PUBLICATIONS

2024

  1. Doi K, Mori K, Komatsu M, Shinoda A, Tashiro K, Higuchi Y, Nakayama J, Takegawa K. Molecular mechanisms of complex-type N-glycan breakdown and metabolism by the human intestinal bacterium Barnesiella intestinihominis. J Biosci Bioeng. 2024 Nov 6:S1389-1723(24)00304-9. doi: 10.1016/j.jbiosc.2024.10.006. Epub ahead of print. PMID: 39510934.
  2. Doi K, Mori K, Komatsu M, Shinoda A, Tashiro K, Higuchi Y, Nakayama J, Takegawa K. Molecular mechanisms of complex-type N-glycan breakdown and metabolism by the human intestinal bacterium Barnesiella intestinihominis. J Biosci Bioeng. 2024 Nov 6:S1389-1723(24)00304-9. doi: 10.1016/j.jbiosc.2024.10.006. Epub ahead of print. PMID: 39510934.
  3. Rahayu ES, Yoga WK, Komalasari H, Mariyatun M, Yuda WA, Manurung NEP, Hasan PN, Suharman S, Pamungkaningtyas FH, Nurfiana DA, Pramesi PC, Gatya M, Therdtatha P, Nakayama J, Juffrie M, Djaafar TF, Marwati T, Utami T. Probiotic Chocolate Containing Lactobacillus plantarum Dad-13 Alters the Gut Microbiota Composition of Undernourished Children in Lombok: A Randomized Double-Blind Trial. Int J Food Sci. 2024 Aug 3;2024:9493797. doi: 10.1155/2024/9493797. PMID: 39132547; PMCID: PMC11316911.
  4. Shinoda A, Lkhagvajav T, Mishima R, Therdtatha P, Jamiyan D, Purevdorj C, Sonomtseren S, Chimeddorj B, Namdag B, Lee YK, Demberel S, Nakayama J. Gut microbiome signatures associated with type 2 diabetes in obesity in Mongolia. Front Microbiol. 2024 Jun 25;15:1355396. doi: 10.3389/fmicb.2024.1355396. PMID: 38983625; PMCID: PMC11231203.
  5. Ikeda H, Ihara E, Takeya K, Mukai K, Onimaru M, Ouchida K, Hata Y, Bai X, Tanaka Y, Sasaki T, Saito F, Eto M, Nakayama J, Oda Y, Nakamura M, Inoue H, Ogawa Y. The interplay between alterations in esophageal microbiota associated with Th17 immune response and impaired LC20 phosphorylation in achalasia. J Gastroenterol. 2024 May;59(5):361-375. doi: 10.1007/s00535-024-02088-w. Epub 2024 Mar 12. PMID: 38472375.

2023

  1. Mishima R, Tanaka M, Momoda R, Sanefuji M, Morokuma S, Ogawa M, Kato K, Nakayama J. Longitudinal gut mycobiota changes in Japanese infants during first three years of life. J Biosci Bioeng. 2023 Apr;135(4):266-273. doi: 10.1016/j.jbiosc.2023.01.007. Epub 2023 Feb 4. PMID: 36740519.
  2. Oshiro M, Zendo T, Tashiro Y, Nakayama J. Cyclic pairwise interaction representing a rock-paper-scissors game maintains the population of the vulnerable yeast Saccharomyces cerevisiae within a multispecies sourdough microbiome. Microbiol Spectr. 2023 Dec 12;11(6):e0137023. doi: 10.1128/spectrum.01370-23. Epub 2023 Nov 2. PMID: 37916803; PMCID: PMC10714952.
  3. Refai MY, Elazzazy AM, Desouky SE, Abu-Elghait M, Fayed EA, Alajel SM, Alajlan AA, Albureikan MO, Nakayama J. Interception of Epoxide ring to quorum sensing system in Enterococcus faecalis and Staphylococcus aureus. AMB Express. 2023 Nov 9;13(1):126. doi: 10.1186/s13568-023-01633-9. PMID: 37946062; PMCID: PMC10636001.

2022

  1. Therdtatha P, Shinoda A, Nakayama J. Crisis of the Asian gut: associations among diet, microbiota, and metabolic diseases. Biosci Microbiota Food Health. 2022;41(3):83-93. doi: 10.12938/bmfh.2021-085. Epub 2022 Feb 9. PMID: 35854695; PMCID: PMC9246424.
  2. Dai H, Otsuka A, Tanabe K, Yanagita T, Nakayama J, Kitagaki H. Glucosylceramide Changes Bacterial Metabolism and Increases Gram-Positive Bacteria through Tolerance to Secondary Bile Acids In Vitro. Int J Mol Sci. 2022 May 10;23(10):5300. doi: 10.3390/ijms23105300. PMID: 35628110; PMCID: PMC9141989.
  3. Tourlousse DM, Narita K, Miura T, Ohashi A, Matsuda M, Ohyama Y, Shimamura M, Furukawa M, Kasahara K, Kameyama K, Saito S, Goto M, Shimizu R, Mishima R, Nakayama J, Hosomi K, Kunisawa J, Terauchi J, Sekiguchi Y, Kawasaki H. Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements. Microbiol Spectr. 2022 Apr 27;10(2):e0191521. doi: 10.1128/spectrum.01915-21. Epub 2022 Mar 2. PMID: 35234490; PMCID: PMC8941912.
  4. Nagao JI, Kishikawa S, Tanaka H, Toyonaga K, Narita Y, Negoro-Yasumatsu K, Tasaki S, Arita-Morioka KI, Nakayama J, Tanaka Y. Pathobiont-responsive Th17 cells in gut-mouth axis provoke inflammatory oral disease and are modulated by intestinal microbiome. Cell Rep. 2022 Sep 6;40(10):111314. doi: 10.1016/j.celrep.2022.111314. PMID: 36070692.

2021

  1. Watanabe M, Sianoya A, Mishima R, Therdtatha P, Rodriguez A, Ramos DC, Lee YK, Dalmacio LM, Nakayama J. Gut microbiome status of urban and rural Filipino adults in relation to diet and metabolic disorders. FEMS Microbiol Lett. 2021 Dec 7;368(20):fnab149. doi: 10.1093/femsle/fnab149. PMID: 34849762.
  2. Oshiro M, Tanaka M, Momoda R, Zendo T, Nakayama J. Mechanistic Insight into Yeast Bloom in a Lactic Acid Bacteria Relaying-Community in the Start of Sourdough Microbiota Evolution. Microbiol Spectr. 2021 Oct 31;9(2):e0066221. doi: 10.1128/Spectrum.00662-21. Epub 2021 Oct 20. PMID: 34668750; PMCID: PMC8528097.
  3. Onizuka S, Tanaka M, Mishima R, Nakayama J. Cultivation of Spore-Forming Gut Microbes Using a Combination of Bile Acids and Amino Acids. Microorganisms. 2021 Aug 2;9(8):1651. doi: 10.3390/microorganisms9081651. PMID: 34442730; PMCID: PMC8401671.
  4. Inoue T, Funatsu Y, Ohnishi M, Isogawa M, Kawashima K, Tanaka M, Moriya K, Kawaratani H, Momoda R, Iio E, Nakagawa H, Suzuki Y, Matsuura K, Fujiwara K, Nakajima A, Yoshiji H, Nakayama J, Tanaka Y. Bile acid dysmetabolism in the gut- microbiota-liver axis under hepatitis C virus infection. Liver Int. 2022 Jan;42(1):124-134. doi: 10.1111/liv.15041. Epub 2021 Sep 5. PMID: 34411400.
  5. Nishihara Y, Ogino H, Tanaka M, Ihara E, Fukaura K, Nishioka K, Chinen T, Tanaka Y, Nakayama J, Kang D, Ogawa Y. Mucosa-associated gut microbiota reflects clinical course of ulcerative colitis. Sci Rep. 2021 Jul 2;11(1):13743. doi: 10.1038/s41598-021-92870-0. PMID: 34215773; PMCID: PMC8253849.
  6. Therdtatha P, Song Y, Tanaka M, Mariyatun M, Almunifah M, Manurung NEP, Indriarsih S, Lu Y, Nagata K, Fukami K, Ikeda T, Lee YK, Rahayu ES, Nakayama J. Gut Microbiome of Indonesian Adults Associated with Obesity and Type 2 Diabetes: A Cross-Sectional Study in an Asian City, Yogyakarta. Microorganisms. 2021 Apr 22;9(5):897. doi: 10.3390/microorganisms9050897. PMID: 33922321; PMCID: PMC8147061.
  7. Kamil RZ, Murdiati A, Juffrie M, Nakayama J, Rahayu ES. Gut Microbiota and Short-Chain Fatty Acid Profile between Normal and Moderate Malnutrition Children in Yogyakarta, Indonesia. Microorganisms. 2021 Jan 7;9(1):127. doi: 10.3390/microorganisms9010127. PMID: 33430510; PMCID: PMC7826765.
  8. Chumponsuk T, Gruneck L, Gentekaki E, Jitprasertwong P, Kullawong N, Nakayama J, Popluechai S. The salivary microbiota of Thai adults with metabolic disorders and association with diet. Arch Oral Biol. 2021 Feb;122:105036. doi: 10.1016/j.archoralbio.2020.105036. Epub 2021 Jan 2. PMID: 33421657.
  9. Oshiro M, Zendo T, Nakayama J. Diversity and dynamics of sourdough lactic acid bacteriota created by a slow food fermentation system. J Biosci Bioeng. 2021 Apr;131(4):333-340. doi: 10.1016/j.jbiosc.2020.11.007. Epub 2021 Jan 6. PMID: 33358094.

2020

  1. Tanaka M, Onizuka S, Mishima R, Nakayama J. Cultural isolation of spore- forming bacteria in human feces using bile acids. Sci Rep. 2020 Sep 14;10(1):15041. doi: 10.1038/s41598-020-71883-1. PMID: 32929101; PMCID: PMC7490687.
  2. La-Ongkham O, Nakphaichit M, Nakayama J, Keawsompong S, Nitisinprasert S. Age-related changes in the gut microbiota and the core gut microbiome of healthy Thai humans. 3 Biotech. 2020 Jun;10(6):276. doi: 10.1007/s13205-020-02265-7. Epub 2020 May 30. PMID: 32537376; PMCID: PMC7261292.
  3. Khine WWT, Rahayu ES, See TY, Kuah S, Salminen S, Nakayama J, Lee YK. Indonesian children fecal microbiome from birth until weaning was different from microbiomes of their mothers. Gut Microbes. 2020 Nov 9;12(1):1761240. doi: 10.1080/19490976.2020.1761240. Epub 2020 May 26. PMID: 32453977; PMCID: PMC7524161.
  4. Furukawa M, Moriya K, Nakayama J, Inoue T, Momoda R, Kawaratani H, Namisaki T, Sato S, Douhara A, Kaji K, Kitade M, Shimozato N, Sawada Y, Saikawa S, Takaya H, Kitagawa K, Akahane T, Mitoro A, Yamao J, Tanaka Y, Yoshiji H. Gut dysbiosis associated with clinical prognosis of patients with primary biliary cholangitis. Hepatol Res. 2020 Jul;50(7):840-852. doi: 10.1111/hepr.13509. Epub 2020 Jun 10. PMID: 32346970.
  5. Fujiwara M, Kuwahara D, Hayashi M, Zendo T, Sato M, Nakayama J, Sonomoto K. Lowering effect of viable Pediococcus pentosaceus QU 19 on the rise in postprandial glucose. Biosci Microbiota Food Health. 2020;39(2):57-64. doi: 10.12938/bmfh.19-041. Epub 2020 Jan 25. PMID: 32328401; PMCID: PMC7162691.

2019

  1. Fukao M, Zendo T, Inoue T, Fuke N, Moriuchi T, Yamane Y, Nakayama J, Sonomoto K, Fukaya T. Relation between cell-bound exopolysaccharide production via plasmid-encoded genes and rugose colony morphology in the probiotic Lactobacillus brevis KB290. Anim Sci J. 2019 Dec;90(12):1575-1580. doi: 10.1111/asj.13297. Epub 2019 Oct 8. PMID: 31593351.
  2. Tanaka M, Sanefuji M, Morokuma S, Yoden M, Momoda R, Sonomoto K, Ogawa M, Kato K, Nakayama J. The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants. Gut Microbes. 2020;11(2):205-216. doi: 10.1080/19490976.2019.1650997. Epub 2019 Sep 24. PMID: 31550982; PMCID: PMC7053967.
  3. Fukao M, Zendo T, Inoue T, Nakayama J, Suzuki S, Fukaya T, Yajima N, Sonomoto K. Plasmid-encoded glycosyltransferase operon is responsible for exopolysaccharide production, cell aggregation, and bile resistance in a probiotic strain, Lactobacillus brevis KB290. J Biosci Bioeng. 2019 Oct;128(4):391-397. doi: 10.1016/j.jbiosc.2019.04.008. Epub 2019 May 22. PMID: 31126721
  4. Nakayama J, Watanabe K, Jiang J, Matsuda K, Chao SH, Haryono P, La-Ongkham O, Sarwoko MA, Sujaya IN, Zhao L, Chen KT, Chen YP, Chiu HH, Hidaka T, Huang NX, Kiyohara C, Kurakawa T, Sakamoto N, Sonomoto K, Tashiro K, Tsuji H, Chen MJ, Leelavatcharamas V, Liao CC, Nitisinprasert S, Rahayu ES, Ren FZ, Tsai YC, Lee YK. Author Correction: Diversity in gut bacterial community of school-age children in Asia. Sci Rep. 2019 Apr 25;9(1):6530. doi: 10.1038/s41598-019-42780-z. Erratum for: Sci Rep. 2015 Feb 23;5:8397. PMID: 31024062; PMCID: PMC6484003.
  5. Hamajima H, Tanaka M, Miyagawa M, Sakamoto M, Nakamura T, Yanagita T, Nishimukai M, Mitsutake S, Nakayama J, Nagao K, Kitagaki H. Koji glycosylceramide commonly contained in Japanese traditional fermented foods alters cholesterol metabolism in obese mice. Biosci Biotechnol Biochem. 2019 Aug;83(8):1514-1522. doi: 10.1080/09168451.2018.1562877. Epub 2018 Dec 30. PMID: 30595103.

2018

  1. Kisuse J, La-Ongkham O, Nakphaichit M, Therdtatha P, Momoda R, Tanaka M, Fukuda S, Popluechai S, Kespechara K, Sonomoto K, Lee YK, Nitisinprasert S, Nakayama J. Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand. Front Microbiol. 2018 Jun 22;9:1345. doi: 10.3389/fmicb.2018.01345. PMID: 29988433; PMCID: PMC6024022.
  2. Inoue T, Nakayama J, Moriya K, Kawaratani H, Momoda R, Ito K, Iio E, Nojiri S, Fujiwara K, Yoneda M, Yoshiji H, Tanaka Y. Gut Dysbiosis Associated With Hepatitis C Virus Infection. Clin Infect Dis. 2018 Aug 31;67(6):869-877. doi: 10.1093/cid/ciy205. PMID: 29718124.
  3. Adachi K, Ohtani K, Kawano M, Singh RP, Yousuf B, Sonomoto K, Shimizu T, Nakayama J. Metabolic dependent and independent pH-drop shuts down VirSR quorum sensing in Clostridium perfringens. J Biosci Bioeng. 2018 May;125(5):525-531. doi: 10.1016/j.jbiosc.2017.12.019. Epub 2018 Jan 17. PMID: 29373309.

2017

  1. Tanaka M, Korenori Y, Washio M, Kobayashi T, Momoda R, Kiyohara C, Kuroda A, Saito Y, Sonomoto K, Nakayama J. Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood. FEMS Microbiol Ecol. 2017 Aug 1;93(8). doi: 10.1093/femsec/fix099. PMID: 28903469.
  2. Tanaka M, Nakayama J. Development of the gut microbiota in infancy and its impact on health in later life. Allergol Int. 2017 Oct;66(4):515-522. doi: 10.1016/j.alit.2017.07.010. Epub 2017 Aug 18. PMID: 28826938.
  3. Kitazaki K, Koga S, Nagatoshi K, Kuwano K, Zendo T, Nakayama J, Sonomoto K, Ano H, Katamoto H. In vitro synergistic activities of cefazolin and nisin A against mastitis pathogens. J Vet Med Sci. 2017 Sep 12;79(9):1472-1479. doi: 10.1292/jvms.17-0180. Epub 2017 Jul 29. PMID: 28757508; PMCID: PMC5627315.
  4. Nakayama J, Yamamoto A, Palermo-Conde LA, Higashi K, Sonomoto K, Tan J, Lee YK. Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island. Front Microbiol. 2017 Feb 14;8:197. doi: 10.3389/fmicb.2017.00197. PMID: 28261164; PMCID: PMC5306386.
  5. Fujita Y, Tsuno H, Nakayama J. Fermented Papaya Preparation Restores Age- Related Reductions in Peripheral Blood Mononuclear Cell Cytolytic Activity in Tube-Fed Patients. PLoS One. 2017 Jan 6;12(1):e0169240. doi: 10.1371/journal.pone.0169240. PMID: 28060858; PMCID: PMC5218495.

2016

  1. Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J, Nitisinprasert S. Microbial Community of Healthy Thai Vegetarians and Non- Vegetarians, Their Core Gut Microbiota, and Pathogen Risk. J Microbiol Biotechnol. 2016 Oct 28;26(10):1723-1735. doi: 10.4014/jmb.1603.03057. PMID: 27381339.

2015

  1. Nakayama J, Watanabe K, Jiang J, Matsuda K, Chao SH, Haryono P, La-Ongkham O, Sarwoko MA, Sujaya IN, Zhao L, Chen KT, Chen YP, Chiu HH, Hidaka T, Huang NX, Kiyohara C, Kurakawa T, Sakamoto N, Sonomoto K, Tashiro K, Tsuji H, Chen MJ, Leelavatcharamas V, Liao CC, Nitisinprasert S, Rahayu ES, Ren FZ, Tsai YC, Lee YK. Diversity in gut bacterial community of school-age children in Asia. Sci Rep. 2015 Feb 23;5:8397. doi: 10.1038/srep08397. Erratum in: Sci Rep. 2019 Apr 25;9(1):6530. PMID: 25703686; PMCID: PMC4336934.