Publications

2024 Pulications

  • Agricultural and Veterinary Microbiome
    1. Himanshi Jayasinghe, Hao-Xun Chang, Stephen Knobloch, Shan-Hua Yang, D. P. Bhagya Hendalage, Kahandawa G.S.U. Ariyawansa, Po-Yu Liu* (co-corresponding author), Marc Stadler and Hiran A. Ariyawansa*. "Metagenomic Insight to Apprehend the Fungal Communities Associated with Leaf Blight of Welsh Onion in Taiwan." Front. Plant Sci. Volume 15 - 2024 doi:10.3389/fpls.2024.1352997
  • Wildlife and Environmental Microbiome
    1. Hsieh, Y. E., C.-Y. Lu, P.-Y. Liu, J.-M. Kao, S.-Y. Yang, C.-Y. Wu, J.-W. M. Wong, S. Shikina, T.-Y. Fan and S.-H. Yang. "Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations." Ecological Indicators 158. doi:10.1016/j.ecolind.2023.111515.
    2. Po-Shun Chuang, Sheng-Ping Yu, Po-Yu Liu, Ming-Tsung Hsu, Yu-Jing Chiou, Chih-Ying Lu, Sen-Lin Tang. "A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching." ISME Communications ycae001. doi:10.1093/ismeco/ycae001.
  • Algorithm and Bioinformatic Tool Development
    1. Ko, J.T., Li, Y.Y., Chen, P.Y., Liu, P.Y.* (co-corresponding author), Ho, M.Y.* "Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light." Mol Ecol Resour. https://doi.org/10.1111/1755-0998.13871
  • Clinical and Medical Microbiome
    1. Lyu, Q., Chen, R. A., Chuang, H. L., Zou, H. B., Liu, L., Sung, L. K., Liu, P. Y., Wu, H. Y., Chang, H. Y., Cheng, W. J., Wu, W. K., Wu, M. S., & Hsu, C. C. "Bifidobacterium alleviate metabolic disorders via converting methionine to 5'-methylthioadenosine", Gut Microbes 16(1):2300847. doi:10.1080/19490976.2023.2300847.

2023 Pulications

  • Wildlife and Environmental Microbiome
    1. Chuang, P.S., Yamada, Y., Liu, P.Y., Tang, S.L., Mitarai, S. "Bacterial Community Shifts during Polyp Bail-Out Induction in Pocillopora Corals", Microbiol Spectr, e0025723. https://doi.org/10.1128/spectrum.00257-23.
    2. Chiou, Y.J., Chan, Y.F., Yu, S.P., Lu, C.Y., Hsiao, S.S., Chiang, P.W., Hsu, T.C., Liu, P.Y., Wada, N., Lee, Y., Jane, W.N., Lee, D.C., Huang, Y.W., Tang, S.L. "Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas." Sci Adv 9:eadk1910. https://doi.org/10.1126/sciadv.adk1910
  • Clinical and Medical Microbiome
    1. Huang, Y.-J., Tsai, M.-S., Panyod, S., Liu, P.-Y., Lu, K.-H., Weng, C.-Y., ... Sheen, L.-Y. "Garlic essential oil ameliorates depression-like behaviors in unpredictable chronic mild stress by modulating the brain NLRP3 inflammasome pathway and influencing the gut barrier and microbiota", Food & Function. doi:10.1039/d3fo00270e
    2. Tsai, C.-Y, Liu, P.-Y., Huang, M.-C., Chang, C.-I., Chou, Y.-H., Tsai, C.-N., Lin, C.-H. "Abundance of Prevotella copri in gut microbiota is inversely related to a healthy diet in patients with type 2 diabetes", J Food Drug Anal. doi:10.38212/2224-6614.3484
  • Veterinary Microbiome
    1. Liu, P. Y., D. Xia, K. McGonigle, A. B. Carroll, J. Chiango, H. Scavello, R. Martins, S. Mehta, E. Krespan, E. Lunde, D. LeVine, C. L. Fellman, R. Goggs, D. P. Beiting, O. A. Garden. "Immune-mediated hematological disease in dogs is associated with alterations of the fecal microbiota: a pilot study", Anim Microbiome, 2023, 5(1): 46. https://doi.org/10.1186/s42523-023-00268-2.
    2. Hay, M.C., Hinsu, A.T., Koringa, P.G., Pandit, R.J., Liu, P.-Y., Parekh, M.J., Jakhesara, S.J., Dai, X., Crotta, M., Fosso, B., et al. "Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices", Frontiers in Microbiomes, 2023, 2. https://www.frontiersin.org/articles/10.3389/frmbi.2023.1301609/

2022 Pulications

  • Wildlife and Environmental Microbiome
    1. Liu, P.-Y., Yang, S.-Y., Lu, C.-Y., Wada, N., De Palmas, S., Yeh, S.-S., Yamashiro, H., Tang, S.-L., Yang, S.-H. "Ocean Currents May Influence the Endolithic Bacterial Composition in Coral Skeletons", Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.769028.
  • Clinical and Medical Microbiome
    1. Chen RA, Wu WK, Panyod S, Liu PY, Chuang HL, Chen YH, Lyu Q, Hsu HC, Lin TL, Shen TD et al. "Dietary Exposure to Antibiotic Residues Facilitates Metabolic Disorder by Altering the Gut Microbiota and Bile Acid Composition", mSystems 2022:e0017222.
    2. Han D-S, Wu W-K, Liu P-Y, Yang Y-T, Hsu H-C, Kuo C-H, Wu M-S, Wang T-G. "Differences in the gut microbiome and reduced fecal butyrate in elders with low skeletal muscle mass", Clinical Nutrition 2022.
    3. Panyod S, Wu WK, Chen PC, Chong KV, Yang YT, Chuang HL, Chen CC, Chen RA, Liu PY, Chung CH et al. "Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation", NPJ Biofilms Microbiomes 2022, 8(1):4.
  • Algorithm and Bioinformatic Tool Development
    1. Liu PY* (corresponding author), Yang SH, Yang SY. "KTU: K-mer Taxonomic Units improve the biological relevance of amplicon sequence variant microbiota data", Methods in Ecology and Evolution, 2022, 13(3):560-568.

2021 Pulications

  • Clinical and Medical Microbiome
    1. Lin YT, Lin TY, Hung SC, Liu PY, Hung WC, Tsai WC, Tsai YC, Delicano RA, Chuang YS, Kuo MC et al. "Differences in the Microbial Composition of Hemodialysis Patients Treated with and without beta-Blockers", J Pers Med 2021, 11(3).
    2. Lin Y-T, Lin T-Y, Hung S-C, Liu P-Y, Wu P-H, Chuang Y-S, Hung W-C, Chiu Y-W, Kuo M-C, Wu C-Y. "Anti-Acid Drug Treatment Induces Changes in the Gut Microbiome Composition of Hemodialysis Patients", Microorganisms 2021, 9(2).
    3. Liu WD, Yen TY, Liu PY, Wu UI, Bhan P, Li YC, Chi CH, Sheng WH. "Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis", Microorganisms 2021, 9(11).
    4. Tsai CY, Lu HC, Chou YH, Liu PY, Chen HY, Huang MC, Lin CH, Tsai CN. "Gut Microbial Signatures for Glycemic Responses of GLP-1 Receptor Agonists in Type 2 Diabetic Patients: A Pilot Study", Front Endocrinol (Lausanne) 2021, 12:814770.

2020 and before pulications

  • Wildlife and Environmental Microbiome
    1. Liu, P.Y., Cheng, A.C., Huang, S.W., Lu, H.P., Oshida, T., Liu, W., Yu, H.T. "Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels", Sci Rep, 10(1):7809. https://doi.org/10.1038/s41598-020-64833-8.
    2. Liu, P.Y., Cheng, A.C., Huang, S.W., Chang, H.W., Oshida, T., Yu, H.T. "Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem", Microb Ecol, 78(1):223-231.
    3. Lu, H.P., Liu, P.Y. (co-first author), Wang, Y.B., Hsieh, J.F., Ho, H.C., Huang, S.W., Lin, C.Y., Hsieh, C.H., Yu, H.T. "Functional characteristics of the flying squirrel's cecal microbiota under a leaf-based diet, based on multiple meta-omic profiling", Front Microbiol, 8:2622. https://doi.org/10.3389/fmicb.2017.02622.
  • Clinical and Medical Microbiome
    1. Wu P-H, Liu P-Y, Chiu Y-W, Hung W-C, Lin Y-T, Lin T-Y, Hung S-C, Delicano RA, Kuo M-C, Wu C-Y. "Comparative Gut Microbiome Differences between Ferric Citrate and Calcium Carbonate Phosphate Binders in Patients with End-Stage Kidney Disease", Microorganisms 2020, 8(12).
    2. Wu WK, Panyod S, Liu PY, Chen CC, Kao HL, Chuang HL, Chen YH, Zou HB, Kuo HC, Kuo CH et al. "Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery", Microbiome 2020, 8(1):162.
    3. Wu WK, Chen CC, Liu PY, Panyod S, Liao BY, Chen PC, Kao HL, Kuo HC, Kuo CH, Chiu THT et al. "Identification of TMAO-producer phenotype and host-diet-gut dysbiosis by carnitine challenge test in human and germ-free mice", Gut 2019, 68(8):1439-1449.

Others

    1. Yeh, C.C., Huang, S.S., Liu, P.Y., Wang, B.C., Tsai, C.F., Wang, D.Y., Cheng, H.F. "Simultaneous quantification of six indicator compounds in Wen-Qing-Yin by high-performance liquid chromatography-diode array detection", J Food Drug Anal, 2019, 27(3):749-757.
    2. Lo, W.S., Liu, P.Y., Kuo, C.H. "Complete Genome Sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a Bacterium Isolated from Soldier Beetle (Cantharis carolinus)", Genome Announc, 2015, 3(5).

Preprints

    1. Liu, P.-Y., Wu, W.-K., Chen, C.-C., Panyod, S., Sheen, L.-Y., Wu, M.-S. "Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling", bioRxiv 2020:2020.08.18.256818. https://doi.org/10.1101/2020.08.18.256818

Conference papers

2023

  • Algorithm and Bioinformatic Tool Development
    1. Gadhia, N. A., Smyrnakis, M., Liu, P.-Y., Blake, D., Hay, M., Nguyen, A., ... Richards, D. "Formulating a method to analyse the differential expression of co-occurrence networks for small-sampled microbiome data", Presented at the Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, Houston, TX, USA. https://doi.org/10.1145/3584371.3612969