和見共生する多様な細菌由来の配列が混入してくるため、同原生生物の共生細菌ゲノム配列も複数種について、取得中である（いくつかについては事前に取得済み）。これらの共生細菌の相違が原生生物の機能の相違に相関している可能性も高いため、これも重要な解析である。

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  • 単細胞真核生物を題材とした真核生物－原核生物間水平伝播遺伝子の進化過程解明

    Grant number：22K19342  2022.6 - 2025.3

    日本学術振興会  科学研究費助成事業  挑戦的研究(萌芽)

    本郷 裕一

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    Grant amount：\6500000 （ Direct Cost: \5000000 、 Indirect Cost：\1500000 ）

    本研究課題は、単細胞真核生物（原生生物）と原核生物（細菌・アーキア）間で水平伝播した遺伝子の進化過程解明を目的としている。具体的には、シロアリ腸内原生生物の核ゲノム配列と、同原生生物に特異的に細胞内共生する原核生物のゲノム配列を取得し、互いに水平伝播した遺伝子/ゲノム領域を特定し、水平伝播後の進化過程を推定するものである。シロアリ腸内原生生物には宿主種に特異的かつ多様な系統群の細菌が細胞内共生しており、こうした研究課題の材料としては最適と考えている。
    2023年度は、2022年度に引き続き、多様な細菌系統群の複数種の原生生物細胞内共生細菌ゲノム配列を再構築した。特に本課題で焦点を当てている細菌系統群の一つであるクロストリディア綱の複数種の完全長ゲノム配列取得に成功し、そのゲノム中に多数の真核生物由来と考えられる遺伝子が存在することを見出した。これら遺伝子の分子系統解析を実施したところ、半数ほどは宿主原生生物種あるいはその近縁系統群の遺伝子に最も近縁であり、宿主原生生物から水平伝播で獲得した可能性が極めて高い。また、それら共生細菌種だけではなく、データベース上にある近縁な細菌ゲノム配列を解析しても同様の結果であった。つまり、この細菌系統群の進化戦略として、宿主真核生物の遺伝子を取得して宿主細胞の防御機構等を操作する可能性がある。ただ、今のところ、宿主原生生物からの遺伝子水平伝播過程が辿れるほどに原型を留めた状態での遺伝子は見つけられていない。本成果は、微生物生態学分野のトップ雑誌であるThe ISME Journalに2023年11月に掲載された。今後は、さらに宿主原生生物ドラフトゲノム配列の解析を進め、比較作業を行っていく。

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  • 未培養原生生物1細胞ゲノム解析系の確立とシロアリ腸内木質分解性原生生物の機能解明

    Grant number：20H02897  2020.4 - 2023.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    本郷 裕一, 山田 明徳, 瀬川 高弘

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    Grant amount：\17810000 （ Direct Cost: \13700000 、 Indirect Cost：\4110000 ）

    本研究課題の目的は、未培養原生生物（単細胞真核生物）の1細胞ゲノム解析手法の確立である。環境中には多様な原生生物が生息するが、未培養種も多く、それらの生理・生態は未知である。本研究ではシロアリ腸内原生生物群集を材料とするが、それらはシロアリの餌である木材の分解発酵の主要部分を担うと考えられているものの、純粋培養成功例は無く、詳細な機能は不明である。ゲノム解析を行うにしても、原生生物細胞ごとに系統が異なる可能性が高いため、単一細胞からのゲノムと（ゲノム解析補助のための）網羅的転写産物を同時に解析する必要がある。その技術的困難により、原生生物1細胞からの高完成度な新規ゲノム解読例は無く、1細胞転写産物解析も容易ではない。
    2020年度（2021年度繰越含む）には、シロアリ原生生物種1細胞を物理的に単離し、同一細胞からの核DNAの全ゲノム増幅と細胞質中mRNAの逆転写及びcDNAのPCR増幅を行い、ゲノム配列再構築と遺伝子領域同定を行った。総塩基長は約150 Mb（推定完成度7割）、遺伝子数約2.8万で、100以上の糖質分解酵素遺伝子を含んでいた。これまで未知であったアミノ酸やビタミン類の合成経路なども判明しつつある。現段階で高品質の配列が取得できているが、予想した以上に異種生物の非特異的な核酸混入が見られ、その識別方法が大きな課題である。
    また、原生生物には細胞内・表面に特定の細菌種が共生することが多い。これらは非特異的DNA混入とは異なり、必ず混入するものなので、あらかじめそれらのゲノム配列を取得しておくことが望ましい。そこで、同原生生物種の核を除いた部分から全ゲノム増幅を行い、まず細菌16S rRNA配列に基づく群集構造解析を行った。その結果12種類の共生細菌配列を取得した。この情報は、今後のゲノム配列解析の基盤となる。

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  • 異種細菌種間付着共生系の実態解明と生物進化へのインパクトの検証

    Grant number：20H05584  2020.4 - 2022.3

    日本学術振興会  科学研究費助成事業  新学術領域研究(研究領域提案型)

    本郷 裕一

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    Grant amount：\8320000 （ Direct Cost: \6400000 、 Indirect Cost：\1920000 ）

    本研究課題の目的は、異種細菌間での種特異的な付着型相利共生系の実態をゲノム情報等を基に解明し、細菌間付着共生がゲノム進化へ与える影響を検証することである。特に、真核細胞の起源である「原核生物間での細胞内共生」の初期段階としての特異的付着共生の可能性を考察する。細菌間の種特異的な付着共生は極めて稀な現象だが、シロアリ腸内原生生物細胞表面において、未培養細菌系統群とスピロヘータあるいは硫酸還元菌との付着・近接共生系が観察されている。こうした共生細菌群は未培養（おそらく人工培養不能）であるが、本研究では1細胞ゲノム解析等の分子生態学的手法を駆使することで、これら共生細菌の機能を予測し、細菌間相互作用の解明を試みる。
    2020年度（2021年度への繰越し含む）は、硫酸還元菌と近接共生する未培養アルファプロテオバクテリアについて両者のゲノム配列を取得し、代謝系を予測した。その結果、前者は多くの硫酸還元菌同様に水素を硫酸あるいはフマル酸で酸化することでエネルギーを得ていると予測され、後者はリケッチア同様にATPや核酸、アミノ酸などを宿主から奪取する寄生者であることが予測された。しかしながら、なぜ両者が特異な近接共生構造を取るのかは、まだ不明である。
    上記の硫酸還元菌とアルファプロテオバクテリアとの近接共生系に加えて、アルファプロテオバクテリアとスピロヘータの特異的付着共生系について、その共生頻度や局在パターンの情報も取得中で、電子顕微鏡観察による局在の詳細な観察も試みている。

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  • Genome analysis of ancient samples preserved in Antarctica

    Grant number：18H04139  2018.4 - 2021.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

    Motoyama Hideaki

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    Grant amount：\43550000 （ Direct Cost: \33500000 、 Indirect Cost：\10050000 ）

    Ice cores provide direct genetic information on old ages, but the amount of microorganisms in ice cores is low and the DNA is fragmented. A method for detecting low amounts of DNA in ice cores has been developed, and microbiological DNA analysis of Antarctic Dome Fuji ice core samples was carried out using the established method. The results showed that there were differences in the taxonomic compositions and origins of bacteria detected between glacial and interglacial periods, and that the microorganisms in Antarctic ice cores can be used as paleoenvironmental indicators. Ancient DNA analysis of mummified Weddell seal remains collected in Antarctica was also conducted to elucidate how Antarctic animal population dynamics have been affected by environmental change. The result showed that Weddell seals have a complex population dynamic history of genetic differentiation and interbreeding between populations.

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  • Posibilty of sympatric speciation of protists by cellular symbiosis

    Grant number：17K19423  2017.6 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Exploratory)

    Hongoh Yuichi, Fukuda Shinji, Sakai Miho

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    Grant amount：\6500000 （ Direct Cost: \5000000 、 Indirect Cost：\1500000 ）

    This study aimed to test my hypothesis that single-celled eukaryotes (protists) can speciate by acquiring symbiotic prokaryotes. For this purpose, I selected a termite-gut protist genus as the material to be examined. Although the protist genus has been regarded monospecific, I demonstrated that it comprises two distinct species and that the two species can be discriminated by the presence or absence of endosymbiotic archaea. The genome analysis of the symbiotic archaeon indicated that the genome is very similar to its free-living relatives; the symbiosis has emerged relatively recently. Thus, this study strongly suggests that cellular symbiosis with prokaryotes can lead to speciation of a protist, though further studies are needed to prove this.

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  • An impact of evolution of the intestinal symbioses to the host insects:interdisciplinary approaches with micro-metabolomic and genomic analyses

    Grant number：17H01510  2017.4 - 2022.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

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    Grant amount：\36140000 （ Direct Cost: \27800000 、 Indirect Cost：\8340000 ）

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  • Deciphering the mechanism of acquisition and evolution of symbiotic microbes in the termite gut

    Grant number：16H04840  2016.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Hongoh Yuichi, Igai Katsura, Morikawa Takahiro, Takahashi Yudai

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    Grant amount：\17550000 （ Direct Cost: \13500000 、 Indirect Cost：\4050000 ）

    This study aimed to decipher how termites have acquired their gut microbes that are responsible for digesting dead plant matter (lignocellulose). For this purpose, I focused on one clade of higher termites that has relatively recently re-acquired protists as a dominant component of the gut microbiota after the loss of the original cellulolytic protist assemblages. As a result, my research team revealed that the novel protists are ubiquitous in diverse termite lineages but have become dominant only in the specific termite clade. In addition, we found that the protist cytoplasm is filled with wood particles, and the gut compartment containing the protists showed significant cellulolytic activities. Thus, in this study, we obtained fundamental information on this new group of protists for future studies.

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  • Adaptive management model for fishery resources: practice and development of genetic population monitoring techniques

    Grant number：15KT0034  2015.7 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    YAMADA Akinori, TAKAHASHI Motomitsu, FUKUWAKA Masa-aki, TANAKA Shuichi, AOSHIMA Takashi, IKEDA Natsuki, INOUE Kazuki, ISHIKAWA Makoto, ONITSUKA Minami, OHNO Haruka, SUGIHARA Yuma, SAGARA Haruka, MORI Ryohei

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    Grant amount：\17940000 （ Direct Cost: \13800000 、 Indirect Cost：\4140000 ）

    In order to sustainably utilize fishery resources, it is essential to understand variable factors affecting them for their appropriate management. The present study aims to contribute to the development of effective management strategy by clarifying spatiotemporal dynamics of the genetic diversity and population structure of fishery resources. Mitochondrial D-loop sequences of chub mackerel (Scomber japonicus), Japanese horse mackerel (Trachurus japonicus), and Japanese sardine (Sardinops melanostictus) mainly caught in Nagasaki and Tottori were obtained and analyzed. The results indicated that genetic diversity of these fish species were extremely high all the year-round and their populations in the South China Sea, East China Sea, and Pacific Ocean apparently consisted of a single genetically-identical population. This strongly confirms the importance of internationally cooperative management of fishery resources.

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  • Effects of global environmental changes on glacier ecosystems

    Grant number：26241020  2014.4 - 2018.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

    Kohshima Shiro

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    Grant amount：\40560000 （ Direct Cost: \31200000 、 Indirect Cost：\9360000 ）

    We genetically analyzed microorganisms collected from the glaciers in various part of the world and found regional difference in species composition of bacteria and cyanobacteria in cryoconites, biogenic dark granules on the glacier that accelerate glacier melting. We could also identify symbiotic bacteria of glacier animals. We developed mathematical model simulating changes in cryoconite holes, melt holes on the glacier formed by cryoconite, to establish the mass valance model of the glacier including biological albedo reducing process.

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  • Metagenomic analysis of phages in the termite gut and potential for application in pest control

    Grant number：26650158  2014.4 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Exploratory Research

    Hongoh Yuichi

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    Grant amount：\4030000 （ Direct Cost: \3100000 、 Indirect Cost：\930000 ）

    Termites feed exclusively on dead plant matter. They play important roles in the global carbon cycle, although they are also destructive pests of wooden buildings. Their ability to digest lignocellulose is mostly attributable to the symbiotic gut microorganisms. In this study, a bacteriophage community that infects the symbiotic gut bacteria was comprehensively analyzed, and specific bacterial hosts of some phages were successfully identified.

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  • Study on novel functions of nitrogen fixation and hydrogen utilization in bacteria of the order Bacteroidales

    Grant number：26292047  2014.4 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    OHKUMA Moriya, HONGOH Yuichi, YUKI Masahiro, INOUE Jun-ichi

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    Grant amount：\16640000 （ Direct Cost: \12800000 、 Indirect Cost：\3840000 ）

    We found bacterial species in the order Bacteroidales that harbor genes for nitrogen fixation or genes homologous to archaea for hydrogen utilization in the genomes, and we detected the respective activities in their representative cultured strains. We identified an endosymbiotic spirochete species of a termite-gut cellulolytic protist species that contributes to the activities for both nitrogen fixation and hydrogen-utilizing reductive acetogenesis in the gut. Through single-cell genome sequencing, we investigated functions and symbiotic mechanisms of this endosymbiont and two ectosymbiotic Bacteroidales species attached onto cell surface of termite-gut protists.

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  • Explorations of metabolic factors involved in efficient cellulolytic systems in insects

    Grant number：26292177  2014.4 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    TOKUDA Gaku, HONGOH Yuichi, KINJO Yukihiro, KUMARA Rohitha P., NALEPA Christine A., PARK Yung Chul

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    Grant amount：\11050000 （ Direct Cost: \8500000 、 Indirect Cost：\2550000 ）

    The present study explored metabolic factors that involved in invention of efficient cellulolytic systems during evolution from wood roaches to termites. In evolution of wood roaches to lower termites, we found some overlaps of metabolic networks between endo- and intestinal symbioses, which had led to relaxed selection of some genes in endosymbionts and increased in dependence of the host insects in intestinal symbionts. In lower termites, we analyzed a genome sequence of a Japanese subterranean lower termite. Endogenous cellulase genes were duplicated in the genome, while a few of them appeared to differentiate their functions. Furthermore, we analyzed transcripts of the so-called “the mixed segment” in the gut of a higher termite, which expressed a variety of transporter genes. Among them, V-ATPases and NHE transporters were assumed to be involved in the gut alkalization, which may contribute to solubilize lignin to facilitate cellulose degradation by the intestinal bacteria.

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  • Research about environmental symbiotic system by using of advanced genome and transcriptome analysis

    Grant number：23117003  2011.4 - 2016.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Moriya Shigeharu, Ohkuma Moriya, Hongoh Yu-ichi, Kihara Kumiko

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    Grant amount：\89700000 （ Direct Cost: \69000000 、 Indirect Cost：\20700000 ）

    We obtain the results about non-cellulose type factors affect to ligno-cellulose utilization by termite symbiotic system. Also, our single cell genome analysis revealed that knowledge of genome rearrangement and metabolism of symbiotic bacteria of symbiotic protist of termite.
    We developed novel total RNAseq analysis pipeline to analyze ecological function of biofilm composing members and mediator for symbiosis between aquatic animal and dinoflagellate.
    These results show that variety factors affect to drive symbiosis depend on environmental condition.

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  • Response prediction and impact statement of glacier ecosystems on global environmental change

    Grant number：22241005  2010.4 - 2014.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

    KOHSHIMA Shiro, USHIDA Kazunari, SHIRAIWA Takayuki, YOSHIMURA Yoshitaka, TAKEUCHI Nozomu, FUJITA Koji

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    Grant amount：\47840000 （ Direct Cost: \36800000 、 Indirect Cost：\11040000 ）

    To estimate the response of glacier ecosystems to the global environmental change, we studied ecology of glacier microorganisms and albedo reducing process by microbial activities on the glaciers of various types by field studies at various part of the world. By comparing microbial flora, surface structure, albedo and environmental conditions on glaciers of various types, we could clarify relationship between glacial microbial flora and environmental condition, basic information needed to understand glacial microbial activities and how it affect glacier albedo.

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  • シロアリ腸内共生系研究のためのモデル生物の構築

    Grant number：22658016  2010 - 2012

    日本学術振興会  科学研究費助成事業  挑戦的萌芽研究

    本郷 裕一

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    Grant amount：\2610000 （ Direct Cost: \2400000 、 Indirect Cost：\210000 ）

    近年、化石燃料価格高騰による経済被害や、その消費に伴う地球温暖化ガス放出などの環境破壊が、世界的な問題となっている。その解決策の一つが、植物質由来のバイオマス燃料開発と普及である。植物は空気中のCO_2を吸収して自身の体を構成するため、それを燃焼しても、CO_2濃度は上昇したことにならない(カーボンニュートラル)。しかし、種子を除き、植物の主成分はリグノセルロースという堅固な物質であり、動物は一般にこれを消化できないし、人工的な化学分解もコストが大きい。ところがシロアリは、腸内共生微生物の働きで高効率なリグノセルロース分解を実現している。そのため、シロアリの能力をバイオ燃料開発に応用しようという試みが、世界中で行われている。
    問題は、シロアリ腸内共生微生物群が難培養性で、従来の培養を前提とした微生物学的研究がほぼ不可能ということである。そこで、網羅的なゲノム(全遺伝情報)解析や転写産物解析など、オミックスと呼ばれる手法が必要となる。そのためには、腸内共生微生物叢を単純化したモデル生物の使用が望ましいが、存在しない。
    本研究課題では、その「モデルシロアリ」作成を試みている。出発材料として、わずか種類の原生生物しか共生していないシロアリ種を用いた。まずその腸内微生物の群集構造を、培養非依存的な分子生態学的手法により解析した。その結果、わずかに異なる2系統が1つの腸内に混在していた。今後、これを1系統にすることを一試みる。

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  • シングルセル・ゲノミクスによる難培養微生物の機能解明と遺伝子資源化

    Grant number：22241046  2010 - 2012

    日本学術振興会  科学研究費助成事業  基盤研究(A)

    本郷 裕一

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    Grant amount：\33930000 （ Direct Cost: \26100000 、 Indirect Cost：\7830000 ）

    シングルセル・ゲノミクスとは、1細胞のみを用いて、ある生物種のゲノムを解読する研究分野あるいは手法である。ゲノムとは全遺伝情報、すなわち設計図であり、その生物種を用いた基礎・応用研究上、最も重要なデータの一つである。
    細菌ゲノムの解読には10億個以上の同一系統の細胞が必要だが、培養すれば容易に集められる。ゲノムDNAの配列解析に要するコストも年々低下しており、これまでに、細菌を中心に1400以上の生物種・系統のゲノムDNA配列が決定されている。
    ところが、大多数の微生物種は、実は培養法が不明である。これらはゲノム解読が不可能なのはもちろん、従来の微生物学的研究手法が適用できないので、生理・生態なども未知のままである。微生物は生態系の基盤を形成するだけではなく、人類にとっては不可欠の生物資源でもある。しかし培養不能なために、生態系には大きなブラックボックスが残り、人類が利用可能な生物資源も、ごくわずかにすぎないのである。
    そこで本研究課題では、培養を介さずに、1細胞のみでゲノム解読を可能とする手法の確立に取り組んでいる。H22年度においては、まず1細胞を環境中から単離する方法の最適化を行ってきた。いくつかの細胞単離法を試し、また購入予定装置の選定を進めてきた。クリーンルーム、マイクロマニピュレーションシステム、結果を評価するためのリアルタイムPCR装置などの購入・設置を行い、次年度以降(最先端・次世代研究開発支援プログラムで継続)の本格的な研究への準備を完了することができた。

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  • Genome analysis of uncultivable microbes

    Grant number：18687002  2006 - 2008

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (A)

    HONGOH Yuichi

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    Grant amount：\15600000 （ Direct Cost: \12000000 、 Indirect Cost：\3600000 ）

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  • 同翅目昆虫と共生微生物の窒素代謝

    Grant number：97J07594  1998

    日本学術振興会  科学研究費助成事業  特別研究員奨励費

    本郷 裕一

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    Grant amount：\900000 （ Direct Cost: \900000 ）

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  • Ecology and genomics of symbiotic microbes in termite gut

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    Grant type：Competitive

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  • シロアリ腸内共生微生物群の分子生態学

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    Grant type：Competitive

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  • 環境ゲノミクス

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    Grant type：Competitive

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Teaching Experience

  • Fundamental Life Science 1-1

    2020 Institution：Tokyo Institute of Technology

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  • 進化生物学

    2016 Institution：東京工業大学

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  • 環境微生物学

    2016 Institution：東京工業大学大学院

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  • 生命科学基礎第二2

    2016 Institution：東京工業大学

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  • 環境微生物学

    2015 Institution：東京大学 大学院農学生命科学研究科

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  • 分子生態学

    2010 - 2014 Institution：東京工業大学大学院

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  • 生命科学基礎実験

    2009 Institution：東京工業大学

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  • 多様性生物学

    2009 - 2015 Institution：東京工業大学

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  • 基礎生物学

    2009 - 2015 Institution：東京工業大学

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Social Activities

  • 日本の大学における研究・教育の実情 〜研究者として生きるということ〜

    Role(s)： Lecturer

    武蔵高等学校同窓会  12 月木曜会講演会  2024.12

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    Audience： Junior students,　High school students,　College students,　Graduate students,　Guardians,　Researchesrs,　General,　Company

    Type：Lecture

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  • オープンキャンパスでの研究室公開

    東京工業大学  オープンキャンパス  2024.8

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    Audience： Junior students,　High school students

    Type：University open house

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  • Associate Editor (Microbes and Environments)

    Role(s)： Editer

    Microbes and Environments  2017

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    Audience： Researchesrs,　Scientific,　Company

    Type：Promotional material

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Media Coverage

  • シロアリはなぜ「木だけ」で生きられる？「100年の謎」を解いた東工大 本郷氏に聞いた Internet

    ビジネス＋IT  2024.7

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