石川県の野鼠の腸内微生物叢
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| Published in | 衛生動物 Vol. 76; no. 1; pp. 25 - 31 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
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日本衛生動物学会
25.03.2025
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| ISSN | 0424-7086 2185-5609 |
| DOI | 10.7601/mez.76.25 |
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| Author | 及川, 陽三郎 望月, 恒太 所, 正治 Arifah, Lacante Siti 村上, 学 |
|---|---|
| Author_xml | – sequence: 1 fullname: Arifah, Lacante Siti – sequence: 1 fullname: 所, 正治 – sequence: 1 fullname: 望月, 恒太 – sequence: 1 fullname: 及川, 陽三郎 – sequence: 1 fullname: 村上, 学 |
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| ContentType | Journal Article |
| Copyright | 2025 日本衛生動物学会 |
| Copyright_xml | – notice: 2025 日本衛生動物学会 |
| DOI | 10.7601/mez.76.25 |
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| Discipline | Public Health Zoology |
| EISSN | 2185-5609 |
| EndPage | 31 |
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| PublicationDate | 2025/03/25 |
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The gut microbiota of wild mice. PLoS One, 10: e0134643. Aivelo, T. and Norberg, A. 2018. Parasite-microbiota interactions potentially affect intestinal communities in wild mammals. J. Anim. Ecol., 87: 438–447. Hugerth, L. W., Muller, E. E., Hu, Y. O., Lebrun, L. A., Roume, H., Lundin, D., Wilmes, P. and Andersson, A. F. 2014. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One, 9: e95567. Popovic, A., Cao, E. Y., Han, J., Nursimulu, N., Alves-Ferreira, E. V. C., Burrows, K., Kennard, A., Alsmadi, N., Grigg, M. E., Mortha, A. and Parkinson, J. 2024. Commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota. ISME J., 18: wrae023. Han, B. A., Schmidt, J. P., Bowden, S. E. and Drake, J. M. 2015. Rodent reservoirs of future zoonotic diseases. Proc. Natl. Acad. Sci. U.S.A., 112: 7039–7044. Reynolds, L. A., Finlay, B. B. and Maizels, R. M. 2015. Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity. J. Immunol., 195: 4059–4066. Brosschot, T. P. and Reynolds, L. A. 2018. The impact of a helminth-modified microbiome on host immunity. Mucosal Immunol., 11: 1039–1046. Midha, A., Jarquin-Diaz, V. H., Ebner, F., Lober, U., Hayani, R., Kundik, A., Cardilli, A., Heitlinger, E., Forslund, S. K. and Hartmann, S. 2022. Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host. Microbiome, 10: 229. Sasaki, M., Anders, L. A. and Nakao, M. 2021. Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes. Species Divers., 26: 255–272. Sugden, S., Sanderson, D., Ford, K., Stein, L. Y. and St Clair, C. C. 2020. An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health. Sci. Rep., 10: 22207. Stevens, E. J., Bates, K. A. and King, K. C. 2021. Host microbiota can facilitate pathogen infection. PLoS Pathog., 17: e1009514. Holm, J. B., Sorobetea, D., Kiilerich, P., Ramayo-Caldas, Y., Estelle, J., Ma, T., Madsen, L., Kristiansen, K. and Svensson-Frej, M. 2015. Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli. PLoS One, 10: e0125495. Kim, S. L., Choi, J. H., Yi, M. H., Lee, S., Kim, M., Oh, S., Lee, I. Y., Jeon, B. Y., Yong, T. S. and Kim, J. Y. 2022. Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius. Parasit. Vectors, 15: 486. Fuirst, M., Veit, R. R., Hahn, M., Dheilly, N. and Thorne, L. H. 2018. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS One, 13: e0209200. Magoc, T. and Salzberg, S. L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27: 2957–2963. Apprill, A., McNally, S., Parsons, R. and Weber, L. 2015. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol., 75: 129–137. Mistrick, J., Kipp, E. J., Weinberg, S. I., Adams, C. C., Larsen, P. A. and Craft, M. E. 2024. Microbiome diversity and zoonotic bacterial pathogen prevalence in Peromyscus mice from agricultural landscapes and synanthropic habitat. Mol. Ecol., 33: e17309. Tsunesumi, N., Sato, G., Iwasa, M., Kabeya, H., Maruyama, S. and Tohya, Y. 2012. Novel murine norovirus-like genes in wild rodents in Japan. J. Vet. Med. Sci., 74: 1221–1224. Appelbee, A. J., Thompson, R. C. and Olson, M. E. 2005. Giardia and Cryptosporidium in mammalian wildlife--current status and future needs. Trends Parasitol., 21: 370–376. Suzuki, T. A., Martins, F. M. and Nachman, M. W. 2019. Altitudinal variation of the gut microbiota in wild house mice. Mol. Ecol., 28: 2378–2390. Bui, T. H., Nguyen, K. T., Ikeuchi, S., Yanagawa, H., Sato, Y., Tran, T. H. T., Okumura, M., Niwa, T., Taniguchi, T. and Hayashidani, H. 2021. A long-term observation for ecology of pathogenic Yersinia in wild rodents living in Fukushima Prefecture, Japan. J. Vet. Med. Sci., 83: 1790–1794. Heni, A. C., Fackelmann, G., Eibner, G., Kreinert, S., Schmid, J., Schwensow, N. I., Wiegand, J., Wilhelm, K. and Sommer, S. 2023. Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances. Anim. Microbiome, 5: 22. Ono, K., Tsuji, H., Rai, S. K., Yamamoto, A., Masuda, K., Endo, T., Hotta, H., Kawamura, T. and Uga, S. 2001. Contamination of river water by Cryptosporidium parvum oocysts in western Japan. Appl. Environ. Microbiol., 67: 3832–3836. Walk, S. T., Blum, A. M., Ewing, S. A., Weinstock, J. V. and Young, V. B. 2010. Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides polygyrus. Inflamm. Bowel Dis., 16: 1841–1849. Wang, J., Linnenbrink, M., Kunzel, S., Fernandes, R., Nadeau, M. J., Rosenstiel, P. and Baines, J. F. 2014. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proc. Natl. Acad. Sci. U.S.A., 111: E2703–E2710. Kounosu, A., Murase, K., Yoshida, A., Maruyama, H. and Kikuchi, T. 2019. Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Sci. Rep., 9: 15789. Goertz, S., de Menezes, A. B., Birtles, R. J., Fenn, J., Lowe, A. E., MacColl, A. D. C., Poulin, B., Young, S., Bradley, J. E. and Taylor, C. H. 2019. Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale. PLoS One, 14: e0222501. Condlova, S., Horcickova, M., Havrdova, N., Sak, B., Hlaskova, L., Perec-Matysiak, A., Kicia, M., McEvoy, J. and Kvac, M. 2019. Diversity of Cryptosporidium spp. in Apodemus spp. in Europe. Eur. J. Protistol., 69: 1–13. McKenney, E. A., Williamson, L., Yoder, A. D., Rawls, J. F., Bilbo, S. D. and Parker, W. 2015. Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta. Gut Microbes, 6: 182–193. Phillips, J. N., Berlow, M. and Derryberry, E. P. 2018. The Effects of Landscape Urbanization on the Gut Microbiome: An Exploration Into the Gut of Urban and Rural White-Crowned Sparrows. Front. Ecol. Evol., 6: 148. Kreisinger, J., Bastien, G., Hauffe, H. C., Marchesi, J. and Perkins, S. E. 2015. Interactions between multiple helminths and the gut microbiota in wild rodents. Philos. Trans. R. Soc. Lond. B Biol. Sci., 370: 20140295. Linnenbrink, M., Wang, J., Hardouin, E. A., Kunzel, S., Metzler, D. and Baines, J. F. 2013. The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Mol. Ecol., 22: 1904–1916. Raulo, A., Allen, B. E., Troitsky, T., Husby, A., Firth, J. A., Coulson, T. and Knowles, S. C. L. 2021. Social networks strongly predict the gut microbiota of wild mice. ISME J., 15: 2601–2613. Roble, G. S., Gillespie, V. and Lipman, N. S. 2012. Infectious disease survey of Mus musculus from pet stores in New York City. J. Am. Assoc. Lab. Anim. Sci., 51: 37–41. Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodriguez, A. M., Chase, J., Cope, E. K., Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S. 2nd, Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vazquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. and Caporaso, J. G. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol., 37: 852–857. Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. and Holmes, S. P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods, 13: 581–583 |
| References_xml | – reference: Hugerth, L. W., Muller, E. E., Hu, Y. O., Lebrun, L. A., Roume, H., Lundin, D., Wilmes, P. and Andersson, A. F. 2014. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One, 9: e95567. – reference: Kounosu, A., Murase, K., Yoshida, A., Maruyama, H. and Kikuchi, T. 2019. Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Sci. Rep., 9: 15789. – reference: Han, B. A., Schmidt, J. P., Bowden, S. E. and Drake, J. M. 2015. Rodent reservoirs of future zoonotic diseases. Proc. Natl. Acad. Sci. U.S.A., 112: 7039–7044. – reference: Suzuki, T. A., Martins, F. M. and Nachman, M. W. 2019. Altitudinal variation of the gut microbiota in wild house mice. Mol. Ecol., 28: 2378–2390. – reference: Stevens, E. J., Bates, K. A. and King, K. C. 2021. Host microbiota can facilitate pathogen infection. PLoS Pathog., 17: e1009514. – reference: Holm, J. B., Sorobetea, D., Kiilerich, P., Ramayo-Caldas, Y., Estelle, J., Ma, T., Madsen, L., Kristiansen, K. and Svensson-Frej, M. 2015. Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli. PLoS One, 10: e0125495. – reference: Fuirst, M., Veit, R. R., Hahn, M., Dheilly, N. and Thorne, L. H. 2018. Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus. PLoS One, 13: e0209200. – reference: Heni, A. C., Fackelmann, G., Eibner, G., Kreinert, S., Schmid, J., Schwensow, N. I., Wiegand, J., Wilhelm, K. and Sommer, S. 2023. Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances. Anim. Microbiome, 5: 22. – reference: Magoc, T. and Salzberg, S. L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27: 2957–2963. – reference: Anders, J. L., Moustafa, M. A. M., Mohamed, W. M. A., Hayakawa, T., Nakao, R. and Koizumi, I. 2021. Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents. Sci. Rep., 11: 19929. – reference: Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodriguez, A. M., Chase, J., Cope, E. K., Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S. 2nd, Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vazquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. and Caporaso, J. G. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol., 37: 852–857. – reference: Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. and Holmes, S. P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods, 13: 581–583. – reference: Condlova, S., Horcickova, M., Havrdova, N., Sak, B., Hlaskova, L., Perec-Matysiak, A., Kicia, M., McEvoy, J. and Kvac, M. 2019. Diversity of Cryptosporidium spp. in Apodemus spp. in Europe. Eur. J. Protistol., 69: 1–13. – reference: Walk, S. T., Blum, A. M., Ewing, S. A., Weinstock, J. V. and Young, V. B. 2010. Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides polygyrus. Inflamm. Bowel Dis., 16: 1841–1849. – reference: Kreisinger, J., Bastien, G., Hauffe, H. C., Marchesi, J. and Perkins, S. E. 2015. Interactions between multiple helminths and the gut microbiota in wild rodents. Philos. Trans. R. Soc. Lond. B Biol. Sci., 370: 20140295. – reference: Goertz, S., de Menezes, A. B., Birtles, R. J., Fenn, J., Lowe, A. E., MacColl, A. D. C., Poulin, B., Young, S., Bradley, J. E. and Taylor, C. H. 2019. Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale. PLoS One, 14: e0222501. – reference: Wang, J., Linnenbrink, M., Kunzel, S., Fernandes, R., Nadeau, M. J., Rosenstiel, P. and Baines, J. F. 2014. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proc. Natl. Acad. Sci. U.S.A., 111: E2703–E2710. – reference: McKenney, E. A., Williamson, L., Yoder, A. D., Rawls, J. F., Bilbo, S. D. and Parker, W. 2015. Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta. Gut Microbes, 6: 182–193. – reference: Midha, A., Jarquin-Diaz, V. H., Ebner, F., Lober, U., Hayani, R., Kundik, A., Cardilli, A., Heitlinger, E., Forslund, S. K. and Hartmann, S. 2022. Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host. Microbiome, 10: 229. – reference: Phillips, J. N., Berlow, M. and Derryberry, E. P. 2018. The Effects of Landscape Urbanization on the Gut Microbiome: An Exploration Into the Gut of Urban and Rural White-Crowned Sparrows. Front. Ecol. Evol., 6: 148. – reference: Raulo, A., Allen, B. E., Troitsky, T., Husby, A., Firth, J. A., Coulson, T. and Knowles, S. C. L. 2021. Social networks strongly predict the gut microbiota of wild mice. ISME J., 15: 2601–2613. – reference: Bui, T. H., Nguyen, K. T., Ikeuchi, S., Yanagawa, H., Sato, Y., Tran, T. H. T., Okumura, M., Niwa, T., Taniguchi, T. and Hayashidani, H. 2021. A long-term observation for ecology of pathogenic Yersinia in wild rodents living in Fukushima Prefecture, Japan. J. Vet. Med. Sci., 83: 1790–1794. – reference: Popovic, A., Cao, E. Y., Han, J., Nursimulu, N., Alves-Ferreira, E. V. 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| Title | 石川県の野鼠の腸内微生物叢 |
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