跳到主要內容

臺灣博碩士論文加值系統

(44.213.60.33) 您好!臺灣時間:2024/07/17 04:30
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

我願授權國圖
: 
twitterline
研究生:何政緯
研究生(外文):Ho, Cheng-Wei
論文名稱:以海鮮替代調查驅動的生魚片微生物菌相的全面調查
論文名稱(外文):An extensive microbiome investigation of served sashimi dishes motivated by a prior seafood substitution investigation
指導教授:劉宗榮劉宗榮引用關係梁恭豪鄒瀚興
指導教授(外文):Liu, Tsung-YunLiang, Kung-HaoTsou, Han-Hsing
口試委員:劉宗榮梁恭豪鄒瀚興郭志鴻鄭彥甫
口試委員(外文):Liu, Tsung-YunLiang, Kung-HaoTsou, Han-HsingKuo, Chih-HorngCheng, Yen-Fu
口試日期:2021-11-23
學位類別:碩士
校院名稱:國立陽明交通大學
系所名稱:食品安全及健康風險評估研究所
學門:醫藥衛生學門
學類:其他醫藥衛生學類
論文種類:學術論文
論文出版年:2021
畢業學年度:110
語文別:英文
論文頁數:100
中文關鍵詞:海鮮替代DNA條形碼16s-rRNA 基因微生物菌相次世代定序
外文關鍵詞:Seafood mislabelingDNA Barcoding16s-rRNA geneMicrobiomeNGS
相關次數:
  • 被引用被引用:0
  • 點閱點閱:144
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
Content
摘要 I
ABSTRACT II
CONTENT III
LIST OF FIGURES VI
LIST OF TABLES VII
ABBREVIATION VIII
CHAPTER 1: INTRODUCTION 1
1.1 SEAFOOD 1
1.1.1 Seafood in Food culture of Taiwan 1
1.1.2 Raw seafood in Taiwan 1
1.1.3 Fish species used as ingredients for sashimi 2
1.1.4 Nutrition of raw seafood 3
1.1.5 Potential health risk of raw seafood 3
1.1.5 Source and supply chain of seafood in Taiwan 5
1.1.6 Substitution issue of raw seafood in Taiwan 6
1.2 MICROBIOME 7
1.2.1 Definition and introduction 7
1.2.2 Methodologies of microbiome research 8
1.2.3 Microbiome in fish 10
1.2.4 Factors influence composition of microbiome in fish 11
1.2.5 Distribution of microbiome in fish 13
CHAPTER 2: MOTIVATION AND AIMS 15
2.1 MOTIVATION 15
2.1.1 PILOT STUDY OF FOOD RELATED MICROBIOME 15
2.1.2 IMPORTANCE OF MICROBIOME IN RAW SEAFOOD 15
2.1.3 A PAUCITY OF MICROBIOME RESEARCH FOCUSED ON SEAFOOD 16
2.2 AIMS 16
2.2.1 Working hypothesis 16
2.2.2 Validation of prior food microbiome study. 17
2.2.3 To identify deterministic factors influencing microbiome in sashimi 17
2.2.4 To investigate characteristics of the sashimi microbiome 18
CHAPTER 3: MATERIALS AND METHODS 19
3.1 WORKFLOW OF STUDY 19
3.2 SAMPLE COLLECTION 19
3.2.1 Sample source 19
3.2.2 Fish types of sashimi 20
3.2.3 Equipment and materials 20
3.2.4 Sampling method 20
3.3 SAMPLE PREPARATION 21
3.3.1 Equipment and materials 21
3.3.2 Procedure 21
3.4 DNA EXTRACTION 22
3.4.1 Basic information 22
3.4.2 Equipment and materials 23
3.4.3 Procedure 23
3.6 POLYMERASE CHAIN REACTION FOR DNA AMPLIFICATION 25
3.6.1 Basic information 25
3.6.2 Equipment and materials 26
3.6.3 Procedure 26
3.7 GEL ELECTROPHORESIS 27
3.7.1 Basic information 27
3.7.2 Equipment and materials 28
3.7.3 Procedure 29
3.8 SANGER SEQUENCING 29
3.8.1 Basic information 29
3.8.2 Equipment and materials 30
3.8.3 Procedure 30
3.9 POST SEQUENCING ANALYSIS 31
3.9.1 Basic information 31
3.9.2 Equipment and materials 32
3.9.3 Procedure 32
3.10 SPECIES IDENTIFICATION 32
3.10.1 Basic information 32
3.10.2 Equipment and materials 33
3.10.3 Procedure 33
3.11 NEXT-GENERATION SEQUENCING 33
3.11.1 Basic information 33
3.11.2 Workflow of Illumina sequencing [57, 58] 36
3.11.3 Post sequencing data preparation 38
3.11.4 Data analysis 40
3.12 STATISTICAL ANALYSIS 44
CHAPTER 4: RESULTS 45
4.1 SAMPLE COLLECTION 45
4.2 DNA EXTRACTION 45
4.3 PCR AMPLIFICATION AND SANGER SEQUENCING 46
4.4 SPECIES IDENTIFICATION OF SASHIMI SAMPLES 47
4.5 MICROBIOME ANALYSIS 47
4.5.1 Raw data statistics 48
4.5.2 Evaluating of sequencing depths by rarefaction curve 49
4.5.3 Alpha diversity of microbiome across fish species 49
4.5.4 Structural diversity of microbial communities 50
4.5.5 Analysis of microbial compositions based on OTU analysis. 52
4.5.6 Identification of the key bacterial species which shaped the tilapia and salmon microbiome. 54
CHAPTER 5: DISCUSSION 55
5.1 TILAPIA SASHIMI AND FOOD SAFETY ISSUE 55
5.2 CHARACTERISTICS OF SASHIMI MICROBIOME 56
5.3 DETERMINISTIC FACTORS CONTRIBUTING TO VARIATION OF MICROBIAL STRUCTURE. 59
5.4 THE DISTINCTLY DIFFERENT MICROBIAL COMPOSITION ACROSS FISH SPECIES 61
5.5 HIGH VARIATION OF MICROBIAL COMMUNITIES IN SALMON SASHIMI 61
5.6 THE HIGH LEVEL OF AMONG SAMPLE VARIATION WITHIN THE SAME SAMPLE TYPE 62
5.7 THE IMPACT OF DIFFERENT SOURCES TO SASHIMI MICROBIOTA 63
5.8 OTHER FOOD-RELATED MICROBIOME STUDY 64
5.9 THE CHALLENGE OF SAMPLE COLLECTION 64
5.10 THE DNA EXTRACTION METHOD INFLUENCE THE RESULT OF MICROBIOME DATA 65
5.11 LIMITATION OF STUDY 66
CHAPTER 6: CONCLUSION 70
REFERENCE 71
APPENDIX 1 98
APPENDIX 2 99
APPENDIX 3 100


1. TFDA, National Food Consumption Database. 108.
2. 衛生福利部國民健康署, 每日飲食指南. 2018.
3. Chiang, C.-f., et al., Core food model of the Taiwan food supply for total diet study. Food Additives & Contaminants: Part A, 2018. 35(11): p. 2088-2098.
4. Nawa, Y., C. Hatz, and J. Blum, Sushi delights and parasites: the risk of fishborne and foodborne parasitic zoonoses in Asia. Clinical infectious diseases, 2005. 41(9): p. 1297-1303.
5. USFDA, Fish and Fishery Products Hazards and Controls Guidance.
6. Oehlenschläger, J., Seafood: nutritional benefits and risk aspects. International journal for vitamin and nutrition research, 2012. 82(3): p. 168-176.
7. McManus, A. and W. Newton, Seafood, nutrition and human health: A synopsis of the nutritional benefits of consuming seafood. 2011.
8. Rimm, E.B., et al., Seafood long-chain n-3 polyunsaturated fatty acids and cardiovascular disease: a science advisory from the American Heart Association. Circulation, 2018. 138(1): p. e35-e47.
9. Ouellet, V., et al., Dietary cod protein improves insulin sensitivity in insulin-resistant men and women: a randomized controlled trial. Diabetes Care, 2007. 30(11): p. 2816-2821.
10. Rudkowska, I., et al., Fish nutrients decrease expression levels of tumor necrosis factor-α in cultured human macrophages. Physiological Genomics, 2010. 40(3): p. 189-194.
11. Ait-Yahia, D., et al., Dietary fish protein lowers blood pressure and alters tissue polyunsaturated fatty acid composition in spontaneously hypertensive rats. Nutrition, 2003. 19(4): p. 342-346.
12. Baki, M.A., et al., Concentration of heavy metals in seafood (fishes, shrimp, lobster and crabs) and human health assessment in Saint Martin Island, Bangladesh. Ecotoxicology and environmental safety, 2018. 159: p. 153-163.
13. Steuerwald, U., et al., Maternal seafood diet, methylmercury exposure, and neonatal neurologic function. The Journal of pediatrics, 2000. 136(5): p. 599-605.
14. IARC, ARSENIC AND ARSENIC COMPOUNDS. 2004.
15. Bernard, A., Renal dysfunction induced by cadmium: biomarkers of critical effects. Biometals, 2004. 17(5): p. 519-523.
16. Sathe, S.K., C. Liu, and V.D. Zaffran, Food allergy. Annual review of food science and technology, 2016. 7: p. 191-220.
17. Whittle, K. and S. Gallacher, Marine toxins. British medical bulletin, 2000. 56(1): p. 236-253.
18. Iwamoto, M., et al., Epidemiology of seafood-associated infections in the United States. Clinical microbiology reviews, 2010. 23(2): p. 399-411.
19. 行政院農委會漁業署, 漁業統計年報. 2019.
20. The nature conservancy, Making Sense of Wild Seafood Supply Chains. 2015.
21. OCEANA, Deceptive Dishes : Seafood Swaps Found Worldwide. 2016.
22. Chen, P.-Y., et al., Investigating seafood substitution problems and consequences in Taiwan using molecular barcoding and deep microbiome profiling. Scientific Reports, 2020. 10(1): p. 1-9.
23. Konopka, A., What is microbial community ecology? The ISME journal, 2009. 3(11): p. 1223-1230.
24. Merriam-Webster Dictionary: Definition of Microbiome.
25. Nature.com: Microbiome.
26. Berg, G., et al., Microbiome definition re-visited: old concepts and new challenges. Microbiome, 2020. 8(1): p. 1-22.
27. Eloe-Fadrosh, E.A. and D.A. Rasko, The human microbiome: from symbiosis to pathogenesis. Annual review of medicine, 2013. 64: p. 145-163.
28. Collado, M.C., et al., The impact of probiotic on gut health. Current drug metabolism, 2009. 10(1): p. 68-78.
29. Charles, J.F., J. Ermann, and A.O. Aliprantis, The intestinal microbiome and skeletal fitness: Connecting bugs and bones. Clinical Immunology, 2015. 159(2): p. 163-169.
30. Ghanbari, M., W. Kneifel, and K.J. Domig, A new view of the fish gut microbiome: advances from next-generation sequencing. Aquaculture, 2015. 448: p. 464-475.
31. Spence, C. and H. Bais, Probiotics for plants: rhizospheric microbiome and plant fitness. Molecular microbial ecology of the rhizosphere, 2013. 1: p. 713-721.
32. Perry, W.B., et al., The role of the gut microbiome in sustainable teleost aquaculture. Proceedings of the Royal Society B, 2020. 287(1926): p. 20200184.
33. Walker-Daniels, J., Microbiome Research Methodologies. 2020.
34. Gómez, G.D. and J.L. Balcázar, A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunology & Medical Microbiology, 2008. 52(2): p. 145-154.
35. Yukgehnaish, K., et al., Gut microbiota metagenomics in aquaculture: Factors influencing gut microbiome and its physiological role in fish. Reviews in Aquaculture, 2020. 12(3): p. 1903-1927.
36. Ross, A.A., A.R. Hoffmann, and J.D. Neufeld, The skin microbiome of vertebrates. Microbiome, 2019. 7(1): p. 1-14.
37. Takeuchi, M., et al., Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum. Scientific reports, 2021. 11(1): p. 1-11.
38. Pérez‐Sánchez, T., et al., Identification and characterization of lactic acid bacteria isolated from rainbow trout, Oncorhynchus mykiss (Walbaum), with inhibitory activity against Lactococcus garvieae. Journal of fish diseases, 2011. 34(7): p. 499-507.
39. Sehnal, L., et al., Microbiome composition and function in aquatic vertebrates: small organisms making big impacts on aquatic animal health. Frontiers in microbiology, 2021. 12: p. 358.
40. Egerton, S., et al., The Gut Microbiota of Marine Fish. Frontiers in Microbiology, 2018. 9(873).
41. Talwar, C., et al., Fish gut microbiome: current approaches and future perspectives. Indian journal of microbiology, 2018. 58(4): p. 397-414.
42. Castillo, D.J., et al., The Healthy Human Blood Microbiome: Fact or Fiction? Frontiers in Cellular and Infection Microbiology, 2019. 9(148).
43. Alikunhi, N.M., et al., Culture-dependent bacteria in commercial fishes: Qualitative assessment and molecular identification using 16S rRNA gene sequencing. Saudi Journal of Biological Sciences, 2017. 24(6): p. 1105-1116.
44. Ampofo, J.A. and G.C. Clerk, Diversity of Bacteria Contaminants in Tissues of Fish Cultured in Organic Waste-Fertilized Ponds Health Implications. 2010.
45. Orlando, M., A. Larsen, and C. Walsh, Microbiome, Macro Benefits. 2015.
46. Lehel, J., et al., Possible food safety hazards of ready-to-eat raw fish containing product (sushi, sashimi). Critical reviews in food science and nutrition, 2021. 61(5): p. 867-888.
47. Hebert, P.D., S. Ratnasingham, and J.R. De Waard, Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences, 2003. 270(suppl_1): p. S96-S99.
48. Haines, A.M., et al., Properties of nucleic acid staining dyes used in gel electrophoresis. Electrophoresis, 2015. 36(6): p. 941-944.
49. Sanger, F. and A.R. Coulson, A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of molecular biology, 1975. 94(3): p. 441-448.
50. Sanger, F., S. Nicklen, and A.R. Coulson, DNA sequencing with chain-terminating inhibitors. Proceedings of the national academy of sciences, 1977. 74(12): p. 5463-5467.
51. Benson, D.A., et al., GenBank. Nucleic acids research, 2012. 41(D1): p. D36-D42.
52. Ratnasingham, S. and P.D. Hebert, BOLD: The Barcode of Life Data System (http://www. barcodinglife. org). Molecular ecology notes, 2007. 7(3): p. 355-364.
53. Anderson, M.W. and I. Schrijver, Next generation DNA sequencing and the future of genomic medicine. Genes, 2010. 1(1): p. 38-69.
54. Li, X., et al., Plant DNA barcoding: from gene to genome. Biological Reviews, 2015. 90(1): p. 157-166.
55. Purty, R. and S. Chatterjee, DNA barcoding: an effective technique in molecular taxonomy. Austin J Biotechnol Bioeng, 2016. 3(1): p. 1059.
56. Chakravorty, S., et al., A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Journal of microbiological methods, 2007. 69(2): p. 330-339.
57. Metzker, M.L., Sequencing technologies—the next generation. Nature reviews genetics, 2010. 11(1): p. 31-46.
58. Illumina. Science and Education /Technology: Next-Generation Sequencing (NGS). 2021.
59. Blaxter, M., et al., Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B: Biological Sciences, 2005. 360(1462): p. 1935-1943.
60. Porter, T.M. and M. Hajibabaei, Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis. Molecular ecology, 2018. 27(2): p. 313-338.
61. Jeong, J., et al., The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Scientific reports, 2021. 11(1): p. 1-12.
62. Gomila, M., et al., Phylogenomics and systematics in Pseudomonas. Frontiers in microbiology, 2015. 6: p. 214.
63. Větrovský, T. and P. Baldrian, The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PloS one, 2013. 8(2): p. e57923.
64. Kembel, S.W., et al., Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS computational biology, 2012. 8(10): p. e1002743.
65. 詹滿色, 吳郭魚全球與國內供需市場分析. 2009, 海大漁推.
66. Uren Webster, T.M., et al., Interpopulation variation in the Atlantic salmon microbiome reflects environmental and genetic diversity. Applied and Environmental Microbiology, 2018. 84(16): p. e00691-18.
67. Lokesh, J. and V. Kiron, Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon. Scientific reports, 2016. 6(1): p. 1-10.
68. Dehler, C.E., C.J. Secombes, and S.A. Martin, Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.). Scientific reports, 2017. 7(1): p. 1-11.
69. Ross, A.A., A. Rodrigues Hoffmann, and J.D. Neufeld, The skin microbiome of vertebrates. Microbiome, 2019. 7(1): p. 1-14.
70. Egerton, S., et al., The gut microbiota of marine fish. Frontiers in microbiology, 2018. 9: p. 873.
71. Larsen, A., et al., Diversity of the skin microbiota of fishes: evidence for host species specificity. FEMS Microbiology Ecology, 2013. 85(3): p. 483-494.
72. Urbanczyk, H., J.C. Ast, and P.V. Dunlap, Phylogeny, genomics, and symbiosis of Photobacterium. FEMS microbiology reviews, 2011. 35(2): p. 324-342.
73. Xing, C.-F., et al., Diet supplementation of Pediococcus pentosaceus in cobia (Rachycentron canadum) enhances growth rate, respiratory burst and resistance against photobacteriosis. Fish & shellfish immunology, 2013. 35(4): p. 1122-1128.
74. Kanki, M., et al., Photobacterium phosphoreum caused a histamine fish poisoning incident. International journal of food microbiology, 2004. 92(1): p. 79-87.
75. Dalgaard, P., et al., Importance of Photobacterium phosphoreum in relation to spoilage of modified atmosphere‐packed fish products. Letters in Applied Microbiology, 1997. 24(5): p. 373-378.
76. Minich, J.J., et al., Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. Msphere, 2020. 5(3): p. e00401-20.
77. Park, J. and E.B. Kim, Insights into the gut and skin microbiome of freshwater fish, smelt (Hypomesus nipponensis). Current microbiology, 2021. 78(5): p. 1798-1806.
78. Arias, C., Fish are not alone: characterization of the gut and skin microbiomes of Largemouth Bass (Micropterus salmoides), Bluegill (Lepomis macrochirus), and Spotted Gar (Lepisosteus oculatus)(2019) SDRP Journal of Aquaculture. Fisheries & Fish Science, 2019. 2(2).
79. Zamora, L., et al., Chryseobacterium viscerum sp. nov., isolated from diseased fish. International journal of systematic and evolutionary microbiology, 2012. 62(Pt_12): p. 2934-2940.
80. Ilardi, P., J. Fernandez, and R. Avendano-Herrera, Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish. International journal of systematic and evolutionary microbiology, 2009. 59(12): p. 3001-3005.
81. Leung, M.H., D. Wilkins, and P.K. Lee, Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups. Scientific reports, 2015. 5(1): p. 1-16.
82. Staley, J.T., R.L. Irgens, and D.J. Brenner, Enhydrobacter aerosaccus gen. nov., sp. nov., a gas-vacuolated, facultatively anaerobic, heterotrophic rod. International Journal of Systematic and Evolutionary Microbiology, 1987. 37(3): p. 289-291.
83. Gaüzère, C., et al., Stability of airborne microbes in the L ouvre M useum over time. Indoor air, 2014. 24(1): p. 29-40.
84. Neza, E. and M. Centini, Microbiologically contaminated and over-preserved cosmetic products according Rapex 2008–2014. Cosmetics, 2016. 3(1): p. 3.
85. Ganeswire, R., K.L. Thong, and S. Puthucheary, Nosocomial outbreak of Enterobacter gergoviae bacteraemia in a neonatal intensive care unit. Journal of Hospital Infection, 2003. 53(4): p. 292-296.
86. Bjornsdottir-Butler, K., S. McCARTHY, and R.A. Benner Jr, Characterization and Control of Erwinia spp. and Pluralibacter sp. in Tuna Salad Preparations. Journal of food protection, 2019. 82(6): p. 1071-1081.
87. Kim, P.S., et al., Host Habitat Is the Major Determinant of the Gut Microbiome of Fish. 2021.
88. Wang, J., et al., Microbiota in intestinal digesta of Atlantic salmon (Salmo salar), observed from late freshwater stage until one year in seawater, and effects of functional ingredients: a case study from a commercial sized research site in the Arctic region. Animal microbiome, 2021. 3(1): p. 1-16.
89. Llewellyn, M.S., et al., The biogeography of the Atlantic salmon (Salmo salar) gut microbiome. The ISME journal, 2016. 10(5): p. 1280-1284.
90. De Filippis, F., E. Parente, and D. Ercolini, Metagenomics insights into food fermentations. Microbial biotechnology, 2017. 10(1): p. 91-102.
91. Koyanagi, T., et al., Pyrosequencing analysis of microbiota in Kaburazushi, a traditional medieval sushi in Japan. Bioscience, biotechnology, and biochemistry, 2013. 77(10): p. 2125-2130.
92. Robinson, R.K., Encyclopedia of food microbiology. 2014: Academic press.
93. Teng, F., et al., Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling. Scientific reports, 2018. 8(1): p. 1-12.
94. Prosser, J.I., Replicate or lie. Environmental microbiology, 2010. 12(7): p. 1806-1810.
95. Amann, R.I., W. Ludwig, and K.-H. Schleifer, Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological reviews, 1995. 59(1): p. 143-169.
96. Jovel, J., et al., Characterization of the gut microbiome using 16S or shotgun metagenomics. Frontiers in microbiology, 2016. 7: p. 459.
97. Edgar, R.C., Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics, 2018. 34(14): p. 2371-2375.
98. Johnson, J.S., et al., Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature communications, 2019. 10(1): p. 1-11.
99. Klinger, R.E. and R.F. Floyd, Introduction to freshwater fish parasites. 1998: University of Florida Cooperative Extension Service, Institute of Food and ….
100. Gonçalves, L.T., et al., Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda. Genome, 2021. 99(999): p. 1-13.
電子全文 電子全文(網際網路公開日期:20261130)
連結至畢業學校之論文網頁點我開啟連結
註: 此連結為研究生畢業學校所提供,不一定有電子全文可供下載,若連結有誤,請點選上方之〝勘誤回報〞功能,我們會盡快修正,謝謝!
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
無相關期刊