Research Interests:

Molecular Evolutionary Biology: gene/genome duplications, molecular evolution, phylogeny, population genetics, and ecology of animals (mainly fishes and vertebrates). Bioinformatic and DNA sequencing (NGS) approach

Environmental DNA (eDNA) Analysis : comprehensive analysis of trans-kingdom biota from animals including rare, endangered, and invasive species to environmental pathogens including bacteria, viruses, and plasmids (with ARGs, antibiotic resistance genes). Both metabarcoding & metagenomic (NGS) approaches

Human- and Livestock-associated Microbiomes: human oral, gut, and skin, and livestock gut and environmental microbiomes including pathogenic and ARGs (antibiotic resistance genes) related ones. Both metabarcoding & metagenomic (NGS) approaches

Mitochondrial Genome Structure, Heteroplasmy, and Functions: gene order conservation or rearrangement through mt gene/genome duplications. Mt-gene order and translational/replication efficiency mainly focusing on animals. Bioinformatic approach

Positions Held:

2016-  Senior Lecturer, University of the Ryukyus (2016 - 2021, Center for Strategic Research Project; 2021 - current, Research Laboratory Center, Faculty of Medicine)

2013-2016 Assistant Professor, Tohoku University (Masao Nagasaki Lab.)

2009-2013 Postdoctoral Researcher, National Institute of Genetics (Naruya Saitou & Takashi Gojobori Lab)

Educational Background:

2008-2009 Postdoctoral Fellow, University of Tokyo (Mutsumi Nishida Lab)

2008 Ph. D. (Agr.) University of Tokyo, Japan (Mutsumi Nishida Lab)

2005 M. (Agr.) University of Tokyo, Japan (Mutsumi Nishida Lab)

2003 B. (Agr.) Tohoku University, Japan (Nobuhiko Taniguchi Lab)

Publications:

52.  Yusuke Maruta, Kazuki Tsuji, Yukuto Sato, Shun Kobayashi, Nobuhiko Kotaka, Kaori Tsurui-Sato. 2026. Observations of the feeding behavior on the fragrant screw-pine (Pandanus odorifer) and roadkill cases, and a new finding on the land hermit crab (Coenobita cavipes) as a prey species in the Ryukyu long-furred rat (Diplothrix legata). Mammalian Science, in press. (In Japanese with English abstract)

51. Yukuto Sato, Yuiko Hiyajo, Taisei Tengan, Tsurua Yoshida, Yoichiro Uchima, Michinari Tokeshi, Kaori Tsurui-Sato, Claudia Toma. 2025. DNA metabarcoding analysis revealed a silent prevalence of environmental pathogenic Leptospira in urban area of Okinawa Island, Japan. One Health, 20: 101016.

50. Shun Kobayashi, Yukuto Sato, Masako Izawa. 2024. Omnivorous food habits of the endangered Ryukyu long-furred rat Diplothrix legata (Muridae) estimated using the DNA metabarcoding method. Mammal Study, 50: 1-14.

49. Yukuto Sato*, Kaori Tsurui-Sato, Yoichiro Uchima, Cheryl-Ann Udui, Osiro Lorin, Kashgar Rengulbai, Claudia Toma, Ryo Suzuki*. 2024. A systematic survey of environmental DNA in Palau's lakes and waterfalls reveals an increase in Leptospira levels after flooding. (*equally contributed) One Health, 19: 100898. 

48. Hiroto Nagai, Yukuto Sato, Hideyuki Imai, Tadashi Kajita. 2024. An environmental DNA survey for fish and decapod crustacean fauna in the irrigation waterway of taro fields in Oyama, Ginowan, Okinawa, Japan. Aquatic Animals,  AA2024-20: 1–13. (In Japanese with English abstract)

47. Naoya Nishiyama, Kohei Uechi, Wakako Arakaki, Daisuke Utsumi, Yukuto Sato, Masashi Nakamatsu, Takeshi Kinjo, Kazuko Yamamoto. 2024. Complete genome sequence of a metallo-β-lactamase-producing Aeromonas dhakensis strain, RYU-Ah62, isolated from a patient with an abdominal abscess. Microbiology Resource Announcements, 13: 1–3.

46. Kaori Tsurui-Sato*, Yukuto Sato*, Naotaka Katsube, Haruki Tatsuta, Kazuki Tsuji. 2024. Detection of functionally polymorphic region of opsin LWS-1 gene of guppy Poecilia reticulata using environmental DNA analysis. (*equally contributed) Japanese Journal of Ichthyology,  71: 81–96. (In Japanese with English abstract)

45. Alisa Tobe*, Yukuto Sato*, Nakatada Wachi, Nozomi Nakanishi, Masako Izawa . 2024. Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan. (*equally contributed) Scientific Reports, 14: 7727.

44. Yukuto Sato, Jun Yasuda, Masahiro Sakurai. 2023. Animal-sourced model of human norovirus infection predicted using environmental DNA metabarcoding analysis. Journal of Freshwater Ecology,  39: 2293171. 

43. Tao Zhu, Yukuto Sato, Tetsuya Sado, Masaki Miya, Wataru Iwasaki. 2023. MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in ten years. Molecular Biology and Evolution,  43: msad035.

42. Shingo Fujimoto, Hajime Yaguchi, Taijun Myosho, Hiroaki Aoyama, Yukuto Sato, Ryosuke Kimura. 2022. Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing. Scientific Reports, 12: 19989.

41. Atsushi Tominaga, Natsuhiko Yoshikawa, Masafumi Matsui, Nobuaki Nagata, Yukuto Sato. 2022. The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela). Biological Journal of the Linnean Society, 137: 651–666.

40. Yukari Tanaka, Riu Yamashita, Junko Kawashima, Hiroshi Mori, Ken Kurokawa, Shinji Fukuda, Yasuhiro Gotoh, Keiji Nakamura, Tetsuya Hayashi, Yoshiyuki Kasahara,  Yukuto Sato, Shin Fukudo. 2022. Omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation. Journal of Gastroenterology, 57: 748–760. 

39. Yukuto Sato, Idam Hermawan, Tetsuya Kakita, Sho Okano, Hideyuki Imai, Hiroto Nagai, Ryosuke Kimura, Tetsu Yamashiro, Tadashi Kajita, Claudia Toma. 2022. Analysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan. PLOS Neglected Tropical Diseases, 16: e0010234.

38. Tomoya Suzuki, Kanto Nishikawa, Yukuto Sato, Mamoru Toda. 2021. Development and evaluation of Loop-Mediated Isothermal Amplification (LAMP) assay for quick identification of Japanese salamander, Hynobius tokyoensis. Genes and Genetic Systems, 96: 247−252.

37. Yukuto Sato*, Kaori Tsurui‐Sato*, Mitsuho Katoh, Ryosuke Kimura, Haruki Tatsuta, Kazuki Tsuji. 2021. Population genetic structure and evolution of Batesian mimicry in Papilio polytes from the Ryukyu Islands, Japan, analyzed by genotyping‐by‐sequencing. (*equally contributed) Ecology and Evolution, 11: 872−886.

36. Alisa Tobe, Nozomi Nakanishi, Yukuto Sato, Nakatada Wachi, Masako Izawa. 2020. Diet analysis of two umbrella species using DNA barcoding to conserve the ecosystem of Iriomote-jima Island. Annual Report of Pro Natura Foundation Japan, 29: 238-248.  (In Japanese with English abstract)

35. Chandika D. Gamage*, Yukuto Sato*, Ryosuke Kimura, Tetsu Yamashiro, Claudia Toma. 2020. Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka. (*equally contributed) PLOS Neglected Tropical Diseases, 14: e0008437.

34. Kota Okamoto, Takaki Kurita, Masahiro Nagano, Yukuto Sato, Hiroaki Aoyama, Seikoh Saitoh, Naoya Shinzato, Mamoru Toda. 2020. Development of 22 microsatellite markers for assessing hybridization in the genus Gekko (Squamata: Gekkonidae). Current Herpetology, 39: 66−74.

33. Kaori Tsurui-Sato*, Yukuto Sato*, Emi Kato*, Mitsuho Katoh*, Ryosuke Kimura, Haruki Tatsuta, and Kazuki Tsuji. 2019. Evidence for frequency‐dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan. (*equally contributed) Ecology and Evolution, 9: 5991−6002.

32. Yukuto Sato*, Masaru Mizuyama*, Megumi Sato, Toshifumi Minamoto, Ryosuke Kimura, and Claudia Toma. 2019. Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. (*equally contributed) Scientific Reports, 9: 6575.

31. Yukuto Sato, Masaki Miya, Tsukasa Fukunaga, Tetsuya Sado, and Wataru Iwasaki. 2018. MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Molecular Biology and Evolution, 35: 1553−1555.

30. Hikaru Nakagawa, Satoshi Yamamoto, Yukuto Sato, Tetsuya Sado, Toshifumi Minamoto, and Masaki Miya. 2018. Comparing local- and regional-scale estimations of thediversity of stream fish using eDNA metabarcoding andconventional observation methods. Freshwater Biology, 63: 569−580.

29. Tazro Ohta, Takeshi Kawashima, Natsuko O. Shinozaki, Akito Dobashi, Satoshi Hiraoka, Tatsuhiko Hoshino, Keiichi Kanno, Takafumi Kataoka, Shuichi Kawashima, Motomu Matsui, Wataru Nemoto, Suguru Nishijima, Natsuki Suganuma, Haruo Suzuki, Y-h. Taguchi, Yoichi Takenaka, Yosuke Tanigawa, Momoka Tsuneyoshi, Kazutoshi Yoshitake, Yukuto Sato, Riu Yamashita, Kazuharu Arakawa, and Wataru Iwasaki. 2018. Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago. Journal of Plant Research, 131: 709−717.

28. Masaki Nishioka, Miki Bundo, Junko Ueda, Fumiki Katsuoka, Yukuto Sato, Yoko Kuroki, Takao Ishii, Wataru Ukai, Shigeo Murayama, Eri Hashimoto, Masao Nagasaki, Jun Yasuda, Kiyoto Kasai, Tadafumi Kato, and Kazuya Iwamoto. 2018. Identification of somatic mutations in postmortem human brains by whole genome sequencing and their implications for psychiatric disorders. Psychiatry and Clinical Neurosciences, 72: 280−294.

27. Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Kobayashi Makoto, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, and Masaki Miya. 2017. Environmental DNA enables detection of terrestrial mammals from forest pond water. Molecular Ecology Resources, 17: e63−e75.

26. Satoshi Yamamoto, Reiji Masuda, Yukuto Sato, Tetsuya Sado, Hitoshi Araki, Michio Kondoh, Toshifumi Minamoto, and Masaki Miya. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports, 7: 40368.

25. Junya Yamagishi*, Yukuto Sato*, Natsuko Shinozaki, Bin Ye, Akito Tsuboi, Masao Nagasaki, and Riu Yamashita. 2016. Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of human oral microbes. (*equally contributed) PLoS One, 11: e0154389. [doi:10.1371/journal.pone.0154389]

24. Xiaoqing Pan, Naoki Nariai, Noriko Fukuhara, Sakae Saito, Yukuto Sato, Fumiki Katsuoka, Kaname Kojima, Yoko Kuroki, Inaho Danjoh, Rumiko Saito, Shin Hasegawa, Yoko Okitsu, Aiko Kondo, Yasushi Onishi, Fuji Nagami, Hideyasu Kiyomoto, Atsushi Hozawa, Nobuo Fuse, Masao Nagasaki, Ritsuko Shimizu, Jun Yasuda, Hideo Harigae, and Masayuki Yamamoto. 2016. Monitoring of minimal residual disease in early T-cell precursor acute lymphoblastic leukaemia by next-generation sequencing. British Journal of Haematology, 176: 318-321 [doi:10.1111/bjh.13948]

23. Yamaguchi-Kabata Y, Nariai N, Kawai Y, Sato Y, Kojima K, Tateno M, Katsuoka F, Yasuda J, Yamamoto M, and Nagasaki M. 2015. iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. Human Genome Variation, 2: 15050. [doi:10.1038/hgv.2015.50]

22. Inoue J*, Sato Y*, Sinclair R*, Tsukamoto K, and Nishida M. 2015. Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. (*equally contributed) PNAS, 112: 14918-14923. [doi: 10.1073/pnas.1507669112] 

21. Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Engel JD, Kinoshita K, Kure S, Yaegashi N, ToMMo Japanese Reference Panel Project, and Yamamoto M. 2015. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nature Communications, 6: 8018. [doi:10.1038/ncomms9018]

20. Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto T, Yamanaka H, Araki H, Kondoh M, and Iwasaki W. 2015. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of >230 subtropical marine species. Royal Society Open Science, 2: 150088. [doi:10.1098/rsos.150088]

19. Sato Y*, Yamagishi J*, Yamashita R*, Shinozaki N, Ye B, Yamada T, Yamamoto M, Nagasaki M, and Tsuboi A. 2015. Inter-individual differences in the oral bacteriome are greater than intra-day fluctuations in individuals. (*equally contributed) PLoS One, 10: e0131607. [doi:10.1371/journal.pone.0131607]

18. Mimori T, Nariai N, Kojima K, Sato Y, Kawai Y, Yamaguchi-Kabata Y, and Nagasaki M. 2015. Estimating copy numbers of alleles from population-scale high-throughput sequencing data. BMC Bioinformatics, 16(Suppl 1): S4. [doi:10.1186/1471-2105-16-S1-S4]

17. Nariai N, Kojima K, Saito S, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Yasuda J, and Nagasaki M. 2015. HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. BMC Genomics, 16(Suppl 2): S7. [doi:10.1186/1471-2164-16-S2-S7]

16. Nariai N, Kojima K, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, and Nagasaki M. 2014. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads. BMC Genomics, 15(Suppl 10): S5. [doi:10.1186/1471-2164-15-S10-S5]

15. Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, and Yamamoto M. 2014. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics, 15: 673. [doi:10.1186/1471-2164-15-673]

14. Sato Y, Kojima K, Nariai N, Yamaguchi-Kabata Y, Takahashi M, Mimori T, and Nagasaki M. 2014. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing. BMC Genomics, 15: 664. [doi:10.1186/1471-2164-15-664]

13. Kojima K, Nariai N, Mimori T, Yamaguchi-Kabata Y, Sato Y, Kawai Y, and Nagasaki M. 2014. HapMonster: a statistically unified approach for variant calling and haplotyping based on phase-informative reads. Lecture Notes in Bioinformatics, 8542: 107−118. [doi:10.1007/978-3-319-07953-0_9]

12. Ohtsuki T, Nariai N, Kojima K, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Shibuya T, and Nagasaki M. 2014. SVEM: a structural variant estimation method using multi-mapped reads on breakpoints. Lecture Notes in Bioinformatics, 8542: 208−219. [doi:10.1007/978-3-319-07953-0_17]

11. Mimori T, Nariai N, Kojima K, Takahashi M, Ono A, Sato Y, Yamaguchi-Kabata Y, and Nagasaki M. 2013. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Systems Biology, 7(Suppl 6): S8. [doi:10.1186/1752-0509-7-S6-S8]

10. Kojima K, Nariai N, Mimori T, Takahashi M, Yamaguchi-Kabata Y, Sato Y, and Nagasaki M. 2013. A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. Bioinformatics, 29: 2835−2843. [doi:10.1093/bioinformatics/btt503]

9. Miya M, Friedman M, Satoh TP, Takeshima H, Sado T, Iwasaki W, Yamanoue Y, Nakatani M, Mabuchi K, Inoue JG, Poulsen JY, Fukunaga T, Sato Y, and Nishida M. 2013. Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families. PLoS One, 8: e73535. [doi:10.1371/journal.pone.0073535]

8. Sato Y, Hachiya T, and Iwasaki W. 2012. Next-generation sequencing in aquatic biology: the current status and future directions. Fish Genetics and Breeding Science, 41: 17-32. (In Japanese with English abstract)

7. Satoh TP*, Sato Y*, Masuyama N, Miya M, and Nishida M. 2010. Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation. (*equally contributed) BMC Genomics, 11: 479. [doi:10.1186/1471-2164-11-479]

6. Sato Y and Nishida M. 2010. Teleost fish with specific genome duplication as unique models of vertebrate evolution. Environmental Biology of Fishes, 88: 169−188. [doi:10.1007/s10641-010-9628-7]

5. Sato Y and Nishida M. 2009. Whole genome duplication and the evolution of fishes. Japanese Journal of Ichthyology, 56: 89-109. (In Japanese with English abstract)

4. Sato Y, Hashiguchi Y, and Nishida M. 2009. Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evolutionary Biology, 9: 127. [doi:10.1186/1471-2148-9-127]

3. Sato Y, Hashiguchi Y, and Nishida M. 2009. Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Systems Biology, 3: 23. [doi:10.1186/1752-0509-3-23]

2. Sato Y and Nishida M. 2009. Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties. Gene, 441: 3−11. [doi:10.1016/j.gene.2008.06.026]

1. Sato Y and Nishida M. 2007. Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites. BMC Evolutionary Biology, 7: 204. [doi:10.1186/1471-2148-7-204]

Publication List in Public Databases:

Google Scholar

PubMed

Research Grants (as principal researcher or subject leader):　

2023 JSPS Grant-in-Aid for Scientific Research (B) (environmental DNA correlation analysis for bio-interaction of whole biota)

2020 ERCA Environment Research and Technology Development Fund (subject 2 leader: genomic evaluation for conservation implications of rare and endangered amphibians and reptiles in Japan)

2020 JSPS Grant-in-Aid for Scientific Research (C) (environmental DNA bio-banking in Okinawa, Japan, aiming for trans-kingdom and longitudinal analysis of biota)

2017 JSPS Grant-in-Aid for Grant-in-Aid for Challenging Exploratory Research (pan-animalian environmental DNA analysis development)

2015 JSPS Grant-in-Aid for Young Scientists (B) (pipeline development for environmental DNA analysis of vertebrates)

2010 JSPS Grant-in-Aid for Young Scientists (B) (RNA/cDNA sequencing of non-teleost actinopterygians)

2009 Sasakawa Scientific Research Grant from the Japan Science Society (protein evolution in deep-sea fish)

Awards:

• The 2023 Faculty of Medicine Best Research Award of University of the Ryukyus (April 22, 2024) with a medical student Ms. Yuiko Hiyajo

• Presidential Award from the National Research Council (NRC), Sri Lanka. (November 21, 2023)

    Related publications: [35] Gamage, Sato, et al.  2020. PLOS Neglected Tropical Diseases, 14: e0008437.

• The 2021 Graduate School of Medicine Research Encouragement Award of University of the Ryukyus (March 30, 2022)

Related publications: [35] Gamage, Sato, et al.  2020. PLOS Neglected Tropical Diseases, 14: e0008437; [37]  Sato et al. 2021. Ecology and Evolution, 11: 872−886.

• Best Poster Prize at Annual Meeting for the Society of Evolutionary Studies, Japan (August 23, 2008)

Related publications: [4] Sato, Hashiguchi, and Nishida 2009 BMC Evol Biol 9:127; [22] Inoue, Sato, Sinclair, et al. 2015 PNAS 112:14918-14923 .

Learned Society:

The Ichthyological Society of Japan (2019-)

BioinfoWakate (Japanese Association of Young Scientists in the Field of Bioinformatics) (2009-2015)

The Genetics Society of Japan (2009-2017)

Society of Evolutionary Studies, Japan (2005-2017)

Peer Review Activity (2007- ):

Aquaculture Reports, BMC Ecology and Evolution, BMC Evolutionary Biology, BMC Genomics, BMC Microbiology, Cladistics, Environmental Advances, Environmental Biology of Fishes, Evolutionary Bioinformatics, Gene, Genome Biology and Evolution, GigaScience, Global Ecology and Conservation, Heliyon, Ichthyological Research, Infectious Diseases of Poverty, Journal of Molecular Evolution, Marine Biotechnology, Marine Genomics, Metabarcoding and Metagenomics, Molecular Biology and Evolution, Molecular Ecology Resources, New Zealand Journal of Zoology, PLoS One, Proceedings of the Royal Society B, Reproduction, Scientific Data, Scientific Reports, Zoological Science, Biological Science (In Japanese 生物科学), Fish Genetics and Breeding Science (In Japanese 水産育種), Japanese Journal of Ichthyology (In Japanese 魚類学雑誌), and others (e.g., some Chapters of text books and dictionaries)