2025 Publications
- Algorithm and Bioinformatic Tool Development
- 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
- 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
- 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
- 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.
- 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
- 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
- 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.
- 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.
- 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.
- 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
- 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
- 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.
- 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
- 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
- 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
- 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.
- 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
- 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
- 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.
- 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.
- 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
- 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
- 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).
- 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).
- 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).
- 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
- 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.
- 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.
- 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
- 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).
- 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.
- 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
- 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.
- 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
2023
- Algorithm and Bioinformatic Tool Development
- 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