Microbial Ecology and Technology Research Group
PUBLICATIONS

Refereed Papers (since 2015)

2022

  1. Yamamoto K, Yoneda Y, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H.: Complete Genome Sequence of Luteitalea sp. Strain TBR-22, Microbiol Resour Announc. 11(2): e00455-21 (2022). DOI:10.1128/mra.00455-21.
  2. Yamamoto K, Yoneda Y, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H.: Draft Genome Sequence of Bryobacteraceae Strain F-183, Microbiol Resour Announc. 11(2): e00453-21 (2022). DOI:10.1128/mra.00453-21.
  3. Yamamoto K, Yamamoto N, Ayukawa S, Yasutake Y, Ishiya K, N Nakashima.: Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa, Sci Rep. (in press).
  4. Ishiya K, Kosaka H, Inaoka T, Kimura K, Nakashima N.,: Comparative genome analysis of three Komagataeibacter strains used for practical production of nata-de-coco, Frontiers in Microbiology, 12:798010 (2022). DOI:10.3389/fmicb.2021.798010.
  5. Ishiya K, Nakashima N.,: Comparative Genome Analysis Reveals Accumulation of Single-Nucleotide Repeats in Pathogenic Escherichia Lineages, Current Issues in Molecular Biology, 44(2) 498-504 (2022). DOI:10.3390/cimb44020034.

2021

  1. Ishiya K, Aburatani S.,: Multivariate statistical monitoring system for microbial population dynamics, Physical Biology, 19(1) (2021). DOI:10.1088/1478-3975/ac3ad6.
  2. Kurashita H, Kuroda K, Maki S, Sato T, Takagi M, Goto M, Kariya T, Hatamoto M, Tomita S, Narihiro T.: Chemical and microbial characteristics of blackening disease in lotus (Nelumbo nucifera Gaertn.) caused by Hirschmanniella diversa Sher, Agronomy, 11(12): 2517 (2021).
  3. Shimada S*, Nakai R*, Aoki K, Kudoh S, Imura S, Shimoeda N, Ohno G, Watanabe K, Miyazaki Y, Ishii Y, Tateda K. (*equal contribution): Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. Microbiol Spectr., 9:e00424-21(2021). DOI=10.1128/Spectrum.00424-21.
  4. Kuroda K, Kurashita H, Takagi M, Narihiro T, Hatamoto M, Yamaguchi T.: Phylogenetic analyses of the lotus root-parasitic nematodes Hirschmanniella diversa Sher and H. imamuri Sher based on the 18S ribosomal RNA (rRNA) gene and 5.8S rRNA gene/internal transcribed spacer region. Nematol Res., 51: 5-9.
  5. Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M.: Ecogenomics reveals microbial metabolic networks in a psychrophilic methanogenic bioreactor treating soy sauce production wastewater. Microbes Environ 36(4) (2021). DOI=10.1264/jsme2.ME21045.
  6. Yamada T, Hamada M, Kurobe M, Narihiro T, Tsuji H, Daimon H.: Complete Genome Sequence of Gelria sp. Strain Kuro-4, a Thermophilic Anaerobe Isolated from a Thermophilic Anaerobic Digestion Reactor Treating Poly (L-Lactic Acid). Microbiol Resour Announc 10 (33), e00544-21. DOI=10.1128/MRA.00544-21.
  7. Kuroda K, Shinshima F, Tokunaga S, Noguchi TQP, Yamauchi M, Nobu MK, Narihiro T, Yamada M.: Assessing the effect of green tuff as novel natural inorganic carrier on methane producing activity of anaerobic sludge microbiome. Environ Technol Innov 24: 101835 (2021). DOI=10.1016/j.eti.2021.101835.
  8. Zhang Z, Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H.: Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil. Syst Appl Microbiol, 44(5), 126233 (2021). DOI=10.1016/j.syapm.2021.126233.
  9. Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H.: Genome-based taxonomic rearrangement of the order Geobacterales including the description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol, 12:737531 (2021). DOI=10.3389/fmicb.2021.737531.
  10. Nakai R, Naganuma T, Tazato N, Kunihiro T, Morohoshi S, Koide T, Kusada H, Tamaki H, Narihiro T.: Characterization of Terrihabitans soli gen. nov., sp. nov., a novel 0.2 μm-filterable soil bacterium belonging to a widely distributed lineage of Hyphomicrobiales (Rhizobiales). Diversity 13(9):422 (2021). DOI=10.3390/d13090422.
  11. Nakai R*, Kusada H*, Sassa F, Morigasaki S, Hayashi H, Takaya N. Tamaki H.(*equal contribution): Draft genome sequence of novel filterable Rhodospirillales bacterium strain TMPK1, isolated from soil. Microbiol Resour Announc, 10:e00393-21 (2021). DOI=10.1128/MRA.00393-21.
  12. Nakai R, Wakana I, Niki H.: Internal microbial zonation during the massive growth of marimo, a lake ball of Aegagropila linnaei in Lake Akan. iScience 24:102720 (2021). DOI:10.1016/j.isci.2021.102720.
  13. Kurth JM, Nobu MK, Tamaki H, de Jonge N, Berger S, Jetten MSM, Yamamoto K, Mayumi D, Sakata S, Bai L, Cheng L, Nielsen JL, Kamagata Y, Wagner T, Welte CU.: Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J., 15: 3549–3565(2021). DOI:10.1038/s41396-021-01025-6.
  14. Yoneda Y*, Yamamoto K*, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. (*equal contribution): Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds. Microorganisms 9:1133 (2021) DOI:10.3390/microorganisms9061133.
  15. Tu Z, Lopes, HFS, Narihiro T, Yumoto I.: The mechanism underlying of long-term stable indigo reduction state in indigo fermentation using sukumo (composted Polygonum tinctorium leaves). Front Microbiol. DOI:10.3389/fmicb.2021.698674.
  16. Yamamoto K, Kusada H, Kamagata Y, Tamaki H.: Parallel evolution of enhanced biofilm formation and phage-resistance in Pseudomonas aeruginosa during adaptation process in spatially heterogeneous environments. Microorganisms 9:569 (2021). DOI=10.3390/microorganisms9030569.
  17. Iwashita T, Tanaka H, Tamaki H, Nakai R, Yoneda Y, Makino A, Toyama T, Kamagata Y, Morikawa M, Mori K.: Isolation and characterization of novel plant growth-promoting bacteria from frond of duckweeds. Jpn. J. Water Treat. Biol. 57:1-9 (2021). DOI=10.2521/jswtb.57.1.
  18. Shimada S, Nakai R, Aoki K, Shimoeda N, Ohno G, Kudoh S, Imura S, Watanabe K, Miyazaki Y, Ishii Y, Tateda K.: Chasing waterborne pathogens in Antarctic human-made and natural environments with special reference to Legionella spp. Appl. Environ. Microbiol. DOI=10.1128/AEM.02247-20.
  19. Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo, K.: Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int. J. Syst. Evol. Microbiol. DOI=10.1099/ijsem.0.004607.
  20. Masuda Y, Shiratori Y, Ohba H, Ishida T, Takano R, Satoh S, Shen W, Nan G, Itoh H, Senoo K.: Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application. Soil Sci. Plant Nutr. (2021). DOI=10.1080/00380768.2021.1888629.
  21. Ishigami K, Jang S, Itoh H, Kikuchi Y.: Insecticide resistance governed by gut symbiosis in a rice pest, Cletus punctiger, under laboratory conditions. Biol. Lett. 17:20200780 (2021). DOI=10.1098/rsbl.2020.0780.
  22. Jang S, Mergaert P, Ohbayashi T, Ishigami K, Shigenobu S, Itoh H, Kikuchi Y.: Dual oxidase enables insect gut symbiosis by mediating respiratory network formation. Proc. Natl. Acad. Sci. U S A 118: e2020922118 (2021). DOI=10.1073/pnas.2020922118.
  23. Hosokawa S, Kuroda K, Narihiro T, Aoi Y, Ozaki N, Ohashi A, Kindaichi T.: Cometabolism of the superphylum Patescibacteriawith anammox bacteria in a long-term freshwater anammox column reactor. Water 13(2):208 (2021). DOI=DOI: 10.3390/w13020208.
  24. Kurashita H, Kuroda K., Narihiro T, Takagi M, Goto M, Ikeda S, Hirakata Y, Hatamoto M, Maki S, Yamaguchi T, Aoi T.: Accurate evaluation of blackening disease in lotus (Nelumbo nucifera Gaertn.) using a quantitative PCR-based assay for Hirschmanniella diversa Sher and H. imamuri Sher. Crop Protection 139 105380 (2021). DOI:10.1016/j.cropro.2020.105380.
  25. Omine T, Kuroda K (equally contributed 1st author), Hatamoto M, Yamaguchi T, Yamauchi M, Yamada M. Reduction of alkalinity supplementation for acid-based wastewater treatment using a thermophilic multi-feed upflow anaerobic sludge blanket reactor. Environ Technol. 27:1-11 (2021). DOI:10.1080/09593330.2019.1620864.

2020

  1. Mei R, Nobu MK, Narihiro T, Liu WT.: Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Frontiers in Microbiology 11:593006 (2020). DOI=10.3389/fmicb.2020.593006 .
  2. Quaiyum S, Igarashi K, Narihiro T, Kato S.: Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes and Environments. 35:ME20002 (2020). DOI=10.1264/jsme2.ME20002 .
  3. Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P.: Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int. J. Syst. Evol. Microbiol. 70:5972-6016 (2020). DOI=10.1099/ijsem.0.004213.
  4. Nakajima Y, Kojima K, Kashiyama Y, Doi S, Nakai R, Sudo Y, Kogure K, Yoshizawa S: Bacterium lacking a known gene for retinal biosynthesis constructs functional rhodopsins. Microbes Environ. 35: ME20085 (2020). DOI=10.1264/jsme2.ME20085.
  5. Chen YT, Zeng Y, Li J, Zhao XY, Yi Y, Gou M, Kamagata Y, Narihiro T, Nobu MK, Tang YQ.: Novel syntrophic isovalerate-degrading bacteria and their energetic cooperation with methanogens in methanogenic chemostats. Environmental Science & Technology 54(15):9618-9628 (2020). doi:10.1021/acs.est.0c01840.
  6. Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT: Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome. 8(1):111. (2020). doi:10.1186/s40168-020-00885-y.
  7. Kosakamoto H, Yamauchi T, Akuzawa-Tokita Y, Nishimura K, Soga T, Murakami T, Mori H, Yamamoto K, Miyazaki R, Koto A, Miura M, Obata F: Local necrotic cells trigger systemic immune activation via gut microbiome dysbiosis in Drosophila, Cell Rep. 32(3) 107938 (2020). doi:10.1016/j.celrep.2020.107938.
  8. Nakai R, Naganuma T, Tazato N, Morohoshi S, Koide T.: Cell plasticity and genomic structure of a novel filterable Rhizobiales bacterium that belongs to a widely distributed lineage. Microorganisms, 8(9): 1373 (2020), doi:10.3390/microorganisms8091373.
  9. Kuroda K, Kurashita H, Arata T, Miyata A, Kawazoe M, Nobu MK, Narihiro T, Ohike T, Hatamoto M, Maki S, Yamaguchi T.: Influence of Green Tuff Fertilizer Application on Soil Microorganisms, Plant Growth, and Soil Chemical Parameters in Green Onion (Allium fistulosum L.) Cultivation. Agronomy, 10: 929 (2020). DOI:10.3390/agronomy10070929.
  10. Masuda Y, Yamanaka H, Xu Z, Shiratori Y, Aono T, Amachi S, Senoo K, Itoh H. Diazotrophic ability of Anaeromyxobacter isolated from soils. Appl. Environ. Microbiol. (2020). DOI:10.1128/AEM.00956-20.
  11. Kawano K, Ushijima N, Kihara M, Itoh H. Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov. Int. J. Syst. Evol. Microbiol. (2020). DOI:10.1099/ijsem.0.004254.
  12. Xu, Z.; Masuda, Y.; Hayakawa, C.; Ushijima, N.; Kawano, K.; Shiratori, Y.; Senoo, K.; Itoh, H. Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.. Microorganisms 8:634 (2020). DOI:10.3390/microorganisms8050634.
  13. Shimada S*, Nakai R*, Aoki K, Shimoeda N, Ohno G, Miyazaki Y, Kudoh S, Imura S, Watanabe K, Ishii Y, Tateda K (*equal contribution): Complete genome sequence of novel psychrotolerant Legionella strain TUM19329, isolated from Antarctic lake sediment. Microbiol Resour Announc. 9(16):e00253-20 (2020).  DOI:10.1128/MRA.00253-20.
  14. Wang HZ, Li J, Yi Y, Nobu MK, Narihiro T, Tang YQ: Response to inhibitory conditions of acetate-degrading methanogenic microbial community. Journal of Bioscience and Bioengineering 129 (4), 476-485 (2020). DOI:10.1016/j.jbiosc.2019.10.006.
  15. Chen YT, Zeng Y, Wang HZ, Zheng D, Kamagata Y, Narihiro T, Nobu MK, Tang YQ: Different interspecies electron transfer patterns during mesophilic and thermophilic syntrophic propionate degradation in chemostats. Microb Ecol. (2020).  DOI:10.1007/s00248-020-01485-x.

2019

  1. Takeshita K, Yamada T, Kawahara Y, Narihiro T, Ito M, Kamagata Y, Shinzato N: Tripartite symbiosis of an anaerobic scuticociliate with two hydrogenosome-associated endosymbionts, a Holospora-related alphaproteobacterium and a nethanogenic archaeon. Appl Environ Microbiol. 85(24). pii: e00854-19. (2019). DOI:10.1128/AEM.00854-19.
  2. Wang HZ, Lv XM, Yi Y, Zheng D, Gou M, Nie Y, Hu B, Nobu MK, Narihiro T, Tang YQ. Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats. Sci Rep. 9(1):17396 (2019). DOI:10.1038/s41598-019-53849-0
  3. Zheng D, Wang HZ, Gou M, Nobu MK, Narihiro T, Hu B, Nie Y, Tang YQ. Identification of novel potential acetate-oxidizing bacteria in thermophilic methanogenic chemostats by DNA stable isotope probing. Appl Microbiol Biotechnol. 103(20):8631-8645 (2019). DOI:10.1007/s00253-019-10078-9
  4. Chen SC, Weng CY, Lai MC, Tamaki H, Narihiro T: Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus. Marine Genomics. 47, 100673 (2019). DOI:10.1016/j.margen.2019.03.008.
  5. Wang HZ, Yan YC, Gou M, Yi Y, Xia ZY, Nobu MK, Narihiro T, Tang YQ: Response of propionate-degrading methanogenic microbial communities to inhibitory conditions. Applied Biochemistry and Biotechnology, 189 (1), 233-248 (2019). DOI:10.1007/s12010-019-03005-1.
  6. Yamada T, Harada J, Kurobe M, Giri S, Nobu MK, Narihiro T, Tsuji H, Daimon H. Draft genome sequence of Thermodesulfovibrio sp. strain Kuro-1, a thermophilic, lactate-degrading anaerobe isolated from a thermophilic anaerobic digestion reactor. Microbiol Resour Announc. 8(29). pii: e00709-19 (2019) . DOI:10.1128/MRA.00709-19.
  7. Sun H, Narihiro T, Ma X, Zhang XX, Ren H, Ye L: Diverse aromatic-degrading bacteria present in a highly enriched autotrophic nitrifying sludge. Sci Total Environ. 666:245-251 (2019). DOI:10.1016/j.scitotenv.2019.02.172.
  8. Leng L, Nobu MK, Narihiro T, Yang P, Amy Tan GY, Lee PH: Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: pathways and mechanisms. Water Res. 148:281-291 (2019). DOI:10.1016/j.watres.2018.10.063.
  9. Narihiro T, Nobu MK, Hori T, Aoyagi T, Sato Y, Inaba T, et al.: Effects of the wastewater flow rate on interactions between the genus Nitrosomonas and diverse populations in an activated sludge microbiome. Microbes Environ. 34(1):89-94 (2019). DOI:10.1264/jsme2.ME18108.
  10. Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing, Sci Rep. 4;9(1):12783 (2019). DOI:10.1038/s41598-019-49290-y.
  11. Yagi F, Minami Y, Yamada M, Kuroda K, Yamauchi M. Development of animal feeding additives from mushroom waste media of shochu lees, International Journal of Recycling of Organic Waste in Agriculture, 8(2) :215–220 (2019). DOI:10.1007/s40093-018-0234-6.
  12. Maharjan N, Kuroda K, Okada M, Nakamura S, Aburatani H, Yamaguchi T, Ichitsubo M. Generic skills assessment through implementation of group based learning to understand SDGs, Journal of Education and practice, 10(6): 14–23 (2019). DOI:10.7176/JEP
  13. Itoh H, Jang S, Takeshita K, Ohbayashi T, Ohnishi N, Meng XY, Mitani Y, Kikuchi Y. Host-symbiont specificity determined by microbe-microbe competition in an insect gut. Proc Natl Acad Sci U S A. 116(45):22673-22682 (2019). DOI:10.1073/pnas.1912397116.
  14. Xu Z, Masuda Y, Itoh H, Ushijima N, Shiratori Y, Senoo K. Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov. Front. Microbiol. 25(10):2201 (2019). DOI:10.3389/fmicb.2019.02201.
  15. Itoh, H., Kawano, K., Kihara, M.: Draft Genome Sequence of Agarivorans sp. Strain Toyoura001, Isolated from an Abalone Gut. Microbiol Resour Announc. 8(19):e00169-19 (2019). DOI:10.1128/MRA.00169-19.
  16. Ohbayashi, T., Itoh, H., Lachat, J., Kikuchi, Y., and Mergaert, P.: Burkholderia gut symbionts associated with European and Japanese populations of the dock bug Coreus marginatus (Coreoidea : Coreidae). Microbes Environ. 34(2):219-222 (2019). DOI:10.1264/jsme2.ME19011.
  17. Faluaburu MS, Nakai R, Imura S, Naganuma T: Phylotypic characterization of mycobionts and photobionts of rock tripe lichen in East Antarctica. Microorganisms 7(7):203 (2019). DOI:10.3390/microorganisms7070203.
  18. Yamamoto K, Hackley K, Kelly W, Panno S, Sekiguchi Y, Sanford R, Liu WT, Kamagata Y, Tamaki H. Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Sci. Rep. 9(1):13484 (2019). DOI:10.1038/s41598-019-49996-z.
  19. Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, Suga H, Shimizu K. Microbial basis of Fusarium wilt suppression by Allium cultivation. Sci. Rep. 9(1):1715 (2019). DOI:10.1038/s41598-018-37559-7.

2018

  1. Mei R, Nobu MK, Narihiro T, Yu J, Sathyagal A, Willman E, et al.: Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Res. 147:403-12 (2018). DOI:10.1016/j.watres.2018.10.026.
  2. Narihiro T, Nobu MK, Bocher BTW, Mei R, Liu WT: Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environ Microbiol Rep. 10(6):673-85 (2018). DOI:10.1111/1758-2229.12689.
  3. Hidalgo-Ahumada CAP, Nobu MK, Narihiro T, Tamaki H, Liu WT, Kamagata Y, et al.: Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environ Microbiol. 20(12):4503-11 (2018). DOI:10.1111/1462-2920.14388.
  4. Harada J, Yamada T, Giri S, Hamada M, Nobu MK, Narihiro T, et al.: Draft genome sequence of Moorella sp. strain Hama-1, a novel acetogenic bacterium isolated from a thermophilic digestion reactor. Genome Announcements. 6(24) (2018). DOI:10.1128/genomeA.00517-18.
  5. Masuda, Y., Itoh, H., Shiratori, Y., Senoo, K.: Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils. Soil Sci. Plant Nutr. 64(4):455-464 (2018). DOI:10.1080/00380768.2018.1457409.
  6. Itoh, H., Hori, T., Sato, Y., Nagayama, A., Tago, K., Hayatsu, M., Kikuchi, Y.: Infection dynamics of insecticide-degrading symbionts from soil to insects in response to insecticide spraying. ISME J. 12:909-920 (2018). DOI:10.1038/s41396-017-0021-9.
  7. Naganuma T, Iinuma Y, Nishiwaki H, Murase R, Masaki K, Nakai R: Enhanced bacterial growth and gene expression of D-amino acid dehydrogenase with D-glutamate as the sole carbon source. Front Microbiol. 9:2097 (2018). DOI:10.3389/fmicb.2018.02097.

2017

  1. Nobu MK, Narihiro T, Liu M, Kuroda K, Mei R, Liu WT: Thermodynamically diverse syntrophic aromatic compound catabolism. Environ. Microbiol. 18: 2495-2506 (2017). DOI:10.1111/1462-2920.13922.
  2. Mei R, Nobu MK, Narihiro T, Kuroda K, Muñoz Sierra J, Wu Z, Ye L, Lee PKH, Lee PH, van Lier JB, McInerney MJ, Kamagata Y, Liu WT: Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Res. 124:77-84 (2017). DOI:10.1016/j.watres.2017.07.050.
  3. Okamoto T, Aino K, Narihiro T, Matsuyama H, Yumoto I: Analysis of microbiota involved in the aged natural fermentation of indigo. World J. Microbiol. Biotechnol. 33:70 (2017). DOI:10.1007/s11274-017-2238-1.
  4. Jia, H., Hanate, M., Aw, W., Itoh, H., Saito, K., Kobayashi, S., Hachimura, S., Fukuda, S., Tomita, M., Hasebe, Y., Kato, H.: Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis. Sci. Rep. 7: 43993 (2017). DOI:10.1038/srep43993.
  5. Masuda, Y., Itoh, H., Shiratori, Y., Isobe, K., Otsuka, S., Senoo, K.: Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ. 32:180-183 (2017). DOI:10.1264/jsme2.ME16179.
  6. Itoh, H., Matsuura, Y., Hosokawa, T., Fukatsu T., Kikuchi, Y.: Obligate gut symbiotic association in the sloe bug Dolycoris baccarum (Hemiptera: Pentatomidae). Appl. Entomol. Zool. 52:51-59 (2017). DOI:10.1007/s13355-016-0453-0.
  7. Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S, Pitt A, Nakai R, Naganuma T, Lang E: Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. Int J Syst Evol Microbiol. 67(8):2555-2568 (2017). DOI:10.1099/ijsem.0.001965.

2016

  1. Mei R, Narihiro T, Nobu MK, Liu WT: Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate. Lett. Appl. Microbiol. 63: 356-362. (2016). DOI:10.1111/lam.12629.
  2. Shinzato N, Aoyama H, Saitoh S, Nikoh N, Nakano K, Shimoji M, Shinzato M, Satou K, Teruya K, Hirano T, Yamada T, Nobu MK, Tamaki H, Shirai Y, Park S, Narihiro T, Liu WT, Kamagata Y: Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum. Genome Announc. 4: pii: e01032-16 (2016). DOI:10.1128/genomeA.01032-16.
  3. Nobu MK, Narihiro T, Kuroda K, Mei R, Liu WT: Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J. 10:2478-87 (2016). DOI:10.1038/ismej.2016.33.
  4. Mei R, Narihiro T, Nobu MK, Kuroda K, Liu WT: Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Sci Rep. 6:34090 (2016). DOI:10.1038/srep34090.
  5. Narihiro T, Kusada H, Yoneda Y, Tamaki H: Draft genome sequences of Methanoculleus horonobensis strain JCM 15517, Methanoculleus thermophilus strain DSM 2373, and Methanofollis ethanolicus strain JCM 15103, hydrogenotrophic methanogens belonging to the family Methanomicrobiaceae. Genome Announc. 4: pii: e00199-16 (2016). DOI:10.1128/genomeA.00199-16.
  6. Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Liu WT: Draft Genome sequence of Syntrophomonas wolfei subsp. methylbutyratica strain 4J5T (JCM 14075), a mesophilic butyrate- and 2-methylbutyrate-degrading syntroph. Genome Announc. 4: pii: e00047-16 (2016). DOI:10.1128/genomeA.00047-16.
  7. Kuroda K, Nobu MK, Mei R, Narihiro T, Bocher BT, Yamaguchi T, Liu WT: A single-granule-level approach reveals ecological heterogeneity in an upflow anaerobic sludge blanket reactor. PLoS One 11: e0167788 (2016). DOI:journal.pone.0167788.
  8. Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT: Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microbes Environ. 31:288-292 (2016). DOI:10.1264/jsme2.ME16057.
  9. Narihiro T, Kanosue Y, Hiraishi A: Cultural, transcriptomic, and proteomic analyses of water-stressed cells of actinobacterial strains isolated from compost: Ecological implications in the fed-batch composting process. Microbes Environ. 31:127-136 (2016). DOI:10.1264/jsme2.ME15199.
  10. Dao HT, Kuroda K, Nakahara N, Danshita T, Hatamoto M, Yamaguchi T. 16S rRNA gene-based comprehensive analysis of microbial community compositions in a full-scale leachate treatment system, J Biosci Bioeng. 122(6):708-715 (2016). DOI:10.1016/j.jbiosc.2016.06.003.
  11. Hirakata Y, Oshiki M, Kuroda K, Hatamoto M, Kubota K, Yamaguchi T, Harada H, Araki N. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge. Microbes Environ. 31(3):279-87 (2016). DOI:10.1264/jsme2.ME16067.
  12. Maharjan N, Kuroda K, Dehama K, Hatamoto M, Yamaguchi T. Development of slow sponge sand filter (SpSF) as a post-treatment of UASB-DHS reactor effluent treating municipal wastewater. Water Sci Technol. 74(1):65-72 (2016). DOI:10.2166/wst.2016.164.
  13. Nakai R, Fujisawa T, Nakamura Y, Baba T, Nishijima M, Karray F, Sayadi S, Isoda H, Naganuma T, Niki H: Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. Stand Genomic Sci. 11:90 (2016). DOI:10.1186/s40793-016-0210-6.
  14. Nakai R, Fujisawa T, Nakamura Y, Nishide H, Uchiyama I, Baba T, Toyoda A, Fujiyama A, Naganuma T, Niki H: Complete genome sequence of Aurantimicrobium minutum type strain KNCT, a planktonic ultramicrobacterium isolated from river water. Genome Announc. 4(3): e00616-16 (2016). DOI:10.1128/genomeA.00616-16.
  15. Mayumi D, Mochimaru H, Tamaki T, Yamamoto K, Yoshioka H, Suzuki Y, Kamagata Y, Sakata S. Methane production from coal by a single methanogen. Science 354(6309): 222-225 (2016). DOI:10.1126/science.aaf8821.
  16. Tamazawa S*, Yamamoto K*, Takasaki K, Mitani Y, Hanada S, Kamagata Y, Tamaki H. In situ gene expression responsible for sulfide oxidation and CO2 fixation of an uncultured large sausage-shaped Aquificae bacterium in a sulfidic hot spring. Microbes Environ. 31(2):194-198 (2016). DOI:10.1264/jsme2.ME16013.

2015

  1. Nobu MK, Narihiro T, Tamaki H, Qiu YL, Sekiguchi Y, Woyke T, Goodwin L, Davenport KW, Kamagata Y, Liu WT: The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol, 17(12):4861-4872 (2015)
  2. Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT: Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. 9: 1710-1722 (2015).
  3. Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y: Isolation of microorganisms involved in reduction of crystalline iron (III) oxides in natural environments. Frontiers in Microbiol, 6: e368 (2015).
  4. Narihiro T, Nobu MK, Kim NK, Kamagata Y, Liu WT: The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey. Environ Microbiol. 17(5):1707-20 (2015)
  5. Narihiro T, Kim NK, Mei R, Nobu MK, Liu WT: Microbial community analysis of anaerobic reactors treating soft drink wastewater. PLOS One, 10(3):e0119131 (2015)
  6. Kuroda K, Chosei T, Nakahara N, Hatamoto M, Wakabayashi T, Kawai T, Araki N, Syutsubo K, Yamaguchi T. High organic loading treatment for industrial molasses wastewater and microbial community shifts corresponding to system development. Bioresour Technol. 196:225-34 (2015).
  7. Kuroda K, Hatamoto M, Nakahara N, Abe K, Takahashi M, Araki N, Yamaguchi T. Community composition of known and uncultured archaeal lineages in anaerobic or anoxic wastewater treatment sludge, Microb Ecol, 69(3): 586–596 (2015).
  8. Aida AA, Kuroda K, Yamamoto M, Nakamura A, Hatamoto M, Yamaguchi T. Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage. Microbes Environ. 30(2):157-63 (2015).
  9. Watari T, Thanh NT, Tsuruoka N, Tanikawa D, Kuroda K, Huong NL, Tan NM, Hai HT, Hatamoto M, Syutsubo K, Fukuda M, Yamaguchi T. Development of a BR-UASB-DHS system for natural rubber processing wastewater treatment. Environ Technol. 37(4):459-465 (2015).
  10. Hirakata Y, Oshiki M, Kuroda K, Hatamoto M, Kubota K, Yamaguchi T, Harada H, Araki N. Identification and Detection of Prokaryotic Symbionts in the Ciliate Metopus from Anaerobic Granular Sludge. Microbes Environ. 30(4):335-8 (2015).
  11. Tourlousse DM, Matsuura N, Sun L, Toyonaga M, Kuroda K, Ohashi A, Cruz R, Yamaguchi T, Sekiguchi Y. Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System. Genome Announc. 3(5). pii: e01168-15 (2015).
  12. Matsuura N, Tourlousse DM, Sun L, Toyonaga M, Kuroda K, Ohashi A, Cruz R, Yamaguchi T, Sekiguchi Y. Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System. Genome Announc. 3(5). pii: e01104-15 (2015).
  13. Hatamoto M, Saito Y, Dehama K, Nakahara N, Kuroda K, Takahashi M, Yamaguchi T. Microbial community structure of a simultaneous nitrogen and phosphorus removal reactor following treatment in a UASB-DHS system. Water Sci Technol. 71(3):454-61 (2015).
  14. Watari T, Tanikawa D, Kuroda K, Nakamura A, Fujii N, Yoneyama F, Wakisaka O, Hatamoto M, Yamaguchi T. Development of UASB-DHS system for treating industrial wastewater containing ethylene glycol. Journal of Water and Environment Technology, 13(2), 131–140 (2015).
  15. Takeshita, K., Matsuura, Y., Itoh, H., Navarro, R., Hori, T., Sone, T., Kamagata, Y., Mergaert, P., Kikuchi, Y.: Burkholderia of plant-beneficial group are symbiotically associated with bordered plant bugs (Heteroptera: Pyrrhocoroidea: Largidae). Microbes Environ. 30:321-329 (2015).
  16. Navarro, R. R., Aoyagi, T., Kimura, M., Itoh, H., Sato, Y., Kikuchi, Y., Ogata, A., Hori, T.: High resolution dynamics of microbial communities during dissimilatory selenate reduction in an anoxic soil. Environ. Sci. Technol. 49: 7684–7691 (2015).
  17. Aoyagi, T., Hanada, S., Itoh, H., Sato, Y., Ogata, A., Friedrich, M. W., Kikuchi, Y., Hori, T.: Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients. Environ. Microbiol. Rep. 7: 282-287 (2015). 
  18. Tago, K., Okubo, T., Itoh, H., Kikuchi, Y., Hori, T., Sato, Y., Nagayama, A., Hayashi, K., Ikeda, S., Hayatsu, M.: Insecticide-degrading Burkholderia symbionts of the stinkbug naturally occupy various environments of sugarcane fields in a southeast island of Japan. Microbs Environ. 30: 29-36 (2015).
  19. Aoyagi T., Kimura M., Yamada N., Navarro R.R., Itoh H., Ogata A., Sakoda A., Katayama Y., Takasaki M., Hori T.: Dynamic transition of chemolithotrophic sulfur-oxidizing bacteria in response to amendment with nitrate in deposited marine sediments. Front. Microbiol. 6:426 (2015).
  20. Nakai R, Baba T, Niki H, Nishijima M, Naganuma T: Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water. Int J Syst Evol Microbiol 65(11): 4072-4079 (2015).

Reviews, book chapters, and other publications (since 2015)

2020

  1. Nakai R: Size matters: ultra-small and filterable microorganisms in the environment. Microbes Environ 35(2) (2020). DOI=10.1264/jsme2.ME20025.
  2. Ichitsubo M (Ed.), Aburatani H (Ed.), Fujii K, Murayama K, Okada M, Sugihara Y, Kuroda K, Maharjan N, Ichitsubo H, Sumits K, L3 Inc. (Molly JD). Transforming for Sustainability –The guide for your action on the SDG 7 & 9–, Maruzen-Yushodo Co., Ltd., Tokyo, Japan (2020).

2019

  1. Ichitsubo M (Ed.), Yamaguchi T, Fujii K, Maharjan N, Drier B, Kuroda K, Maruyama N, Takimoto Y, Putra AA, Thao TP, Ohmine N, Arata T, Kurashita H, Kotsusa M. SDGs Fun Learning Book – A bright future for all of us -, Maruzen-Yushodo Co., Ltd., Tokyo, Japan (2019).
  2. Nakai R, Imura S, Naganuma T: Chapter 2: Patterns of microorganisms inhabiting Antarctic freshwater lakes with special reference to aquatic moss pillars, pp.25-43, In: Castro-Sowinski S (ed) The Ecological Role of Micro-organisms in the Antarctic Environment, Springer Polar Sciences, (2019).

2018

  1. Itoh, H., Tago, K., Hayatsu, M., Kikuchi, Y.: Detoxifying symbiosis: microbe-mediated detoxification of phytotoxins and pesticides in insects. Nat. Prod. Rep. 35(5):434-454 (2018).
  2. Haruta S, Yamamoto K. Model microbial consortia as tools for understanding complex microbial communities. Curr. Genomics 19(8):723-733 (2018).

2017

  1. Narihiro T, Kamagata Y: Genomics and metagenomics in microbial ecology: recent advances and challenges. Microbes Environ. 32:1-4 (2017).

2016

  1. Narihiro T, Kamagata Y: Anaerobic Cultivation, pp. 2.1.2-1-2.1.2-12. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC (2016).
  2. Kamagata Y, Narihiro T: Symbiosis studies in microbial ecology. Microbes Environ. 31: 201-203 (2016).
  3. Narihiro T: Microbes in the water infrastructure: underpinning our society. Microbes Environ. 31:89-92 (2016).
  4. Kudoh S, Takahashi KT, Ishihara T, Tsujimoto M, Nakai R, Suzuki AC, Tanabe Y, Uchida M, Imura S: Limnological parameters in Sôya Coats lakes between the 55th and 56th Japanese Antarctic Research Expeditions in 2014–2015 —Long-term monitoring study —. JARE Data Reports, 344 (Terrestrial Biology 14): 1-7 (2016).

2015

  1. Narihiro T, Nobu MK, Mei R, Liu WT: Microbial Community Involved in Anaerobic Purified Terephthalic Acid Treatment Process, pp. 31-48. In Fang HHP, Zhang T. (ed.), Anaerobic Biotechnology: Environmental Protection and Resource Recovery. World Scientific Publishing, Singapore (2015).
  2. Narihiro T, Sekiguchi Y: Primers: Functional Genes and 16S rRNA Genes for Methanogens, pp. 79-139. In McGenity TJ, Timmis KN, Nogales B. (ed.), Hydrocarbon and Lipid Microbiology Protocols. Springer Berlin Heidelberg, New York (2015).
  3. Kudoh S, Takahashi KT, Ishihara T, Tsujimoto M, Nakai R, Suzuki AC, Tanabe Y, Uchida M, Imura S: Meteorological data from ice-free areas in Yukidori Zawa, Langhovde, Kizahashi Hama, Skarvsnes and Skallen in Sôya Coast, East Antarctica during 2014– 2015. JARE Data Reports, 339 (Terrestrial Biology 11): 1-6 (2015).

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Bioproduction Research Institute

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