INDEX

 

main

research

publications

members

Japanese

 

Publications (2012~)

 

Scientific Papers (reviewed)

Forthcoming

• Asai, T., Ikushima, S., Sugiyama, M., Morimoto, T., Sudo, A., Minamoto, T. (accepted) Application of dietary content analysis using dropped feces to assess damage to fisheries by great cormorants. Ornithological Science.
• Nakagawa, H., Fujiki, D., Numata, H., Wu, L., Mori, T., Minamoto, T. (accepted) Regional-scale effects of deer-induced forest degradation on river ecosystem dynamics. Poulation Ecology. LINK

2024

• Sato, T., Uemura, K., Yasuda, M., Maeda, A., Minamoto, T., Harada, K., Sugiyama, M., Ikushima, S., Yokota, S., Horiuchi, M., Takahashi, S., Asai, T. (2024) Traces of pandemic fluoroquinolone-resistant Escherichia coli clone ST131 transmitted from human society to aquatic environments and wildlife in Japan. One Health 18, 199715. LINK
• Hidaka, S., Jo, T. S., Yamamoto, S., Katsuhara, K. R., Tomita, S., Miya, M., Ikegami,M., Ushimaru, A., Minamoto, T. (2024) Sensitive and efficient surveillance of Japanese giant salamander (Andrias japonicus) distribution in western Japan using multi-copy nuclear DNA marker. Limnology 25, 189-198. LINK
• Oyabu, A., Wu, L., Matsumoto, T., Kihara, N., Yamanaka, H., Minamoto, T. (2024) The effect of artificial light at night on wild fish community: manipulative field experiment and species composition analysis using environmental DNA. Environmental Advances 15, 100457 LINK
• Wu, L., Osugi, T., Inagawa, T., Okitsu, J., Sakamoto, S., Minamoto, T. (2024) Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons. Molecular Ecology Resources 24, e13875. LINK

2023

• Hashizume, H., Taga, S., Sakata, M. K., Hussein, M., Siddig, E. E., Minamoto, T., Fahal, A. H., Kaneko, S. (2023) Environmental detection of eumycetoma pathogens using multiplex real-time PCR for soil DNA in Sennar State, Sudan. Tropical Medicine and Health 51, 71. LINK
• Akatsuka, M., Iimura, K., Takayama, Y., Minamoto, T. (2023) A study on the distribution characteristics of environmental DNA associated with seagrass beds and the sampling area selection procedure. Japanese Journal of JSCE 79, 23-27158. (in Japanese) LINK
• Yano, N., Minamoto, T., Yamaguchi, H., Goto, T., Nishikata, T. (2023) Comparison of evolutionary relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens globins provide evidence of gene cooption and convergent evolution. International Journal of Molecular Sciences, 24, 16009. LINK
• Takahara, T., Doi, H., Kosuge, T., Nomura, N., Maki, N., Minamoto, T., Watanabe, K. (2023) Effective environmental DNA collection for an endangered catfish species: testing for habitat and daily periodicity. Ichthyological Research, 70, 409-418.　LINK
• Kanamori, A., Kitani, R., Oota, A., Hirano. K., Myosho, T., Kobayashi, T., Kawamura, K., Kato, N., Ansai, S., Kinoshita, M. (2023) Wnt4a is indispensable for genital duct elongation but not for gonadal sex differentiation in the Medaka, Oryzias latipes. Zoological Science, 40, 348-359. LINK
• Wu, Q., Zhou, J., Komoto, T., Ishikawa, T., Goto, N., Sakata, M. K., Kitazawa, D., Minamoto, T. (2023) Opposite trends in environmental DNA distributions of two freshwater species under climate change. Ecosphere 14, e4651. LINK
• Miki, T., Yamanaka, H., Sogabe, A., Omori, K., Saito, Y., Minamoto, T., Uchii, K., Honjo, M. N., Suzuki, A. A., Kohmatsu, Y., Kawabata, Z. (2023) Spatial epidemiology model can explain the seasonal dynamics of infectious disease Cyprinid herpesvirus 3 (CyHV-3) by thermoregulation behavior of the host, common carp (Cyprinus carpio). Theoretical Ecology 16, 195-208. LINK
• Sato, M., Minamoto, T., Ushimaru, A. (2023) An interdisciplinary approach to environmental conservation policy: A case of Satoyama re-development in the peri-urban area. International Journal of Economic Policy Studies 17, 403-419. LINK
• Doi, H., Matsuoka, S., Matsuzaki, S. S., Nagano, M., Sato, H., Yamanaka, H., Matsuhashi, S., Yamamoto, S., Minamoto, T., Araki, H., Ikeda, K., Kato, A., Kamei, K., Maki, N., Mitsuzuka, T., Takahara, T., Toki, K., Ueda, N., Watanabe, T., Yamazoe, K., Miya, M. (2023) Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities. Freshwater Biology 68, 1346-1358.　LINK
• Mori, K., Imamura, A., Hirayama, I., Minamoto, T. (2023) Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water. PeerJ 11, e15431. LINK
• Sakata, M. K., Takeshita, D., Nishizawa, R., Sato, T., Minamoto, T. (2023) An efficient environmental DNA detection method for rare species: a case study of a small salamander (Hynobius boulengeri). Analytical Sciences 39, 721-728. LINK
• Wu, Q., Minamoto, T. (2023) Improvement of recovery yield of macro-organismal environmental DNA from seawater samples. Analytical Sciences 39, 713-720. LINK
• Souma, R., Katano, I., Doi, H., Takahara, T., Minamoto, T. (2023) Comparing environmental DNA with whole pond survey to estimate the total biomass of fish species in ponds. Freshwater Biology 68, 727-736. LINK
• Aoshima, I., Nakao, R., Minamoto, T., Ushimaru, A., Sato, M. (2023) Heterogeneous preference for biodiversity in Japanese urban blue spaces based on people's nature experiences: Analysis using eDNA and satisfaction data. City and Environment Interactions 18, 100101. LINK
• Okanishi, M., Kohtsuka, H., Wu, Q., Shinji, J., Shibata, N., Tamada, T., Nakano, T., Minamoto, T. (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Mebarcoding and Metagenomics 7, e94298. LINK
• Takahara, T., Fukui, K., Hiramatsu, D., Doi, H., Fujii, M., Minamoto, T. (2023) Development of primer-probe sets for environmental DNA-based monitoring of pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon. Landscape and Ecological Engineering 19. 11-19. LINK
• Nishizawa, R., Nakao, R., Ushimaru, A., Minamoto, T. (2023) Development of environmental DNA detection assays for snakes in paddy fields in Japan. Landscape and Ecological Engineering 19, 3-10. LINK
• Wu, L., Wu, Q., Inagawa, T., Okitsu, J., Sakamoto, S., Minamoto, T. (2023) Estimating the spawning activity of fish species using nuclear and mitochondrial environmental DNA concentrations and their ratios. Freshwater Biology 68, 103-114. LINK

2022

• Nakagawa, H., Fukushima, K., Sakai, M., Wu, L., Minamoto, T. (2022) Relationships between the eDNA concentration obtained from metabarcoding and stream fish abundance estimated by the removal method under field conditions. Environmental DNA 4, 1369-1380. LINK
• Akatsuka, M., Muchebve, E., Takayama, Y., Oda, Y., Minamoto, T. (2022) Influence of flow in seagrass bed monitoring utilizing environmental ANA analysis. J.JSCE, Ser.B2, Coastal Engineering 78, I_865─I_870. (in Japanese)
• Jo, T.*, Sato, M.*, Minamoto, T.*, Ushimaru A.* (2022) Valuing the cultural services from urban blue space ecosystems in Japanese megacities during the COVID-19 pandemic. People and Nature 4, 1176-1189. (*equal contribution) LINK
• Asai, T., Sugiyama, M., Omatsu, T., Yoshikawa, M., Minamoto, T. (2022) Isolation of extended-spectrum beta-lactamase-producing Escherichia coli from Japanese red fox (Vulpes vulpes japonica). MicrobiologyOpen 11, e1317. LINK
• Wakiya, R., Itakura, H., Hirae, T., Igari T., Manabe, M., Matsuya N., Miyata, K., Sakata, M. K., Minamoto, T. (2022) Slower growth of farmed eels stocked into rivers with higher wild eel density. Journal of Fish Biology 101, 613-627. LINK
• Sakata, M. K., Sato, M., Sato, M. O., Watanabe, T., Mitsuishi, H., Hikitsuchi, T., Kobayashi, J., Minamoto, T. (2022) Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens. PLoS ONE 17, e0272653. LINK
• Koizumi, N., Minamoto, T., Shirako, T., Nakamura, M. (2022) Applicability of environmental DNA research and diffusion distance of environmental DNA in agriculture canals. Water, Land and Environmental Engeneering 90, 11-14.
• Wu, L., Yamamoto, Y., Yamaguchi, S., Minamoto, T. (2022) Spatiotemporal changes in environmental DNA concentrations caused by fish spawning activity. Ecological Indicators 142, 109213. LINK
• Minamoto, T. (2022) Environmental DNA analysis for macro-organisms: Species distribution and more. DNA Research, 29, dsac018. LINK
• Jo, T., Takao, K., Minamoto, T. (2022) Linking the state of environmental DNA to its application for biomonitoring and stock assessment: targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes. Environmental DNA 4, 271-283. LINK
• Hashizume, H., Taga, S., Sakata, M. K., Taha M. H. M., Siddig, E. E., Minamoto, T., Fahal, A. H., Kaneko, S. (2022) Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan. PLoS Neglected Tropical Diseases 16, e0010274. LINK
• Sakata, M. K., Kawata, M. U., Kurabayashi, A., Kurita, T., Nakamura, M., Shirako, T., Kakehashi R., Nishikawa, K., Hossman, M. Y., Nishijima, T., Kawamoto, J., Miya, M., Minamoto, T. (2022) Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. Metabarcoding and Metagenomics 6, 15-26. LINK
• Nagayama, S., Oota, M., Fujita, T., Kitamura, J., Minamoto, T., Mori, S., Kato, M., Takeyama, N., Takino, F., Yonekura, R., Yamanaha, H. (2022) Autumn dispersal and limited success of reproduction of the deepbody bitterling (Acheilognathus longipinnis) in terrestrialized floodplain. Knowledge and Management of Aquatic Ecosystems, 423, 4. LINK
• Sasano, S., Murakami, H., Suzuki, K. W., Minamoto, T., Yamashita, Y., Masuda R. (2022) Seasonal changes in the distribution of black sea bream Acanthopagrus schlegelii estimated by environmental DNA. Fisheries Science 88, 91-107 LINK
• Murakami, H., Masuda, R., Yamamoto, S., Minamoto, T., Yamashita, Y. (2022) Environmental DNA emission by two carangid fishes in single and mixed-species tanks. Fisheries Science 88, 55-62. LINK
• Tsuji, S., Nakao, R., Saito, M., Minamoto, T., Akamatsu, Y. (2022) Pre-centrifugation before DNA extraction mitigates extraction efficiency reduction of environmental DNA caused by the preservative solution (benzalkonium chloride) remaining in the filters. Limnology 23, 9-16. LINK

2021

• Seguchi, Y., Yamamoto, Y., Takemon, Y., Minamoto, T. (2021) Discovery of residual Ayu fish in the backwater area of the Yodo River Barrage. Japanese Journal of Ichthyology 68, 163-172. (in Japanese) (*equal contribution) LINK
• Jo, T., Sakata, M. K., Murakami, H., Masuda, R., Minamoto, T. (2021) Universal performance of benzalkonium chloride for the preservation of environmental DNA in seawater samples. Limnology and Oceanography: Methods 19, 758-768. LINK
• Akatsuka, M., Takayama, Y., Muchebve, E., Ito, K., Watanabe, K., Kuwae, T., Minamoto, T. (2021) Study on an environmental DNA analysis protocol for seagrass bed monitoring. J.JSCE, Ser.B2, Coastal Engineering 77, I_895-I_900. LINK (in Japanese)
• Fukuda, A., Usui, M., Uchiyama, K., Shrestha, D., Hashimoto, N., Sakata, M. K., Minamoto, T., Yoshida, O., Murakami, K., Tamura, Y., Asai, T. (2021) Prevalence of antimicrobial-resistant Escherichia coli in the migratory bird (Anser albifrons) and their habitat in Miyajimanuma, Japan. Journal of Wildlife Diseases 57, 954-958. LINK
• Osathanunkul, M., Minamoto, T. (2021) eDNA based detection of a vulnerable crocodile newt (Tylototriton uyenoi) to influence government policy and raise public awareness. Diversity and Distributions 27, 1958-1965. LINK
• Ogata, M., Masuda, R., Marino, H., Sakata, M. K., Hatakeyama, M., Yokoyama, K., Yamashita, Y., Minamoto, T. (2021) Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Scientific Reports 11, 16830. LINK
• Wu, Q.*, Sakata, M. K.*, Wu, D., Yamanaka, H., Minamoto, T. (2021) Application of environmental DNA metabarcoding in a lake with extensive algal blooms. Limnology 22, 363-370. LINK (*equal contribution)
• Fukaya, K., Murakami, H., Yoon, S., Minami, K., Osada, Y., Yamamoto, S., Masuda, R., Kasai, A., Miyahira, K., Minamoto, T., Kondoh, M. (2021) Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling. Molecular Ecology 30, 3057-3067. LINK プレスリリース
• Jo, T., Ikeda, S., Fukuoka, A., Inagawa, T., Okitsu, J., Katano, I., Doi, H., Nakai, K., Ichiyanagi, H., Minamoto, T. (2021) Utility of environmental DNA analysis for effective monitoring of invasive fish species in reservoirs. Ecosphere 12, e03643. LINK
• Jo, T., Minamoto, T. (2021) Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses. Molecular Ecology Resources 21, 1490-1503. LINK
• Osathanunkul, M., Minamoto, T. (2021) Molecular detection of giant snakeheads, Channa micropeltes (Cuvier, 1831), one of the most troublesome fish species. Scientific Reports 11, 9943. LINK
• Yasashimoto, T., Sakata, M. K., Sakita, T., Nakajima, S., Ozaki, M., Minamoto, T. (2021) Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples. Scientific Reports 11, 10712. LINK
• Doi, H.*, Minamoto, T.*, Takahara, T., Tsuji, S., Uchii, K., Yamamoto, S., Katano, I., Yamanaka, H. (2021) Compilation of real-time PCR conditions toward the standardization of eDNA methods. Ecological Research, 36 (3), 379-388. (*equal contribution) LINK
• Tenma, H., Tsunekawa, K., Fujiyoshi, R., Takai, H., Hirose, M., Masai, N., Sumi, K., Takihana, Y., Yanagisawa, S., Tsuchida, K., Ohara, K., Jo, T., Takagi, M., Ota, A., Iwata, H., Yaoi, Y., Minamoto, T. (2021) Spatio-temporal distribution of Flavobacterium psychrophilum and ayu Plecoglossus altivelis in rivers revealed by environmental DNA analysis. Fisheries Science 87, 321-330. LINK プレスリリース
• Sakata, M. K., Watanabe, T., Maki, N., Ikeda, K., Kosuge, T., Okada, H., Yamanaka, H., Sado, T., Miya, M., Minamoto, T. (2021) Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river. Limnology 22, 221-235. LINK プレスリリース
  
• Hoshino, T., Nakao, R., Doi, H., Minamoto, T. (2021) Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique. Scientific Reports 11, 4372. LINK
• Aratani, T., Koide, N., Hayami, K., Sugiyama, M., Minamoto, T., Asai, T. (2021) Continuous prevalence of VEB-3 extended-spectrum β-lactamase-producing Aeromonas hydrophila in a local river in Gifu City, Japan. Microbiology and Immunology 65, 99-100. LINK
• Doi, H., Akamatsu, Y., Goto, M., Inui, R., Komuro, T., Nagano, M., Minamoto, T. (2021) Broad-scale detection of environmental DNA for an invasive macrophyte and the relationship between DNA concentration and coverage in rivers. Biological Invasions 23, 507-520. LINK
  
• Tsuri, K., Ikeda, S., Hirohara, T., Shimada, Y., Minamoto, T., Yamanaka, H. (2021) Messenger RNA-typing of environmental RNA (eRNA): a case study on zebrafish tank water with perspectives for the future development of eRNA analysis on aquatic vertebrates. Environmental DNA 3, 14-21. LINK プレスリリース
  
• Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M., Nakamura, K., Takahara, T., Yamamoto, S., Yamanaka, H., Araki, H., Iwasaki, W., Kasai, A., Masuda, R., Uchii, K. (2021) An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environmental DNA 3, 8-13. LINK
  
• Sugiura, K., Tomita, S., Minamoto, T., Mishina, T., Iwata, A., Abe, T., Yamamoto, S., Watanabe, K. (2021) Characterizing the spatial and temporal occurrence patterns of the endangered botiid loach Parabotia curtus by environmental DNA analysis using a newly developed species-specific primer set. Ichthyological Research 68, 152-157. LINK
• Chen J. -W., Chen, Z., Liu S. -S. Guo, W. -J., Li D., Minamoto, T., Gao, T. -X. (2021) Revealing an invasion risk of fish species in Qingdao Underwater World by Eevironmental DNA metabarcoding. Journal of Ocean University of China, 20 (1), 124-136. LINK
• Chen, Z., Minamoto, T., Lin, L. -S., Gao, T. -X. (2021) An optional low-cost method of extracting environmental DNA of macro-organisms from filter membranes in large scale eDNA surveys. Pakistan Journal of Zoology, 53 (1), 263-372. LINK

2020

• Osathanunkul, M., Minamoto, T. (2020) A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ, 8, e10338. LINK
  
• Matsumoto, T., Arakawa, H., Murakami, T., Yanai, S. (2020) Settlement patterns of two sesarmid megalopae in the Sai River Estuary, Ishikawa Prefecture, Japan. Plankton and Benthos Research 15(4), 306-316. LINK
  
• Jo, T., Tomita, S., Kohmatsu, Y., Osathanunkul, M., Ushimaru, A., Minamoto, T. (2020) Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set. Endangered Species Research 43, 341-352. LINK
  
• Muchebve, E., Takayama, Y., Akatsuka, M., Ito, K., Minamoto, T. (2020) Feasibility study for seagrass beds monitoring using environmental DNA. Journal of Japan Society of Civil Engineers (B2) 76 (2), I_949-I_954. LINK
  
• Akatsuka, M., Takayama, Y., Muchebve, E., Ito, K., Watanabe, K., Kuwae, T., Minamoto, T. (2020) Seasonal changes of environmental DNA in seagrass beds and examination of water sampling procedure. Journal of Japan Society of Civil Engineers (B2) 76 (2), I_943-I_948. LINK
  
• Imamura, A., Hayami, K., Sakata, M. K., Minamoto, T. (2020) Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout. Biodiversity Data Journal, 8, e56876. LINK
  
• Kudoh, A., Minamoto, T., Yamamoto, S. (2020) Detection of herbivory: eDNA detection from feeding marks on leaves. Environmental DNA, 2, 627-634. LINK プレスリリース
• Sakata, M. K., Yamamoto, S., Gotoh, R. O., Miya, M., Yamanaka, H., Minamoto, T. (2020) Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA, 2, 505-518. LINK
• Kuwae, M., Tamai, H., Doi, H., Sakata, M. K., Minamoto, T., Suzuki, Y. (2020) Sedimentary DNA tracks decadal-centennial changes in fish abundance. Communications Biology, 3, 558. LINK
• Tsuji, S., Maruyama, A., Miya, M., Ushio, M., Sato, H., Minamoto, T., Yamanaka, H. (2020) Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population. Molecular Ecology Resources, 20 (5), 1248-1258. LINK
• Takahara, T., Taguchi, J., Yamagishi, S., Doi, H., Ogata, S., Yamanaha, H., Minamoto, T. (2020) Suppression of eDNA degradation in water samples associated with different storage temperature and period using benzalkonium chloride. Limnology and Oceanography: Methods 18, 437-445. LINK
• Takeshita, D., Terui, S., Ikeda, K., Mitsuzuka, T., Osathanunkul, M., Minamoto, T. (2020) Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan. PeerJ 8, e9764. LINK
  
• Itakura, H., Wakiya, R., Sakata, M. K., Hsu H. -Y., Chen, S, -C., Yang, C. -S., Han, Y. -S., Minamoto, T. (2020) Estimations of riverine distribution, abundance and biomass of anguillid eels in Japan and Taiwan using environmental DNA analysis. Zoological Studies 59, 17. LINK
• Hayami, K., Sakata, M. K., Inagawa, T., Okitsu, J., Katano, I., Doi, H., Nakai, K., Ichiyanagi, H., Gotoh, R. O., Miya, M., Sato, H., Yamanaka, H., Minamoto, T. (2020) Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs. Ecology and Evolution 10 (12), 5354-5367. LINK
• Jo, T., Murakami, H., Masuda, R., Minamoto, T. (2020) Selective collection of long fragments of environmental DNA using larger pore size filter. Science of the Total Environment 735, 139462. LINK
• Takahashi, S., Sakata, M. K., Minamoto, T., Masuda, R. (2020) Comparing the efficiency of open and enclosed filtering systems in fish and jellyfish environmental DNA quantification. PLOS ONE 15 (4), e0231718 LINK
• Jo, T., Arimoto, M., Murakami, H., Masuda, R., Minamoto, T. (2020) Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass. Environmental DNA 2 (2), 140-151. LINK
• Yatsuyanagi, T., Ishida, R., Sakata, M. K., Kanbe, T., Mizumoto, H., Kobayashi, Y., Namba S., Nii H., Minamoto, T., Araki, H. (2020) Environmental DNA monitoring for short-term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus). Environmental DNA 2 (2), 130-139. LINK
• Jo, T., Fukuoka, A., Uchida, K., Ushimaru A., Minamoto, T. (2020) Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biological Invasions 22 (2), 455-471. LINK
• Tsuji, S., Miya, M., Ushio, M., Sato, H., Minamoto, T., Yamanaka, H. (2020) Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water. Environmental DNA 2, 42-52. LINK
• Chen, Z., Song, N., Minamoto, T., Wu, Q., Gao, T. (2020) The eDNA Collection method of Zhoushan coastal waters. Acta Hydrobiologica Sinica 44, 1-7.

2019

• Kakuda, A., Kakuda, A., Doi, H., Souma, R., Nagano, M., Minamoto, T., Katano, I. (2019) Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality. PeerJ 7, e815. LINK
• Fornillos, R. J. C, Sato, M. O., Tabios, I. K. B., Sato, M., Leonardo, L. R., Chigusa, Y., Minamoto, T., Kikuchi, M., Legaspi E. R., Fontanilla, I. K. (2019) Detection of Schistosoma japonicum and Oncomelania hupensis quadrasi environmental DNA and its potential utility to schistosomiasis japonica surveillance in the Philippines. PLOS ONE 14, e0224617. LINK
• Uchii, K., Doi, H., Okahashi, T., Katano, I., Yamanaka, H., Sakata, M. K., Minamoto, T. (2019) Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA. Environmental DNA 1, 359-367. LINK
• Akatsuka, M., Takayama, Y., Ito, K., Watane, K., Kuwae, T., Osawa, R., Morimoto, T., Minamoto, T. (2019) Study on seasonal, daily and morphological change of environmental DNA for seagrass bed. Journal of Japan Society of Civil Engineers (B2) 75 (2), I_1075─I_1080.
• Takayama, Y., Akatsuka, M., Ito, I., Minamoto, T. (2019) A feasibility study in a monitoring method of non-moving aquatic organism using environmental DNA. Journal of Japan Society of Civil Engineers (B2) 75 (2), I_1087─I_1092.
• Calata, F. I., Caranguian, C., Mendoza, J. E., Fornillos, R. J., Tabios, I. K., Fontanilla, I. K., Leonardo, L., Sunico, L., Chigusa, Y., Kikuchi, M., Sato, M. O., Minamoto, T., Sato, M., Baoanan, Z. （2019) Analysis of environmental DNA and edaphic factors for the detection of the snail intermediate host Oncomelania hupensis quadrasi. Pathogens 8, 160. LINK
• Sakai, Y., Kusakabe, A., Tsuchida, K., Tsuzuku, Y., Okada, S., Kitamura, T., Tomita, S., Mukai, T., Tagami, M., Takagi, M., Yaoi, Y., Minamoto, T. (2019) Discovery of an unrecorded population of Yamato salamander (Hynobius vandenburghi) by GIS and eDNA analysis. Environmental DNA 1, 281-289. LINK Press release (Kobe U.)
• Horiuchi, T., Masuda, R., Murakami H., Yamamoto, S., Minamoto, T. (2019) Biomass-dependent emission of environmental DNA in jack mackerel Trachurus japonicus juveniles. Journal of Fish Biology 95, 979-981. LINK
• Matsuhashi, S., Minamoto, T., Doi, H. (2019) Seasonal change in environmental DNA concentration of a submerged aquatic plant species. Freshwater Science 38, 654-660. LINK
• Jo, T., Arimoto, M., Murakami, H., Masuda, R., Minamoto, T. (2019) Particle size distribution of environmental DNA from the nuclei of marine fish. Environmental Science & Technology 53, 9947-9956. LINK
• Imamura, A., Hayami, K., Sakata M. K., Minamoto, T. (2019) Are Salvelinus species on Hokkaido Island, Japan, endangered by damming and invasive rainbow trouts? ~based on the results of eDNA analysis. Japanese Journal of Conservation Ecology 24, 71-81. (in Japanese).
• Kano, K., Kudo, M., Yoshizawa, G., Mizumachi, E., Suga, M., Akiya, N., Ebina, K., Goto, T., Itoh, M., Joh, A., Maenami, H., Minamoto, T., Mori, M., Morimura, Y., Motoki, T., Nakayama, A., Takanashi, K. (2019) How science, technology and innovation can be placed in broader visions? -Public opinions from inclusive public engagement activities-. Journal of Science Communication 18, A02. LINK
• Wu, Q., Kawano, K., Ishikawa, T., Sakata, M. K., Nakao, R., Hiraiwa, M. K., Tsuji, S., Yamanaka, H., Minamoto, T. (2019) Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan – an eDNA-based study. Environmental DNA 1, 54-63. LINK
• Matsuhashi, S., Minamoto, T., Doi, H. (2019) Seasonal change in environmental DNA concentration of a submerged aquatic plant species.　Freshwater Science.
• Sato, Y., Mizuyama, M., Sato, M., Minamoto, T., Kimura, R., Toma, C. (2019) Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Scienctific Reports 9, 6575. LINK
• Wu, Q., Takami, Y., Minamoto, T., Ishikawa, T. (2019) The life history with seasonal migration of the lacustrine shrimp Palaemon paucidens in an ancient lake in Japan. Ecosphere 10, 4, e02628. LINK
• Takahara, T., Ikebuchi, T., Doi, H., Minamoto, T. (2019) Using environmental DNA to estimate the seasonal distribution and habitat preferences of a Japanese basket clam in Lake Shinji, Japan. Estuarine, Coastal and Shelf Science 221, 15-20. LINK
• Itakura, H., Wakiya, R., Yamamoto, S., Kaifu, K., Sato, T., Minamoto, T. (2019) Environmental DNA analysis reveals the spatial distribution, abundance and biomass of Japanese eels at the river basin scale. Aquatic Conservation: Marine and Freshwater Ecosystems 29, 361-373. LINK
• Murakami, H., Yoon, S., Kasai, A., Minamoto, T., Yamamoto, S., Sakata, M. K., Horiuchi, T., Sawada, H., Kondoh, M., Yamashita, Y., Masuda, R. (2019) Dispersion and degradation of environmental DNA from caged fish in a marine environment. Fisheries Science 85, 327-337. LINK
• Jo, T., Murakami, H.,Yamamoto, S., Masuda, R., Minamoto, T. (2019) Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution. Ecology and Evolution 9, 1135-1146. LINK
• Minamoto, T., Hayami, K., Sakata M. K., Imamura, A. (2019) Real-time PCR assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: application to winter surveys. Ecological Research 34, 237-242. LINK
• Takeuchi, A., Watanabe, S., Yamamoto, S., Miller, M. J., Fukuba, T., Miwa, T., Okino, T., Minamoto, T., Tsukamoto, K. (2019) First attempt of an oceanic environmental DNA survey of the spawning ecology of the Japanese eel Anguilla japonica. Marine Ecology Progress Series 609, 187-196. LINK

2018

• Niwa, H., Sakata, M. K., Minamoto, T., Kiyono, M. (2018) River fish detection by environmental DNA analysis and conventional field sampling survey in 500 m intervals. Japanese Journal of Conservation Ecology 23 (2), 257-264. (in Japanese)　LINK
• Sato, M. O., Rafalimanantsoa, A., Ramarokoto, C., Rahetilahy, A. M., Ravoniarimbinina, P., Kawai, S., Minamoto, T., Sato, M., Kirinoki, M., Rasolofo, V., De Calan M., Chigusa, Y. (2018) Usefulness of environmental DNA for detection of Schistosoma mansoni in Madagascar. International Journal of Infectious Diseases 76, 130-136. LINK
• Akatsuka, M., Takayama, Y., Ito, K., Morimoto, T., Minamoto, T. (2018) Study on appropriate environmental DNA and applicability of tidal flow analysis for seagrass bed. Journal of Japan Society of Civil Engineers (B2), 74 (2), I_1225-I_1230. (in Japanese)　LINK
• Takayama, Y., Akatsuka, M., Ito, K., Minamoto, T. (2018) A feasibility study in a monitoring method of seagrass bed using environmental DNA. Journal of Japan Society of Civil Engineers (B2), 74 (2), I_1231-I_1236. (in Japanese)　LINK
• Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T., Miya, M. (2018) Comparing local- and regional-scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshwater Biology 63 (6), 569-580. LINK
• Wu, Q., Kawano, K., Uehara, Y., Okuda, N., Hongo, M., Tsuji, S., Yamanaka, H., Minamoto, T. (2018) Environmental DNA reveals non-migratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters. Freshwater Science 37 (2), 307-314. LINK
• Ushio, M., Murakami, H., Masuda, R., Sado, T., Miya, M., Sakurai, S., Yamanaka, H., Minamoto, T., Kondoh, T. (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding & Metagenomics 2, e23297. LINK

2017

• Doi, H., Akamatsu, Y., Watanabe, Y., Goto, M., Inui, R., Katano, I., Nagano, M., Takahara, T., Minamoto, T. (2017) Water sampling for environmental DNA surveys by using an unmanned aerial vehicle. Limnology and Oceangraphy: Methods 15, 939-944. LINK
• Jo, T., Murakami, H., Masuda, R., Sakata, M. K., Yamamoto, S., Minamoto, T. (2017) Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA. Molecular Ecology Resources 17 (6), e25-e33. LINK
• Sakata, M. K., Maki, N., Sugiyama, H., Minamoto, T. (2017) Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan. The Science of Nature - Naturwissenschaften 104, 100. LINK
• Sato, M., Ushimaru, A., Minamoto, T. (2017) The effect of different personal histories on valuation of forest ecosystem services in urban areas: a case study of Mt. Rokko, Kobe, Japan. Urban Forestry & Urban Greening 28, 110-117. LINK
• Uchii, K., Doi, H., Yamanaka, H., Minamoto, T. (2017) Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA. Ecology and Evolution 7(20): 8515-8522. LINK
• Kouduka, M., Tanabe, A.S., Yamamoto, S., Yanagawa, K., Nakamura, Y., Akiba, F., Tomaru, H., Toju, H., Suzuki, Y. (2017) Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea. Geobiology 15 (5): 715-727. LINK
• Katano, I., Harada, K., Doi, H., Souma, R., Minamoto, T. (2017) Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods. PLOS ONE 12(5): e0176541. LINK
• Hashizume, H., Sato, M., Sato, M. O., Ikeda, S., Yoounan, T., Sanguankiat, S., Pongvongsa, T., Moji, K., Minamoto, T. (2017) Application of environmental DNA analysis for the detection of Opisthorchis viverrini DNA in water samples. Acta Tropica 169, 1-7. LINK
• Tsuji, S., Ushio, M., Sakurai, S., Minamoto, T. Yamanaka, H. (2017) Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLOS ONE 12(4): e0176608. LINK
• Yamanaka, H., Minamoto, T., Matsuura, J., Sakurai, S., Tsui, S., Motozawa, H., Hongo, M., Sogo, Y., Kakimi, N., Teramura, I., Sugita, M., Baba, M., Kondo, A. (2017) A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology 17 (2), 233-241. LINK
• Minamoto, T., Uchii, K., Takahara, T., Kitayoshi, T., Tsuji, S., Yamanaka, H., Doi, H. (2017) Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Molecular Ecology Resources 17 (2), 324-333. LINK
• Minamoto, T., Fukuda, M., Katsuhara, K.R., Fujiwara, A., Hidaka, S., Yamamoto, S., Takahashi, K., Masuda, R. (2017) Environmental DNA reflects spatial and temporal jellyfish distribution. PLOS ONE 12 (2), e0173073. LINK
  
• Doi, H., Uchii, K., Matsuhashi, S., Takahara, T., Yamanaka, H., Minamoto, T. (2017) Isopropanol precipitation method for collecting fish environmental DNA. Limnology and Oceanography: Methods, 15 (2), 212-218. LINK
• Yamamoto, S., Masuda, R., Sato, Y., Sado, T., Araki, H., Kondoh, M., Minamoto, T., Miya, M. (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports 7, 40368. LINK
• Tsuji, S., Yamanaka, H., Minamoto, T. (2017) Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples. Limnology 18 (1), 1-8. LINK
• Doi, H., Inui, R., Akamatsu, Y., Kanno, K., Yamanaka, H., Takahara, T., Minamoto, T. (2017) Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshwater Biology 62 (1), 30-39. LINK

2016

• Miya, M., Minamoto, T., Yamanaka, H., Oka, S., Sato, K., Yamamoto, S., Sado, T., Doi, H. (2016) Use of a filter cartridge for filtration of water samples and extraction of environmental DNA. Journal of Visualized Experiments 117, e54741. LINK
• Takahara, T., Yamanaka, H., Minamoto, T., Doi, H., Uchii, K. (2016) Current state of biomonitoring method using environmental DNA analysis. Japanese Journal of Ecology 66 (3), 583-599. (in Japanese)
• Yamanaka, H., Minamoto, T., Takahara, T., Uchii, K., Doi, H. (2016) Environmental DNA analysis in field research. Japanese Journal of Ecology 66 (3), 601-611. (in Japanese)
• Fukuoka, A.,Takahara, T., Matsumoto, M., Biology Club of Hyogo Prefectural Agricultural High School, Ushimaru, A., Minamoto T. (2016) Establishment of detection system for native rare species, Hemigrammocypris rasborella, using environmental DNA. Japanese Journal of Ecology 66 (3), 613-620. (in Japanese)
• Yamanaka, H., Motozawa, H., Tsuji, S., Miyazawa, R. C., Takahara, T., Minamoto, T. (2016) On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation. Ecological Research 31 (6), 963-967. LINK
• Matsuhashi, S., Doi, H., Fujiwara, A., Watanabe, S., Minamoto, T. (2016) Evaluation of the environmental DNA method for estimating distribution and biomass of submerged aquatic plants. PLOS ONE 11(6), e0156217. LINK
• Fujiwara, A., Matsuhashi, S., Doi, H., Yamamoto, S., Minamoto, T. (2016) Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds. Freshwater Science 35 (2), 748-754. LINK
• Yamamoto, S., Minami, K., Fukaya, K., Takahashi, K., Sawada, H., Murakami, H., Tsuji, S., Hashizume, H., Kubonaga, S., Horiuchi, T., Hongo, M., Nishida, J., Okugawa, Y., Fujiwara, A., Fukuda, M., Hidaka, S., Suzuki, K. W., Miya, M., Araki, H., Yamanaka, H., Maruyama, A., Miyashita, K., Masuda, R., Minamoto, T., and Kondoh, M. (2016) Environmental DNA as a 'snapshot' of fish distribution: a case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan. PLOS ONE 11(3), e1249786. LINK
• Toju, H., Yamamoto, S., Tanabe, A.S., Hayakawa, T., Ishii, H.S. (2016) Network modules and hubs in plant-root fungal biome. Journal of the Royal Society Interface 13, 20151097. LINK
• Ino, K., Kouduka, M., Hirota, A., Togo, Y., Fukuda, A., Komatsu, D., Tsunogai, U., Tanabe, A.S., Yamamoto, S., Iwatsuki, T., Mizuno, T., Ito, K., Suzuki, Y. (2016) Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes. Environmental Microbiology Reports 8, 285–294. LINK
• Uchii, K., Doi, H., Minamoto, T. (2016) A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes. Molecular Ecology Resources 16 (2), 415-422. LINK
• Minamoto, T., Yamamoto, S., Kasai, A., Kondoh, M. (2016) Coastal fish monitoring using environmental DNA. Bulletin on Coastal Oceanograph 53 (2), 173-178. (in Japanese with English abstrct)
• Yamanaka, H., Minamoto, T. (2016) The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecological Indicators 62, 147-153. LINK
• Minamoto, T., Naka, T., Moji, K.,Maruyama, A. (2016) Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction. Limnology 17 (1), 23-32. LINK
• Yamamoto, S., Beljaev, E., Sota, T. (2016) Phylogenetic analysis of the winter geometrid genus Inurois reveals repeated reproductive season shifts. Molecular Phylogenetics and Evolution 94 part A, 47-54. LINK

2015

• Matsumae, H., Ishiwata, R., Minamoto, T., Ishida, N., Ogishima, S., Tanaka, H. (2015) Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis. Artificial Life and Robotics 20 (4), 347-352. LINK
• Miya, M., Sato, Y. Fukunaga, T., Sado, T., Poulsen, J.Y., Sato., K., Minamoto, T., Yamamoto, S., Yamanaka, H., Araki, H., Kondoh, M., Iwasaki, W. (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than　230 subtropical marine species. Royal Society Open Science 2, 150088. LINK
• Koizumi, N., Takahara, T., Minamoto, T., Doi, H., Mori, Atsushi, Watanabe, K., Takemura, T. (2015) Preliminary experiment for detection method of fish inhabiting agricultural drainage canals using environmental DNA. Irrigation, Drainage and Rural Engineering Journal 297 (83-3), IV_7-IV_8. LINK
• Doi, H., Takahara, T., Minamoto, T., Matsuhashi, S., Uchii, K., Yamanaka, H. (2015) Droplet digital Polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species. Environmental Science and Technology 49 (9), 5601-5608. LINK
• Doi, H., Uchii, K., Takahara, T., Matsuhashi, S., Yamanaka, H., Minamoto, T. (2015) Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLOS ONE 10(3): e0122763. LINK
• Fukumoto S., Ushimaru A., Minamoto T. (2015) A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: A case study of giant salamanders in Japan. Journal of Applied Ecology 52 (2) 358-365. LINK
• Takahara T., Minamoto T., Doi H. (2015) Effects of sample processing on the detection rate of environmental DNA from the Common Carp (Cyprinus carpio). Biological Conservation, 183, 64-69. LINK
• Minamoto T., Pu X., Xie J., Dong Y., Wu D., Kong H., Yang X., Takahara T., Honjo M. N., Yamanaka H., Kawabata Z. (2015) Monitoring of fish pathogenic viruses in natural lakes in Yunnan, China. Limnology 16(1), 69-77. LINK

2014

• Maruyama A., Nakamura K., Yamanaka H., Kondoh M., Minamoto T. (2014) The release rate of environmental DNA from juvenile and adult fish. PLoS ONE. 9 (12), e114639 LINK
• Mizumachi E., Kano K., Itoh M., Minamoto T., Nakayama A., Ebina K., Akiya N. (2014) Public comment workshops on the draft of“ Basic plan on space policy”. Japanese Journal of Science Communication, 15, 123-136. (in Japanese) LINK
• Takahara T., Honjo M. N. Uchii K., Minamoto T., Doi H., Ito T., Kawabata Z. (2014) Effects of daily temperature fluctuation on the survival of carp infected with Cyprinid herpesvirus 3. Aquaculture 433, 208-213. LINK
• Takahara T., Minamoto T., Doi H., Ito T., Kawabata Z. (2014) Differences between domesticated Eurasian and Japanese indigenous strains of the common carp (Cyprinus carpio) in cortisol release following acute stressor. Ichthyological Research 61 (2) 165-168. LINK
• Uchii K., Minamoto T., Honjo M.N., Kawabata Z. (2014) Seasonal reactivation enables Cyprinid herpesvirus 3 to persist in a wild host population. FEMS Microbiol. Ecol. 87 (2) 536-542. LINK

2013

• Uchii K., Okuda N., Minamoto T., Kawabata Z. (2013) An emerging infectious pathogen endangers an ancient lineage of common carp by acting synergistically with conspecific exotic strains. Animal Conservation 16(3), 324-330. LINK
• Xie J., Wu D., Chen X., Kong H., Pu X., Yang X., Minamoto T., Yamanaka H., Honjo M. N., Kawabata Z., Li M. (2013) Relationship between aquatic vegetation and water quality in the littoral zones of Lake Dianchi and Lake Erhai. Environmental Science & Technology (Wuhan) 36 (2) 61-65. (in Chinese with English abstract) LINK
• Takahara T., Minamoto T., Doi H. (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLOS ONE. 8(2): e56584. LINK

2012

• Minamoto T.*, Yamanaka H.*, Takahara T., Honjo M. N., Kawabata Z. (2012) Surveillance of fish species composition using environmental DNA. Limnology 13(2), 193-197. (*equal contribution) LINK
• Minamoto T., Honjo M. N., Yamanaka H., Uchii K., Kawabata Z. (2012) Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Res. Vet. Sci. 93 (1) 508-514. LINK
• Yamanaka H., Minamoto T., Wu D., Kong H., Wei Z.-H., Liu B., Kawabata Z. (2012) Spatial-temporal analysis of water temperatures during spring in Lake Erhai, China: implications for fisheries. Inland Waters 2(3), 129-136. LINK　関連する写真がInland Waters誌の表紙に採用されました
• Takahara T., Minamoto T., Yamanaka H., Doi H., Kawabata Z. (2012) Estimation of fish biomass using environmental DNA. PLOS ONE, 7 (4), e35868. LINK
• Minamoto T., Fuchikawa, T., Shimizu I. (2012) Expression of spliced variants of period mRNA in the Japanese honeybee Apis cerana japonica. Biol. Rhythm Res. 43 (2), 125-135. LINK
• Honjo M. N., Minamoto T., Kawabata Z. (2012) Reservoirs of Cyprinid herpesvirus 3 (CyHV-3) DNA in sediments of natural lakes and ponds. Vet. Microbiol. 155 (2-4), 183-190. LINK
• Minamoto T., Wada E., Shimizu I. (2012) A new method for random mutagenesis by error-prone polymerase chain reaction using heavy water. J. Biotech. 157 (1), 71-74. LINK

 

Other Publications

• Asai, T., Ikushima, S., Sugiyama, M., Morimoto, T., Sudo, A., Minamoto, T. (accepted) Application of dietary content analysis using dropped feces to assess damage to fisheries by great cormorants. Ornithological Science.
• Yamanaka, H., Doi, H., Araki, A., Uchii, K., Minamoto, T. (2024) The eDNA Society International Meeting 2023, “Moving from knowledge into practice”. Environmental DNA 5, 1191-1195. LINK
  
• Yamamoto, Y. (2023) Fish distribution surveys using environmental DNA. National Parks, 816, 18. (in Japanese)
  
• Minamoto, T. (2022) Introduction to Environmental DNA: What Drifting Genes Tell Us. Iwanami Shoten. (in Japanese)
  
• Minamoto, T. (2022) Assessing the distribution of invasive alien ants by environmental DNA analysis of soils. Pest Control 198, 20-25. (in Japanese)
  
• Minamoto, T. (2022) Environmental DNA analysis for macro-organisms: Species distribution and more. DNA Research. LINK
• Sakata, M. K., Jo, T., Minamoto,T. (2021) Overview of Environmental DNA Analysis（Ed. by H. Doi and M. Kondoh) Environmental DNA: Deciphering the True Nature of Ecosystems (Ed. by H. Doi and M. Kondoh) (in Japanese). Kyoritsu Syuppan, pp 1-35.
  
• Minamoto, T. (2021) Standardization of Methods in Environmental DNA Analysis（Ed. by H. Doi and M. Kondoh) Environmental DNA: Deciphering the True Nature of Ecosystems (Ed. by H. Doi and M. Kondoh) (in Japanese). Kyoritsu Syuppan, pp 249-253.
  
• Minamoto, T. (2020) Attempt to obtain information on aquatic organisms using environmental nucleic acids. JMOA Report No.19, 1-10.
  
• Minamoto, T. (2019) Development and application of environmental DNA analysis for macro-organisms. KAGAKU 89, 1029-1035.
  
• Minamoto, T. (2019) Environmental DNA: A novel monitoring tool for aquatic organisms. Seiryu-Seiko 146, 10-11.
  
• Minamoto, T. (2019) Outline of environmental DNA analysis and detection of rare species: Distribution of endangered species discovered by a cup of water. Kagaku to Seibutsu (Chemistry and Biology) 57 (3), 181-186.
  
• Minamoto, T. (2018) Environmental DNA. Ed. The Ichthyological Society of Japan. ENcyclopedia of Icthyology. Maruzen Publishing, Tokyo, pp. 492-493.
  
• Minamoto, T. (2018) Ecological surveys of macro-organisms based on species-specic detection of environmental DNA. Journal of Japan Society on Water Environment 41A (4), 123-127.
  
• Ikeda, K., Doi, H.,Minamoto, T. (2018) Environmental DNA: A new tool for biological monitoring with a bottle of water. IPEJ Journal 30 (3), 20-21.
  
• Minamoto, T. (2018) What is environmental DNA? Aquabiology (Tokyo) 40 (1), 3-8.
  
• Masuda, R., Murakami, H., Takahashi, K., Minamoto, T., Miya, M. (2018) Evaluating the efficiency of environmental DNA through tnak experiments and field surveys. Aquabiology (Tokyo) 40 (1), 17-22.
  
• Fukaya, K., Osada, Y., Minamoto, T. (2018) The potential of environmental DNA for the estimation of population abundance and biomass. Aquabiology (Tokyo) 40 (1), 47-53.
  
• Minamoto, T. (2017) Current developmental status of environmental DNA monitoring for aquatic environments . Environmental Conservation Engineering 46 (12), 624-629. (in Japanese)
  
• Minamoto, T., Uchii, K., Takahara, T., Doi, H. (2017) Issues and prospects of environmental DNA monitoring methods. Environmental Conservation Engineering 46 (12), 648-652. (in Japanese)
  
• Minamoto, T. (2017) Expectation for infectious disease studies using environmental DNA. Virus (Tokyo) 66, 171-178. (in Japanese)
  
• Minamoto, T.(2017) Random Mutagenesis by Error-Prone Polymerase Chain Reaction Using a Heavy Water Solvent in "Methods in Molecular Biology Volume 1498 In Vitro Mutagenesis" (Ed. Andrew Reeves), Springer New York, pp. 491-495. LINK
  
• Uchii, K., Minamoto, T.,Doi, H., Takahara, T., Yamanaka, H., Katano, I. (2016) Environmental DNA analysis: a new monitoring tool for aquatic species. Japanese Journal of Ecology 66 (3), 581-582. (in Japanese)
• Minamoto, T., Uchii, K., Yamanaka, H., Takahara, T., Katano, I., Doi, H. (2016) Towards the further developments of environmental DNA analysis. Japanese Journal of Ecology 66 (3), 621-623. (in Japanese)
• Minamoto T. (2016) Aquatic species census using environemntal DNA. BIOINDUSTRY, 33 (6), 60-65. (in Japanese)
• Minamoto T., Itoh, M., Ebina, K. (2016) Supporting research activities of high school students using environmental DNA analysis. Nihon Kagaku Kyouiku Gakkai Kenkyuukai Kenkyuu Houkoku 30, 21-24. (in Japanese)
• Ebina, K., Itoh, M., Umemura, K., Minamoto, T. (2016) Supporting citizens' activity scrutinizing scientific information: citizens' seminar on IPCC reports. Nihon Kagaku Kyouiku Gakkai Kenkyuukai Kenkyuu Houkoku 30, 17-20. (in Japanese)
• Minamoto, T. (2016) Pathogenic mechanism of infectious diseases. Ecological Society of Japan (ed.) Ecology of Infectiuos diseases, Kyoritsu Syuppan (Tokyo), pp39-51.(in Japanese)
• Iwasaki, W., Sato, Y., Minamoto, T., Yamanaka H., Araki, H., Miya, M .(2016) Impact of environmental DNA analysis. Jikken Igaku (Experimental Medicine) 34 , 1 , 103-107. (in Japanese)
• Minamoto, T. (2014) Environmental DNA: A novel tool for Ecohealth research. Igaku-no-Ayumi, 249 (12), pp 1264-1269. (in Japanese)
• Takahara, T., Minamoto. T., Doi, H. (2014) Organisms can be seen by simply examining the water! Biodistribution survey method using environmental DNA. JSLIM Tokai branch (ed). Asakura Publishing (Tokyo), pp. 159-161.
• Minamoto, T., Kawabata, Z. (2014) Environmental Change of Lakes and Infectious Disease. Kawabata, Z. et al. (eds) Our Lakes: From the Present towards a Future Perspective. (RIHN-China Study Series No.3) Syokado, Kyoto, Japan, pp.75-86. (in Japanese and English)
• Xie, Q., Wu, D., Minamoto, T., Yamanaka, H., Honjo, M. N. Kawabata, Z. (2014) An On-site Empirical Study on the Role of Aquatic Plants Improving Lakefront Water Quality. (RIHN-China Study Series No.3) Syokado, Kyoto, Japan, pp. 139-151. (in Japanese and English).
• Minamoto, T. (2014) eDNA monitoring method for aquatic animals. The Research Institute for Humanity and Nature (ed.) A Manual for Global Environmental Studies 2. Asakura Publishing (Tokyo),. pp.68-69. (in Japanese)