Publications

Tsugeki N*, Hashimoto I, Nakane K, Honjo MN, Uchii K* (2024) Establishment success of alien Daphnia in the ancient Lake Biwa: Insights from sedimentary archives Hydrobiologia *Corresponding authors doi: 10.1007/s10750-024-05519-0 Sharing link (View only)

Yamanaka H, Doi H, Araki H, Uchii K, Minamoto T (2023) The eDNA Society International Meeting 2023, “moving from knowledge into practice”  Environmental DNA 5(6): 1191-1195 doi: 10.1002/edn3.465

Miki T, Yamanaka H, Sogabe A, Omori K, Saito Y, Minamoto T, Uchii K, Honjo MN, Suzuki AA, 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 doi: 10.1007/s12080-023-00563-3 Sharing link (View only)

Wakimura K, Uchii K*, Kikko T (2023) Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation. Environmental DNA 5(5): 973-986 doi: 10.1002/edn3.408 Open Access *Corresponding author

Koizumi Y, Ichijo T, Uchii K, Nasu M (2023) Changes in bacterial diversity and community structure in drinking water distribution system revealed by high throughput sequencing. Journal of Microorganism Control 28(1): 27-34 doi: 10.4265/jmc.28.1_27 Open Access

Mimura M, Koizumi Y, Wada M, Ichijo T, Uchii K, Nasu M (2023) Microbial water quality assessment of private wells using 16S rRNA gene amplicon sequencing with a Nanopore Sequencer. Biological and Pharmaceutical Bulletin 46(2): 263-271 doi: 10.1248/bpb.b22-00690

Ichijo T†, Uchii K†, Sekimoto K, Minakami T, Sugita T, Nasu M, Yamazaki T (2022) Bacterial bioburden and community structure of potable water used in the International Space Station. Scientific Reports 12: 16282 doi: 10.1038/s41598-022-19320-3 Open Access  †Co-first authors

Uchii K, Wakimura K, Kikko T, Yonekura R, Kawaguchi R, Komada H, Yamanaka H, Kenzaka T, Tani K (2022) Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens. Limnology 23: 49-56 doi: 10.1007/s10201-021-00665-z

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: 379-388 doi: 10.1111/1440-1703.12217

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 doi: 10.1002/edn3.121 Open Access

Uchii K, Doi H, Okahashi T, Katano I, Yamanaka H, Sakata MK, Minamoto T (2019) Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA. Environmental DNA 1: 359-367 doi: 10.1002/edn3.37 Open Access

• Doi H, Uchii K, Matsuhashi S, Takahara T, Yamanaka H, Minamoto T (2017) Isopropanol precipitation method for collecting fish environmental DNA. Limnology & Oceanography: Methods 15(2): 212-218 doi: 10.1002/lom3.10161

• 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 doi: 10.1111/1755-0998.12586

• 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) doi: 10.18960/seitai.66.3_601

• Takahara T, Yamanaka H, Minamoto T, Doi H, Uchii K (2016) Current state of biomonitoring method using environment DNA analysis. Japanese Journal of Ecology 66(3): 583-599 (In Japanese) doi: 10.18960/seitai.66.3_583

• Maier MA, Uchii K, Peterson TD, Kagami M (2016) Evaluation of daphnid grazing on microscopic zoosporic fungi using comparative CT qPCR. Applied and Environmental Microbiology 82(13):3868-3874 doi: 10.1128/AEM.00087-16 Open Access

• 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 doi: 10.1111/1755-0998.12460

• 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 & Technology doi: 10.1021/acs.est.5b00253 

• 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 doi: 10.1371/journal.pone.0122763 Open Access

• Takahara T, Honjo MN, Uchii K, Minamoto T, Doi H, Ito T, Kawabata A (2014) Effects of daily temperature fluctuation on the survival of carp infected with Cyprinid herpesvirus 3. Aquaculture 433:208-213 doi: 10.1016/j.aquaculture.2014.06.001

• Uchii K, Minamoto T, Honjo MN, Kawabata Z (2014) Seasonal reactivation enables Cyprinid herpesvirus 3 to persist in a wild host population. FEMS Microbiology Ecology 87:536-542 doi: 10.1111/1574-6941.12242 Open Access

• 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 doi: 10.1111/j.1469-1795.2012.00604.x

• Minamoto T, Honjo MN, Yamanaka H, Uchii K, Kawabata Z (2012) Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Research in Veterinary Science 93(1):508-514 doi: 10.1016/j.rvsc.2011.06.004

• Kawabata Z, Minamoto T, Honjo MN, Uchii K, Yamanaka H et al. (2011) Environment-KHV-carp-human linkage as a model for environmental diseases. Ecological Research 26(6):1011-1016 doi: 10.1007/s11284-011-0881-9

• Yamamura N, Telschow A, Uchii K, Kawabata Z (2011) A basic equation for population dynamics with destruction of breeding habitats and its application to outbreak of cyprinid herpesvirus 3. Ecological Research 26(1):181-189 doi: 10.1007/s11284-010-0775-2

• Uchii K, Telschow A, Minamoto T, Yamanaka H, Honjo MN, Matsui K, Kawabata Z (2011) Transmission dynamics of an emerging infectious disease in wildlife through host reproductive cycles. The ISME Journal 5(2):244-251 doi: 10.1038/ismej.2010.123 Open Access

• Honjo MN, Minamoto T, Matsui K, Uchii K, Yamanaka H, Suzuki AA, Kohmatsu Y, Iida T, Kawabata Z (2010) Quantification of cyprinid herpesvirus-3 (CyHV-3) in environmental water using an external standard virus. Applied and Environmental Microbiology 76(1):161-168 doi: 10.1128/AEM.02011-09 Open Access

• Uchii K, Kawabata Z (2009) Biological invasion of a fish pathogen, cyprinid herpesvirus 3, into Japanese freshwater ecosystems. Japanese Journal of Limnology 70(3):267-272 (In Japanese) doi: 10.3739/rikusui.70.267

• Uchii K, Matsui K, Iida T, Kawabata Z (2009) Distribution of the introduced cyprinid herpesvirus 3 in a wild population of common carp, Cyprinus carpio L. Journal of Fish Diseases 32(10):857-864 doi: 10.1111/j.1365-2761.2009.01064.x

• Minamoto T, Honjo MN, Uchii K, Yamanaka H, Suzuki AA, Kohmatsu Y, Iida T, Kawabata Z (2009) Detection of cyprinid herpesvirus 3 DNA in river water during and after an outbreak. Veterinary Microbiology 135(3-4):261-266 doi: 10.1016/j.vetmic.2008.09.081

• Yonekura R, Yamanaka H, Ushimaru A, Matsui K, Uchii K, Maruyama A (2009) Allochthonous prey subsidies provide an asymmetric growth benefit to invasive bluegills over native cyprinids under the competitive conditions in a pond. Biological Invasions 11(6):1347-1355 doi: 10.1007/s10530-008-9342-y

• Matsui K, Honjo M, Kohmatsu Y, Uchii K, Yonekura R, Kawabata Z (2008) Detection and significance of koi herpesvirus (KHV) in freshwater environments. Freshwater Biology 53(6):1262-1272 doi: 10.1111/j.1365-2427.2007.01874.x

• Uchii K (2007) Does gut microbiota help animal adaptations to new environments? Japanese Journal of Ecology 57(3):407-411 (In Japanese) doi: 10.18960/seitai.57.3_407

• Miki T, Matsui K, Yokokawa T, Nishida T, Kobayashi Y, Uchii K (2007) Microbial pool and biodiversity. Japanese Journal of Ecology 57(3):424-431 (In Japanese) doi: 10.18960/seitai.57.3_424

• Yonekura R, Kawamura K, Uchii K (2007) A peculiar relatiohship between genetic diversity and adaptability in invasive exotic species: bluegill sunfish as a model species. Ecological Research 22(6):911-919 doi: 10.1007/s11284-007-0357-0

• Uchii K, Okuda N, Yonekura R, Karube Z, Matsui K, Kawabata Z (2007) Trophic polymorphism in bluegill sunfish (Lepomis macrochirus) introduced into Lake Biwa: evidence from stable isotope analysis. Limnology 8(1):59-63 doi: 10.1007/s10201-006-0196-7

• Uchii K, Matsui K, Yonekura R, Tani K, Kenzaka T, Nasu M, Kawabata Z (2006) Genetic and physiological characterization of the intestinal bacterial microbiota of bluegill (Lepomis macrochirus) with three different feeding habits. Microbial Ecology 51(3):277-284 doi: 10.1007/s00248-006-9018-z