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Tripartite Symbiosis of an Anaerobic Scuticociliate with two Hydrogenosome-Associated Endosymbionts, a Holospora-related Alphaproteobacterium and a Methanogenic Archaeon.

Takeshita K, Yamada T, Kawahara Y, Narihiro T, Ito M, Kamagata Y, Shinzato N.

Appl Environ Microbiol. 2019 Oct 4. pii: AEM.00854-19. doi: 10.1128/AEM.00854-19. [Epub ahead of print]


Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States.

Yamamoto K, Hackley KC, Kelly WR, Panno SV, Sekiguchi Y, Sanford RA, Liu WT, Kamagata Y, Tamaki H.

Sci Rep. 2019 Sep 17;9(1):13484. doi: 10.1038/s41598-019-49996-z.


Molecular evolutionary engineering of xylose isomerase to improve its catalytic activity and performance of micro-aerobic glucose/xylose co-fermentation in Saccharomyces cerevisiae.

Seike T, Kobayashi Y, Sahara T, Ohgiya S, Kamagata Y, Fujimori KE.

Biotechnol Biofuels. 2019 Jun 6;12:139. doi: 10.1186/s13068-019-1474-z. eCollection 2019.


Whole-Genome Sequence of an Isogenic Haploid Strain, Saccharomyces cerevisiae IR-2idA30(MATa), Established from the Industrial Diploid Strain IR-2.

Fujimori KE, Kobayashi Y, Seike T, Sahara T, Ohgiya S, Kamagata Y.

Microbiol Resour Announc. 2019 Apr 25;8(17). pii: e00018-19. doi: 10.1128/MRA.00018-19.


Novel N-Acyl Homoserine Lactone-Degrading Bacteria Isolated From Penicillin-Contaminated Environments and Their Quorum-Quenching Activities.

Kusada H, Zhang Y, Tamaki H, Kimura N, Kamagata Y.

Front Microbiol. 2019 Mar 14;10:455. doi: 10.3389/fmicb.2019.00455. eCollection 2019.


Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.

Takeuchi M, Ozaki H, Hiraoka S, Kamagata Y, Sakata S, Yoshioka H, Iwasaki W.

PLoS One. 2019 Mar 14;14(3):e0213535. doi: 10.1371/journal.pone.0213535. eCollection 2019.


Conductive Iron Oxides Promote Methanogenic Acetate Degradation by Microbial Communities in a High-Temperature Petroleum Reservoir.

Kato S, Wada K, Kitagawa W, Mayumi D, Ikarashi M, Sone T, Asano K, Kamagata Y.

Microbes Environ. 2019 Mar 30;34(1):95-98. doi: 10.1264/jsme2.ME18140. Epub 2019 Feb 15.


"Duckweed-Microbe Co-Cultivation Method" for Isolating a Wide Variety of Microbes Including Taxonomically Novel Microbes.

Tanaka Y, Tamaki H, Tanaka K, Tozawa E, Matsuzawa H, Toyama T, Kamagata Y, Mori K.

Microbes Environ. 2018 Dec 28;33(4):402-406. doi: 10.1264/jsme2.ME18067. Epub 2018 Nov 7.


Novel gene encoding a unique luciferase from the fireworm Odontsyllis undecimdonta.

Mitani Y, Yasuno R, Isaka M, Mitsuda N, Futahashi R, Kamagata Y, Ohmiya Y.

Sci Rep. 2018 Aug 24;8(1):12789. doi: 10.1038/s41598-018-31086-1.


Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism.

Hidalgo-Ahumada CAP, Nobu MK, Narihiro T, Tamaki H, Liu WT, Kamagata Y, Stams AJM, Imachi H, Sousa DZ.

Environ Microbiol. 2018 Dec;20(12):4503-4511. doi: 10.1111/1462-2920.14388. Epub 2018 Oct 30.


Isolation of Previously Uncultured Slow-Growing Bacteria by Using a Simple Modification in the Preparation of Agar Media.

Kato S, Yamagishi A, Daimon S, Kawasaki K, Tamaki H, Kitagawa W, Abe A, Tanaka M, Sone T, Asano K, Kamagata Y.

Appl Environ Microbiol. 2018 Sep 17;84(19). pii: e00807-18. doi: 10.1128/AEM.00807-18. Print 2018 Oct 1.


Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice.

Kusada H, Kameyama K, Meng XY, Kamagata Y, Tamaki H.

Sci Rep. 2017 Dec 22;7(1):18087. doi: 10.1038/s41598-017-18122-2.


Petrothermobacter organivorans gen. nov., sp. nov., a thermophilic, strictly anaerobic bacterium of the phylum Deferribacteres isolated from a deep subsurface oil reservoir.

Tamazawa S, Mayumi D, Mochimaru H, Sakata S, Maeda H, Wakayama T, Ikarashi M, Kamagata Y, Tamaki H.

Int J Syst Evol Microbiol. 2017 Oct;67(10):3982-3986. doi: 10.1099/ijsem.0.002234. Epub 2017 Sep 12.


Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides.

Yasutake Y, Kusada H, Ebuchi T, Hanada S, Kamagata Y, Tamura T, Kimura N.

Sci Rep. 2017 Aug 21;7(1):8946. doi: 10.1038/s41598-017-09399-4.


Phosphate-Catalyzed Hydrogen Peroxide Formation from Agar, Gellan, and κ-Carrageenan and Recovery of Microbial Cultivability via Catalase and Pyruvate.

Kawasaki K, Kamagata Y.

Appl Environ Microbiol. 2017 Oct 17;83(21). pii: e01366-17. doi: 10.1128/AEM.01366-17. Print 2017 Nov 1.


Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome.

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.

Water Res. 2017 Nov 1;124:77-84. doi: 10.1016/j.watres.2017.07.050. Epub 2017 Jul 20.


Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method.

Tanaka Y, Matsuzawa H, Tamaki H, Tagawa M, Toyama T, Kamagata Y, Mori K.

Microbes Environ. 2017 Sep 27;32(3):288-292. doi: 10.1264/jsme2.ME17027. Epub 2017 Jul 22.


Restoration of the growth of Escherichia coli under K+-deficient conditions by Cs+ incorporation via the K+ transporter Kup.

Kato S, Kanata Y, Kitagawa W, Sone T, Asano K, Kamagata Y.

Sci Rep. 2017 May 16;7(1):1965. doi: 10.1038/s41598-017-02024-4.


A Novel Quorum-Quenching N-Acylhomoserine Lactone Acylase from Acidovorax sp. Strain MR-S7 Mediates Antibiotic Resistance.

Kusada H, Tamaki H, Kamagata Y, Hanada S, Kimura N.

Appl Environ Microbiol. 2017 Jun 16;83(13). pii: e00080-17. doi: 10.1128/AEM.00080-17. Print 2017 Jul 1.


A Thermostable Bilirubin-Oxidizing Enzyme from Activated Sludge Isolated by a Metagenomic Approach.

Kimura N, Kamagata Y.

Microbes Environ. 2017;32(1):92. doi: 10.1264/jsme2.ME16106e.


Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges.

Narihiro T, Kamagata Y.

Microbes Environ. 2017;32(1):1-4. doi: 10.1264/jsme2.ME3201rh. No abstract available.


Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production.

Kobayashi Y, Sahara T, Suzuki T, Kamachi S, Matsushika A, Hoshino T, Ohgiya S, Kamagata Y, Fujimori KE.

J Ind Microbiol Biotechnol. 2017 Jun;44(6):879-891. doi: 10.1007/s10295-017-1912-5. Epub 2017 Feb 8.


A Thermostable Bilirubin-Oxidizing Enzyme from Activated Sludge Isolated by a Metagenomic Approach.

Kimura N, Kamagata Y.

Microbes Environ. 2016 Dec 23;31(4):435-441. doi: 10.1264/jsme2.ME16106. Epub 2016 Nov 23. Erratum in: Microbes Environ. 2017;32(1):92.


Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant.

Terashima M, Yama A, Sato M, Yumoto I, Kamagata Y, Kato S.

Microbes Environ. 2016 Dec 23;31(4):449-455. doi: 10.1264/jsme2.ME16097. Epub 2016 Nov 19.


Methane production from coal by a single methanogen.

Mayumi D, Mochimaru H, Tamaki H, Yamamoto K, Yoshioka H, Suzuki Y, Kamagata Y, Sakata S.

Science. 2016 Oct 14;354(6309):222-225.


Symbiosis Studies in Microbial Ecology.

Kamagata Y, Narihiro T.

Microbes Environ. 2016;31(3):201-3. doi: 10.1264/jsme2.ME3103rh. No abstract available.


Complete Genome Sequence of the Intracellular Bacterial Symbiont TC1 in the Anaerobic Ciliate Trimyema compressum.

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.

Genome Announc. 2016 Sep 22;4(5). pii: e01032-16. doi: 10.1128/genomeA.01032-16.


Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field.

Mochimaru H, Tamaki H, Katayama T, Imachi H, Sakata S, Kamagata Y.

Int J Syst Evol Microbiol. 2016 Nov;66(11):4873-4877. doi: 10.1099/ijsem.0.001444. Epub 2016 Aug 23.


Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria.

Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT.

Microbes Environ. 2016 Sep 29;31(3):288-92. doi: 10.1264/jsme2.ME16057. Epub 2016 Jul 16.


In Situ Gene Expression Responsible for Sulfide Oxidation and CO2 Fixation of an Uncultured Large Sausage-Shaped Aquificae Bacterium in a Sulfidic Hot Spring.

Tamazawa S, Yamamoto K, Takasaki K, Mitani Y, Hanada S, Kamagata Y, Tamaki H.

Microbes Environ. 2016 Jun 25;31(2):194-8. doi: 10.1264/jsme2.ME16013. Epub 2016 Jun 7.


Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae.

Tani T, Taguchi H, Fujimori KE, Sahara T, Ohgiya S, Kamagata Y, Akamatsu T.

J Biosci Bioeng. 2016 Oct;122(4):446-55. doi: 10.1016/j.jbiosc.2016.03.008. Epub 2016 Apr 8.


Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica Strain 4J5T (JCM 14075), a Mesophilic Butyrate- and 2-Methylbutyrate-Degrading Syntroph.

Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Liu WT.

Genome Announc. 2016 Mar 3;4(2). pii: e00047-16. doi: 10.1128/genomeA.00047-16.


Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion.

Kato S, Goya E, Tanaka M, Kitagawa W, Kikuchi Y, Asano K, Kamagata Y.

Sci Rep. 2016 Feb 17;6:20041. doi: 10.1038/srep20041.


Keys to Cultivating Uncultured Microbes: Elaborate Enrichment Strategies and Resuscitation of Dormant Cells.

Kamagata Y.

Microbes Environ. 2015;30(4):289-90. doi: 10.1264/jsme2.ME3004rh. No abstract available.


Burkholderia of Plant-Beneficial Group are Symbiotically Associated with Bordered Plant Bugs (Heteroptera: Pyrrhocoroidea: Largidae).

Takeshita K, Matsuura Y, Itoh H, Navarro R, Hori T, Sone T, Kamagata Y, Mergaert P, Kikuchi Y.

Microbes Environ. 2015;30(4):321-9. doi: 10.1264/jsme2.ME15153. Epub 2015 Dec 9.


Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen.

Kanno M, Constant P, Tamaki H, Kamagata Y.

Environ Microbiol. 2016 Sep;18(8):2495-506. doi: 10.1111/1462-2920.13162. Epub 2016 Jan 21.


Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil.

Kato S, Chino K, Kamimura N, Masai E, Yumoto I, Kamagata Y.

Sci Rep. 2015 Sep 24;5:14295. doi: 10.1038/srep14295.


Insect's intestinal organ for symbiont sorting.

Ohbayashi T, Takeshita K, Kitagawa W, Nikoh N, Koga R, Meng XY, Tago K, Hori T, Hayatsu M, Asano K, Kamagata Y, Lee BL, Fukatsu T, Kikuchi Y.

Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5179-88. doi: 10.1073/pnas.1511454112. Epub 2015 Aug 31.


Zincmethylphyrins and coproporphyrins, novel growth factors released by Sphingopyxis sp., enable laboratory cultivation of previously uncultured Leucobacter sp. through interspecies mutualism.

Bhuiyan MN, Takai R, Mitsuhashi S, Shigetomi K, Tanaka Y, Kamagata Y, Ubukata M.

J Antibiot (Tokyo). 2016 Feb;69(2):97-103. doi: 10.1038/ja.2015.87. Epub 2015 Aug 26.


Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments.

Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y.

Front Microbiol. 2015 May 5;6:386. doi: 10.3389/fmicb.2015.00386. eCollection 2015.


pH-induced change in cell susceptibility to butanol in a high butanol-tolerant bacterium, Enterococcus faecalis strain CM4A.

Kanno M, Tamaki H, Mitani Y, Kimura N, Hanada S, Kamagata Y.

Biotechnol Biofuels. 2015 Apr 17;8:69. doi: 10.1186/s13068-015-0251-x. eCollection 2015.


Increase in Bacterial Colony Formation from a Permafrost Ice Wedge Dosed with a Tomitella biformata Recombinant Resuscitation-Promoting Factor Protein.

Puspita ID, Kitagawa W, Kamagata Y, Tanaka M, Nakatsu CH.

Microbes Environ. 2015;30(2):151-6. doi: 10.1264/jsme2.ME14119. Epub 2015 Apr 4.


Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions.

Takeuchi M, Yamagishi T, Kamagata Y, Oshima K, Hattori M, Katayama T, Hanada S, Tamaki H, Marumo K, Maeda H, Nedachi M, Iwasaki W, Suwa Y, Sakata S.

Int J Syst Evol Microbiol. 2015 Jun;65(Pt 6):1749-54. doi: 10.1099/ijs.0.000167. Epub 2015 Mar 4.


Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.

Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT.

ISME J. 2015 Aug;9(8):1710-22. doi: 10.1038/ismej.2014.256. Epub 2015 Jan 23.


Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester.

Kanno M, Katayama T, Morita N, Tamaki H, Hanada S, Kamagata Y.

Int J Syst Evol Microbiol. 2015 Mar;65(Pt 3):805-10. doi: 10.1099/ijs.0.000021. Epub 2014 Dec 6.


The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium.

Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y.

Front Microbiol. 2014 Oct 30;5:575. doi: 10.3389/fmicb.2014.00575. eCollection 2014.


Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor.

Kato S, Yumoto I, Kamagata Y.

Appl Environ Microbiol. 2015 Jan;81(1):67-73. doi: 10.1128/AEM.02767-14. Epub 2014 Oct 10.


Draft Genome Sequence of "Candidatus Phytoplasma asteris" Strain OY-V, an Unculturable Plant-Pathogenic Bacterium.

Kakizawa S, Makino A, Ishii Y, Tamaki H, Kamagata Y.

Genome Announc. 2014 Sep 18;2(5). pii: e00944-14. doi: 10.1128/genomeA.00944-14.

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