Publications

2025 Publications

  • Algorithm and Bioinformatic Tool Development
    1. Nandini Gadhia, Michalis Smyrnakis, Po-Yu Liu, Damer Blake, Melanie Hay, Anh Nguyen, Dominic Richards, Dong Xia, Ritesh Krishna: A novel approach to differential expression analysis of co-occurrence networks for small-sampled microbiome data. IEEE Transactions on Computational Biology and Bioinformatics 2025:1-12 doi:10.1109/TCBBIO.2025.3554740.

2024 Publications

  • Agricultural and Veterinary Microbiome
    1. Jayasingh H, Chang H-X, Knobloch S, Yang S-H, Hendalage DPB, Ariyawansa KGSU, Liu P-Y, Stadler M, Ariyawansa HA: Metagenomic Insight to Apprehend the Fungal Communities Associated with Leaf Blight of Welsh Onion in Taiwan. Front Plant Sci 2024, 15. doi:10.3389/fpls.2024.1352997
    2. Liu P-Y, Liaw J, Soutter F, Ortiz JJ, Tomley FM, Werling D, Gundogdu O, Blake DP, Xia D: Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge. mSystems 2024:e0094724. doi:10.1128/msystems.00947-24.
  • Wildlife and Environmental Microbiome
    1. Hsieh YE, Lu C-Y, Liu P-Y, Kao J-M, Yang S-Y, Wu C-Y, Wong J-WM, Shikina S, Fan T-Y, Yang S-H: Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations. Ecological Indicators 2024, 158. doi:10.1016/j.ecolind.2023.111515.
    2. Chuang P-S, Yu S-P, Liu P-Y, Hsu M-T, Chiou Y-J, Lu C-Y, Tang S-L: A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching. ISME Communications 2024. doi:10.1093/ismeco/ycae001.
  • Algorithm and Bioinformatic Tool Development
    1. Ko JT, Li YY, Chen PY, Liu PY, Ho MY: Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light. Mol Ecol Resour 2024, 24(1):e13871. https://doi.org/10.1111/1755-0998.13871
  • Clinical and Medical Microbiome
    1. Lyu Q, Chen RA, Chuang HL, Zou HB, Liu L, Sung LK, Liu PY, Wu HY, Chang HY, Cheng WJ et al: Bifidobacterium alleviate metabolic disorders via converting methionine to 5'-methylthioadenosine. Gut Microbes 2024, 16(1):2300847. doi:10.1080/19490976.2023.2300847.
    2. Huang J-K, Wu P-H, Chen Z-F, Liu P-Y, Kuo C-C, Chuang Y-S, Lu M-Z, Kuo M-C, Chiu Y-W, Lin Y-T: Identification of Gut Microbiome Signatures Associated with Indole Pathway in Tryptophan Metabolism in Patients Undergoing Hemodialysis. Biomolecules 2024, 14(6). doi:10.3390/biom14060623.
    3. Panyod S, Wu WK, Chang CT, Wada N, Ho HC, Lo YL, Tsai SP, Chen RA, Huang HS, Liu PY et al: Common dietary emulsifiers promote metabolic disorders and intestinal microbiota dysbiosis in mice. Commun Biol 2024, 7(1):749. doi:10.1038/s42003-024-06224-3.
    4. Wong MW, Lo IH, Wu WK, Liu PY, Yang YT, Chen CY, Wu MS, Wong SH, Lei WY, Yi CH et al: Impact of Esophageal Motility on Microbiome Alterations in Symptomatic Gastroesophageal Reflux Disease Patients With Negative Endoscopy: Exploring the Role of Ineffective Esophageal Motility and Contraction Reserve. J Neurogastroenterol Motil 2024, 30(3):332-342. doi:10.5056/jnm22191.
  • Others
    1. Yu H-R, Tsai C-Y, Chen W-L, Liu P-Y, Tain Y-L, Sheen J-M, Huang Y-S, Tiao M-M, Chiu C-Y: Exploring Oxidative Stress and Metabolic Dysregulation in Lung Tissues of Offspring Rats Exposed to Prenatal Polystyrene Microplastics: Effects of Melatonin Treatment . Antioxidants 2024, 13(12). https://doi.org/10.3390/antiox13121459

2023 Publications

  • Wildlife and Environmental Microbiome
    1. Chuang PS, Yamada Y, Liu PY, Tang SL, Mitarai S: Bacterial Community Shifts during Polyp Bail-Out Induction in Pocillopora Corals. Microbiol Spectr 2023:e0025723. https://doi.org/10.1128/spectrum.00257-23.
    2. Chiou YJ, Chan YF, Yu SP, Lu CY, Hsiao SS, Chiang PW, Hsu TC, Liu PY, Wada N, Lee Y et al: Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas. Sci Adv 2023, 9(47):eadk1910. https://doi.org/10.1126/sciadv.adk1910
  • Clinical and Medical Microbiome
    1. Huang YJ, Tsai MS, Panyod S, Liu PY, Lu KH, Weng CY, Huang HS, Hsu CC, Sheen LY: 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 Funct 2023, 14(15):6998-7010. doi:10.1039/d3fo00270e
    2. Tsai C-Y, Liu P-Y, Huang M-C, Chang C-I, Chen H-Y, 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. Journal of Food and Drug Analysis 2023, 31(4). doi:10.38212/2224-6614.3484
  • Veterinary Microbiome
    1. Liu PY, Xia D, McGonigle K, Carroll AB, Chiango J, Scavello H, Martins R, Mehta S, Krespan E, Lunde E et al: 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 MC, Hinsu AT, Koringa PG, Pandit RJ, Liu P-Y, Parekh MJ, Jakhesara SJ, 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 Publications

  • 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 2022, 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 DS, Wu WK, Liu PY, Yang YT, Hsu HC, Kuo CH, Wu MS, Wang TG: Differences in the gut microbiome and reduced fecal butyrate in elders with low skeletal muscle mass. Clin Nutr 2022, 41(7):1491-1500.
    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, 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 Publications

  • Clinical and Medical Microbiome
    1. 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).
    2. 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).
    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 Publications

  • Wildlife and Environmental Microbiome
    1. Liu PY, Cheng AC, Huang SW, Lu HP, Oshida T, Liu W, Yu HT: Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels. Sci Rep 2020, 10(1):7809. https://doi.org/10.1038/s41598-020-64833-8.
    2. Liu PY, Cheng AC, Huang SW, Chang HW, Oshida T, Yu HT: Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem. Microb Ecol 2019, 78(1):223-231.
    3. Lu HP, Liu PY, Wang YB, Hsieh JF, Ho HC, Huang SW, Lin CY, Hsieh CH, Yu HT: Functional characteristics of the flying squirrel's cecal microbiota under a leaf-based diet, based on multiple meta-omic profiling. Front Microbiol 2017, 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 CC, Huang SS, Liu PY, Wang BC, Tsai CF, Wang DY, Cheng HF: 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 WS, Liu PY, Kuo CH: Complete Genome Sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a Bacterium Isolated from Soldier Beetle (Cantharis carolinus). Genome Announc 2015, 3(5).

Preprints

      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 2020:2020.2008.2018.256818. https://doi.org/10.1101/2020.08.18.256818

Conference papers

2023

  • Algorithm and Bioinformatic Tool Development
    1. Gadhia NA, Smyrnakis M, Liu P-Y, Blake D, Hay M, Nguyen A, Xia D, Krishna R, Richards D: Formulating a method to analyse the differential expression of co-occurrence networks for small-sampled microbiome data. In: Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Houston, TX, USA: Association for Computing Machinery; 2023: 1-6. https://doi.org/10.1145/3584371.3612969