VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE FACULTY OF BIOTECHNOLOGY GRADUATION THESIS TITLE: “COMPARATIVE ANALYSIS OF MICROBIAL COMMUNITIES ASSOCIATED WITH ACROPORA FORMOSA AND SEDIMENT IN PHU QUOC ISLAND.” Hanoi - 2022 VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE FACULTY OF BIOTECHNOLOGY GRADUATION THESIS TITLE: “COMPARATIVE ANALYSIS OF MICROBIAL COMMUNITIES ASSOCIATED WITH ACROPORA FORMOSA AND SEDIMENT IN PHU QUOC ISLAND.” Student name : NGUYEN PHAM DAN TRUONG Class : K63CNSHE Student’s code : 637372 Supervisor : NGUYEN HUY DUONG, MSc NGUYEN VAN GIANG, Assoc Prof Department : MICROBIAL TECHNOLOGY Hanoi - 2022 COMMITMENT I hereby declare that the data and results stated in the thesis are honest and have never been published by anyone in other studies In the references section, the graduations with references to papers and action information are mentioned I am completely responsible for the data of this thesis Hanoi, January 9th, 2023 Sincerely Nguyen Pham Dan Truong i ACKNOWLEDGEMENTS Above all else, I would like to express my heartfelt gratitude to MSc Nguyen Huy Duong, an officer of Bioinformatics Department at the Institute of Biotechnology of the Vietnam Academy of Science and Technology, who is my thesis advisor and has also provided me with invaluable guidance, input, and support throughout the thesis work Following that, I'd want to offer my grateful to PhD Bui Van Ngoc with researchers at the Bioinformatics Department at the Institute of Biotechnology of the Vietnam Academy of Science and Technology, have assisted, provided technical support and imparted valuable knowledge as well as research experience The knowledge and skills gained would be beneficial in the future it had been a warm and fruitful experience It would not have been possible to complete this project without the enthusiastically guidelines, cordial supporting of Assoc Prof Nguyen Van Giang, Head of Department of Microbiology Technology at the Vietnam National University of Agriculture, who created opportunities for me to study and work directly at the Bioinformatics Department Without the enthusiastic facilitation of the Board of Directors at Vietnam National University of Agriculture and the teachers of Biotechnology falcuty, I would not have been able to acquire not only the professional foundation necessary to complete this report, but also the wealth of experience that has helped me take my first confident steps along my chosen career path I would have to thank all the seniors in the lab, who also helped me during the preparation of this thesis To wrap up, I'd want to express my gratitude to my family and all who have journeyed with me, encouraged me, and shared in my experiences I sincerely thank you! ii Hanoi, Janury 9th, 2023 Sincerely Nguyen Pham Dan Truong iii Table of Contents COMMITMENT i ACKNOWLEDGEMENTS ii LIST OF TABLES vi LIST OF FIGURES vii LIST OF ABBREVIATIONS viii ABSTRACT ix CHAPTER INTRODUCTION 1.1 State of problem 1.2 Purpose 1.3 Research contents .3 CHAPTER LITERATURE REVIEW 2.1 Coral reefs 2.1.1 Coral and coral reef 2.1.2 Functional importance of coral reefs 2.1.3 The current situation of coral reefs .5 2.2 The coral microbiome .6 2.2.1 The coral holobiont: a multi-partite symbiotic organism 2.2.2 Microbiota of healthy corals .7 2.3 Microbial identification methods in coral reefs 2.3.1 Culture-based methods .8 2.3.2 Methods for unculturable microbes Error! Bookmark not defined 2.4 Bioinformatics analysis of metagenomics 2.4.1 Methods in metagenomics 11 2.5 Current situation of domestic and international research .13 2.5.1 International research 13 2.5.2 Domestic research .14 CHAPTER MATERIALS AND METHODS .16 3.1 Materials 16 iv 3.2 Methods 17 3.2.1 Total DNA extraction for 16S rRNA survey 17 3.2.2 Next-generation sequencing .17 3.2.3 Bioinformatics approach 18 CHAPTER RESULTS 20 4.1 Enhancing data reliability .20 4.1.1 Raw read quality profiles 20 4.1.2 Obtaining cleaned and chimera-free sequences .23 4.2 Data exploration 25 4.2.1 Archaeal data 25 4.2.2 Bacterial data 32 CHAPTER CONCLUSIONS AND RECOMMENDATIONS 41 5.1 Conclusions .41 5.2 Recommendations 41 CHAPTER REFERENCES 42 SUPPLEMENTARY MATERIALS .49 v LIST OF TABLES Table Overview of modern sequencing technologies 11 Table Sample name, sample abbreviation and sample collection location 16 Table 4.1 Abundance of archaeal phyla in the Acropora formosa mucus and the sediment (Abundance > 0.5%) 27 Table 4.2 Abundance of archaeal genera in the Acropora formosa mucus and in the sediment (Abundance > 0.5%) 28 Table 4.3 Statistical summary for alpha diversity indices for archaeal communities 31 Table 4.4 Abundance of bacterial phyla in the Acropora formosa mucus and in the sediment (Abundance > 0.5%) 34 Table 4.5 Abundance of top 10 bacterial genera in the Acropora formosa mucus and in the sediment (Abundance > 0.5%) 36 Table 4.6 Statistical summary for alpha diversity indices for bacterial communities 37 vi LIST OF FIGURES Figure Acropora formosa coral Figure 4.1 Forward read’s quality score of the archaeal data when sequencing ………20 Figure 4.2 Reverse read’s quality score of the archaeal data when sequencing …… 21 Figure 4.3 Forward read’s quality score of the bacterial data when sequencing……… 22 Figure 4.4 Reverse read’s quality score of the bacterial data when sequencing ……….23 Figure 4.5 Quantity of reads that were kept after filtering step in the archaeal data… 24 Figure 4.6 Quantity of reads that were kept after filtering step in the bacterial data 25 Figure 4.7 Composition of microbiota at phylum level…… ……………………………26 Figure 4.8 Composition of microbiota at genus level 28 Figure 4.9 Alpha diversity of archaeal biomes …………………………………………30 Figure 4.10 Beta diversity of the archaeal community 32 Figure 4.11 Composition of microbiota at phylum level 33 Figure 4.12 Composition of microbiota at genus level 35 Figure 4.13 Alpha diversity of bacterial community 38 Figure 4.14 Beta diversity of the bacterial community 40 Supplementary Figure Supplementary Figure Supplementary Figure Supplementary Figure Supplementary Figure Supplementary Figure Composition of microbiota at Class level 53 Composition of microbiota at Order level 54 Composition of microbiota at Family level 55 Composition of microbiota at Class level 56 Composition of microbiota at Order level 57 Composition of microbiota at Family level 58 vii LIST OF ABBREVIATIONS Abbreviation Full word 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