Title Page
Contents
ABSTRACT 8
General Introduction 11
1. Microbiome 11
2. Microbiomes in animals 12
Chapter 1. Impact of epilepsy and Giardia intestinalis infection on the gut microbiome of canine species 15
1.1. Abstract 15
1.2. Introduction 16
1.3. Materials and Methods 17
1.3.1. Data collection 17
1.3.2. Data pre-processing 17
1.3.3. Microbial composition with statistical analysis 17
1.4. Results 19
1.4.1. Gut microbiome community composition 19
1.4.2. Biomarker analysis 24
1.5. Discussion 29
Chapter 2. Comparative analysis of the pig gut microbiome associated with the pig growth performance 33
2.1. Abstract 33
2.2. Introduction 34
2.3. Materials and Methods 36
2.3.1. Animals and sample collections 36
2.3.2. Genomic DNA extraction and amplicon 16S rRNA gene polymerase chain reaction 36
2.3.3. Index polymerase chain reaction and 16S rRNA metagenomic sequencing 37
2.3.4. Microbiome data and 16S rRNA gene analysis 38
2.4. Results 39
2.4.1. Fecal DNA sequence data and Alpha diversity 39
2.4.2. Beta diversity 41
2.4.3. Taxonomic classification of the sequences 44
2.4.4. Fecal microbial shifts at different ages 46
2.5. Discussion 51
Conclusion 55
References 58
Abstract (in Korean) 67
Figure 1. Distance-based redundancy analysis (dbRDA) between disease groups and healthy groups. 20
Figure 2. Relative abundance of TOP 20 genus between the disease groups and healthy group. 22
Figure 3. Evenness of alpha-diversity analysis with pairwise test. 23
Figure 4. Network analysis based on spearman's rank-based correlation coefficient. 25
Figure 5. Box plots with pairwise test of statistical analysis in most significant genus at each category between the disease groups and healthy group for A) Bacteroides, B) Fusobacterium, C) Ligilactobacillus and D)... 28
Figure 6. Box plot showing the alpha diversity index of the pig's internal microorganism. 40
Figure 7. Principal coordinate analysis (PCoA) plots of pig gut microbiota are based on weighted (a) and unweighted (b) UniFrac distances. 42
Figure 8. Principal coordinate analysis (PCoA) plots and taxon abundance of pig gut microbiota based on the weighted UniFrac and unweighted... 43
Figure 9. Taxonomic classification of the sequences at (a) phylum and (b) genus levels. 45
Figure 10. Extended error bar plots identifying significantly different taxa at the genus level. (a) The comparison of the relative abundances of genera at different days of age in group J, (b) The comparison of the relative abundances... 48
Figure 11. Extended error bar plots identifying significantly different taxa at the genus level. (a) The comparison of the relative abundances of genera at different days of age in group T, (b) The comparison of the relative abundances... 49
Figure 12. Extended error bar plots identifying significantly different taxa at the genus level in group D at different ages. 50