publications

peer-reviewed journal articles ( * co-first author, ^ corresponding author )

2024

  1. Nat Micro
    A Marine Group A isolate relies on other growing bacteria for cell wall formation
    T. Katayama, M. K. Nobu*, H. Imachi, N. Hosogi, X. Y. Meng, K. Morinaga, H. Yoshioka, H. A. Takahashi, Y. Kamagata, and H. Tamaki
    Nat Microbiol, 2024
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  2. Microscopic and metatranscriptomic analyses revealed unique cross-domain parasitism between phylum Candidatus Patescibacteria/candidate phyla radiation and methanogenic archaea in anaerobic ecosystems
    K. Kuroda, M. Nakajima, R. Nakai, Y. Hirakata, S. Kagemasa, K. Kubota, T. Q. P. Noguchi, K. Yamamoto, H. Satoh, M. K. Nobu, and T. Narihiro
    mBio, 2024
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  3. PNAS
    Illuminating the coevolution of photosynthesis and Bacteria
    A. Nishihara, Y. Tsukatani, C. Azai, and M. K. Nobu^
    Proc Natl Acad Sci U S A, 2024
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2023

  1. ISME J
    Identification and cultivation of anaerobic bacterial scavengers of dead cells
    Y. Hirakata, R. Mei, K. Morinaga, T. Katayama, H. Tamaki, X. Y. Meng, T. Watari, T. Yamaguchi, M. Hatamoto, and M. K. Nobu^
    ISME J, 2023
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  2. PNAS Nexus
    The origin and evolution of methanogenesis and Archaea are intertwined
    R. Mei, M. Kaneko, H. Imachi, and M. K. Nobu^
    PNAS Nexus, 2023
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  3. ISME J
    Unique H(2)-utilizing lithotrophy in serpentinite-hosted systems
    M. K. Nobu*^, R. Nakai, S. Tamazawa, H. Mori, A. Toyoda, A. Ijiri, S. Suzuki, K. Kurokawa, Y. Kamagata, and H. Tamaki
    ISME J, 2023
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2022

  1. Nat Protoc
    Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study
    H. Imachi, M. K. Nobu*^, M. Miyazaki, E. Tasumi, Y. Saito, S. Sakai, M. Ogawara, A. Ohashi, and K. Takai
    Nat Protoc, 2022
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  2. Elucidation of the biodegradation pathways of bis(2-hydroxyethyl) terephthalate and dimethyl terephthalate under anaerobic conditions revealed by enrichment culture and microbiome analysis
    K. Kuroda, T. Narihiro, Y. Nakaya, T. Q. P. Noguchi, R. Maeda, M. K. Nobu, Y. Ohnishi, Y. Kumaki, T. Aizawa, and H. Satoh
    Chemical Engineering Journal, 2022
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  3. High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation
    K. Kuroda, T. Narihiro, F. Shinshima, M. Yoshida, H. Yamaguchi, H. Kurashita, N. Nakahara, M. K. Nobu, T. Q. P. Noguchi, M. Yamauchi, and M. Yamada
    Water Res, 2022
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  4. Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors
    K. Kuroda, K. Yamamoto, R. Nakai, Y. Hirakata, K. Kubota, M. K. Nobu*, and T. Narihiro
    mBio, 2022
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2021

  1. ISME J
    Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds
    J. M. Kurth, M. K. Nobu*^, H. Tamaki, N. Jonge, S. Berger, M. S. M. Jetten, K. Yamamoto, D. Mayumi, S. Sakata, L. Bai, L. Cheng, J. L. Nielsen, Y. Kamagata, T. Wagner, and C. U. Welte
    ISME J, 2021
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  2. Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes
    S. Sakamoto, M. K. Nobu^, D. Mayumi, S. Tamazawa, H. Kusada, H. Yonebayashi, H. Iwama, M. Ikarashi, T. Wakayama, H. Maeda, S. Sakata, T. Tamura, N. Nomura, Y. Kamagata, and H. Tamaki
    Syst Appl Microbiol, 2021
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2020

  1. Novel Syntrophic Isovalerate-Degrading Bacteria and Their Energetic Cooperation with Methanogens in Methanogenic Chemostats
    Y. T. Chen, Y. Zeng, J. Li, X. Y. Zhao, Y. Yi, M. Gou, Y. Kamagata, T. Narihiro, M. K. Nobu, and Y. Q. Tang
    Environ Sci Technol, 2020
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  2. Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats
    Y. T. Chen, Y. Zeng, H. Z. Wang, D. Zheng, Y. Kamagata, T. Narihiro, M. K. Nobu, and Y. Q. Tang
    Microb Ecol, 2020
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  3. Different inhibitory mechanisms of chlortetracycline and enrofloxacin on mesophilic anaerobic degradation of propionate
    M. Gou, H. Wang, J. Li, Z. Sun, Y. Nie, M. K. Nobu, and Y. Tang
    Environ Sci Pollut Res Int, 2020
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  4. Nature
    Isolation of an archaeon at the prokaryote-eukaryote interface
    H. Imachi, M. K. Nobu*^, N. Nakahara, Y. Morono, M. Ogawara, Y. Takaki, Y. Takano, K. Uematsu, T. Ikuta, M. Ito, Y. Matsui, M. Miyazaki, K. Murata, Y. Saito, S. Sakai, C. Song, E. Tasumi, Y. Yamanaka, T. Yamaguchi, Y. Kamagata, H. Tamaki, and K. Takai
    Nature, 2020
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  5. Nat Comm
    Isolation of a member of the candidate phylum ’Atribacteria’ reveals a unique cell membrane structure
    T. Katayama, M. K. Nobu*, H. Kusada, X. Y. Meng, N. Hosogi, K. Uematsu, H. Yoshioka, Y. Kamagata, and H. Tamaki
    Nat Commun, 2020
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  6. Deep Sequencing Uncovers Caste-Associated Diversity of Symbionts in the Social Ant Camponotus japonicus
    A. Koto, M. K. Nobu*, and R. Miyazaki
    mBio, 2020
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  7. Influence of Green Tuff Fertilizer Application on Soil Microorganisms, Plant Growth, and Soil Chemical Parameters in Green Onion (Allium fistulosum L.) Cultivation
    K. Kuroda, H. Kurashita, T. Arata, A. Miyata, M. Kawazoe, M. K. Nobu, T. Narihiro, T. Ohike, M. Hatamoto, S. Maki, and T. Yamaguchi
    Agronomy, 2020
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  8. Response of Isovalerate-Degrading Methanogenic Microbial Community to Inhibitors
    J. Li, H. Z. Wang, Y. Yi, M. Gou, M. K. Nobu, Y. T. Chen, and Y. Q. Tang
    Appl Biochem Biotechnol, 2020
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  9. Bacterial compositions in inhalable particulate matters from indoor and outdoor wastewater treatment processes
    M. Liu, M. K. Nobu, J. Ren, X. Jin, G. Hong, and H. Yao
    J Hazard Mater, 2020
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  10. Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments
    R. Mei, M. K. Nobu, and W. T. Liu
    Environ Microbiol Rep, 2020
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  11. Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters
    R. Mei, M. K. Nobu, T. Narihiro, and W. T. Liu
    Front Microbiol, 2020
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  12. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses
    M. K. Nobu, T. Narihiro, R. Mei, Y. Kamagata, P. K. H. Lee, P. H. Lee, M. J. McInerney, and W. T. Liu
    Microbiome, 2020
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  13. Nat Eco Evo
    A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism
    M. Preiner, K. Igarashi, K. B. Muchowska, M. Yu, S. J. Varma, K. Kleinermanns, M. K. Nobu, Y. Kamagata, H. Tuysuz, J. Moran, and W. F. Martin
    Nat Ecol Evol, 2020
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  14. Response to inhibitory conditions of acetate-degrading methanogenic microbial community
    H. Z. Wang, J. Li, Y. Yi, M. K. Nobu, T. Narihiro, and Y. Q. Tang
    J Biosci Bioeng, 2020
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2019

  1. Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms
    L. Leng, M. K. Nobu, T. Narihiro, P. Yang, G. Y. Amy Tan, and P. H. Lee
    Water Res, 2019
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  2. Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi
    N. Nakahara, M. K. Nobu, Y. Takaki, M. Miyazaki, E. Tasumi, S. Sakai, M. Ogawara, N. Yoshida, H. Tamaki, Y. Yamanaka, A. Katayama, T. Yamaguchi, K. Takai, and H. Imachi
    Int J Syst Evol Microbiol, 2019
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  3. Effects of the Wastewater Flow Rate on Interactions between the Genus Nitrosomonas and Diverse Populations in an Activated Sludge Microbiome
    T. Narihiro, M. K. Nobu, T. Hori, T. Aoyagi, Y. Sato, T. Inaba, H. Aizawa, H. Tamaki, and H. Habe
    Microbes Environ, 2019
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  4. Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima
    S. Suenami, M. Konishi Nobu, and R. Miyazaki
    Sci Rep, 2019
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  5. Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats
    H. Z. Wang, X. M. Lv, Y. Yi, D. Zheng, M. Gou, Y. Nie, B. Hu, M. K. Nobu, T. Narihiro, and Y. Q. Tang
    Sci Rep, 2019
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  6. Response of Propionate-Degrading Methanogenic Microbial Communities to Inhibitory Conditions
    H. Z. Wang, Y. C. Yan, M. Gou, Y. Yi, Z. Y. Xia, M. K. Nobu, T. Narihiro, and Y. Q. Tang
    Appl Biochem Biotechnol, 2019
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  7. Draft Genome Sequence of Thermodesulfovibrio sp. Strain Kuro-1, a Thermophilic, Lactate-Degrading Anaerobe Isolated from a Thermophilic Anaerobic Digestion Reactor
    T. Yamada, J. Harada, M. Kurobe, S. Giri, M. Konishi Nobu, T. Narihiro, H. Tsuji, and H. Daimon
    Microbiol Resour Announc, 2019
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  8. Identification of novel potential acetate-oxidizing bacteria in thermophilic methanogenic chemostats by DNA stable isotope probing
    D. Zheng, H. Z. Wang, M. Gou, M. K. Nobu, T. Narihiro, B. Hu, Y. Nie, and Y. Q. Tang
    Appl Microbiol Biotechnol, 2019
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  9. Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics
    R. M. Ziels, M. K. Nobu, and D. Z. Sousa
    mSystems, 2019
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2018

  1. Draft Genome Sequence of Moorella sp. Strain Hama-1, a Novel Acetogenic Bacterium Isolated from a Thermophilic Digestion Reactor
    J. Harada, T. Yamada, S. Giri, M. Hamada, M. K. Nobu, T. Narihiro, H. Tsuji, and H. Daimon
    Genome Announc, 2018
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  2. Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism
    C. A. P. Hidalgo-Ahumada, M. K. Nobu*^, T. Narihiro, H. Tamaki, W. T. Liu, Y. Kamagata, A. J. M. Stams, H. Imachi, and D. Z. Sousa
    Environ Microbiol, 2018
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  3. Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors
    R. Mei, M. K. Nobu, T. Narihiro, J. Yu, A. Sathyagal, E. Willman, and W. T. Liu
    Water Res, 2018
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  4. Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors
    T. Narihiro, M. K. Nobu, B. T. W. Bocher, R. Mei, and W. T. Liu
    Environ Microbiol Rep, 2018
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2017

  1. Nat Comm
    Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients
    A. K. Hawley, M. K. Nobu*, J. J. Wright, W. E. Durno, C. Morgan-Lang, B. Sage, P. Schwientek, B. K. Swan, C. Rinke, M. Torres-Beltran, K. Mewis, W. T. Liu, R. Stepanauskas, T. Woyke, and S. J. Hallam
    Nat Commun, 2017
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  2. Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater
    M. Liu, S. Wang, M. K. Nobu, B. T. W. Bocher, S. A. Kaley, and W. T. Liu
    Water Res, 2017
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  3. Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome
    R. Mei, M. K. Nobu, T. Narihiro, K. Kuroda, J. Munoz Sierra, Z. Wu, L. Ye, P. K. H. Lee, P. H. Lee, J. B. Lier, M. J. McInerney, Y. Kamagata, and W. T. Liu
    Water Res, 2017
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  4. Thermodynamically diverse syntrophic aromatic compound catabolism
    M. K. Nobu, T. Narihiro, M. Liu, K. Kuroda, R. Mei, and W. T. Liu
    Environ Microbiol, 2017
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2016

  1. A Single-Granule-Level Approach Reveals Ecological Heterogeneity in an Upflow Anaerobic Sludge Blanket Reactor
    K. Kuroda, M. K. Nobu, R. Mei, T. Narihiro, B. T. Bocher, T. Yamaguchi, and W. T. Liu
    PLoS One, 2016
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  2. Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns
    H. Lu, A. V. Ulanov, M. Nobu, and W. T. Liu
    Appl Microbiol Biotechnol, 2016
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  3. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity
    R. Mei, T. Narihiro, M. K. Nobu, K. Kuroda, and W. T. Liu
    Sci Rep, 2016
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  4. Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate
    R. Mei, T. Narihiro, M. K. Nobu, and W. T. Liu
    Lett Appl Microbiol, 2016
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  5. Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica Strain 4J5T (JCM 14075), a Mesophilic Butyrate- and 2-Methylbutyrate-Degrading Syntroph
    T. Narihiro, M. K. Nobu, H. Tamaki, Y. Kamagata, and W. T. Liu
    Genome Announc, 2016
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  6. Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria
    T. Narihiro, M. K. Nobu*, H. Tamaki, Y. Kamagata, Y. Sekiguchi, and W. T. Liu
    Microbes Environ, 2016
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  7. ISME J
    Phylogeny and physiology of candidate phylum ’Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
    M. K. Nobu, J. A. Dodsworth, S. K. Murugapiran, C. Rinke, E. A. Gies, G. Webster, P. Schwientek, P. Kille, R. J. Parkes, H. Sass, B. B. Jorgensen, A. J. Weightman, W. T. Liu, S. J. Hallam, G. Tsiamis, T. Woyke, and B. P. Hedlund
    ISME J, 2016
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  8. ISME J
    Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen
    M. K. Nobu, T. Narihiro, K. Kuroda, R. Mei, and W. T. Liu
    ISME J, 2016
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2015

  1. Microbial community analysis of anaerobic reactors treating soft drink wastewater
    T. Narihiro, N. K. Kim, R. Mei, M. K. Nobu, and W. T. Liu
    PLoS One, 2015
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  2. The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey
    T. Narihiro, M. K. Nobu*, N. K. Kim, Y. Kamagata, and W. T. Liu
    Environ Microbiol, 2015
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  3. The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow
    M. K. Nobu, T. Narihiro, T. Hideyuki, Y. L. Qiu, Y. Sekiguchi, T. Woyke, L. Goodwin, K. W. Davenport, Y. Kamagata, and W. T. Liu
    Environ Microbiol, 2015
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  4. ISME J
    Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
    M. K. Nobu, T. Narihiro, C. Rinke, Y. Kamagata, S. G. Tringe, T. Woyke, and W. T. Liu
    ISME J, 2015
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2014

  1. Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph
    M. K. Nobu, T. Narihiro, H. Tamaki, Y. L. Qiu, Y. Sekiguchi, T. Woyke, L. Goodwin, K. W. Davenport, Y. Kamagata, and W. T. Liu
    Genome Announc, 2014
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  2. Metagenomic characterization of ’Candidatus Defluviicoccus tetraformis strain TFO71’, a tetrad-forming organism, predominant in an anaerobic-aerobic membrane bioreactor with deteriorated biological phosphorus removal
    M. K. Nobu, H. Tamaki, K. Kubota, and W. T. Liu
    Environ Microbiol, 2014
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