Analysis of whole genome sequence and metabolomic profiles reveals the mode of action of probiotics in olive flounder (Paralichythys olivaceus)
- Alternative Title
- 넙치에서 전장게놈염기서열 및 대사체 프로필 분석을 통한 프로바이오틱스의 작용기작 연구
- Abstract
- The use of probiotics is considered an attractive biocontrol and effective in growth promotion in aquaculture. However, the mode of action of probiotics in fish in terms of growth promotion is still unclear. The present study investigated the benefits of the administration of host-derived probiotics, Lactococcus lactis WFLU12, in the growth promotion of olive flounder by analyzing their intestinal and serum metabolome using capillary electrophoresis mass spectrometry with time-of flight (CE-TOFMS), and comparing with those in a group fed with the basal diet. CE-TOFMS identified 53 (out of 200) and 5 (out of 171) metabolites from the intestinal luminal and serum metabolome, respectively, were present in significantly higher concentrations in the probiotic-fed group than in the control. The concentration of metabolites including citrulline, tricarboxylic acid cycle (TCA) intermediates, short chain fatty acids, vitamins, and taurine was significantly higher in the fish of the probiotic group than those in the control group. Also, our probiotic strain WFLU12 possesses genes encoding enzymes to help in the production of these metabolites. Therefore, it is highly likely that the increased metabolites observed in this study are due to the supplementation of our probiotic strain and are linked to growth promotion in olive flounder. To the best of the authors’ knowledge, this is the first study to show that dietary probiotics can greatly influence metabolome in fish, and the present findings may reveal important implications for maximizing the utilization efficiency of dietary additives and optimizing fish health and growth.
- Issued Date
- 2018
- Awarded Date
- 2018.2
- Type
- Dissertation
- Publisher
- 부경대학교
- Affiliation
- 부경대학교 대학원
- Department
- 대학원 수산생명의학과
- Advisor
- Do-Hyung Kim
- Table Of Contents
- General Introduction 1
Chapter I. Literature review 3
1.1. Probiotics in sustainable strategies for aquaculture 3
1.2. Lactic acid bacteria 6
1.2.1. Lactococcus lactis 6
1.2.2. Application of L. lactis for aquaculture 9
1.3. Bacterial genome study 11
1.3.1. Bacterial genomes 12
1.3.2. The pan-genome concept 15
1.4. Metabolome study 17
1.4.1. Definition and application 19
1.4.2. Use of metabolomics in fish studies 21
1.5. Aims of the present study 23
Chapter II. Improved growth rate and disease resistance in olive flounder, Paralichthys olivaceus, by probiotic Lactococcus lactis WFLU12 isolated from wild marine fish 24
2.1. Introduction 25
2.2. Materials and methods 26
2.2.1. Bacteria and culture conditions 26
2.2.2. Bacterial identification 26
2.2.3. Phenotypic characterization of bacterial cultures 27
2.2.4. Examination of feeding behavior and natural infection in pilot-scale system 28
2.2.5. Determination of probiotic effects of a selected strain 32
2.2.6. Statistical analysis 32
2.3. Results and discussion 33
2.3.1. Microbial diversity and selection of a probiotic candidate 33
2.3.2. Growth performance and resistance against natural infection 40
2.3.3. Resistance against streptococcosis and immune responses 46
2.4. Conclusion 51
Chapter III. Comparative genomics of probiotic Lactococcus lactis strain WFLU12 isolated from the gastrointestinal tract of olive flounder (Paralichythys olivaceus) 53
3.1. Introduction 54
3.2. Materials and methods 55
3.2.1. Bacterial genome extraction and sequencing 55
3.2.2. Genome analysis, assembly and annotation 56
3.2.3. Genome identification and phylogenomic analysis 56
3.2.4. Carbohydrate-active enzymes (CAZy) profiles 57
3.2.5. Pan-genome analysis 57
3.3. Results and discussion 59
3.3.1. General genome features 59
3.3.2. General genome comparison 67
3.3.3. Pan-genomic analysis of L. lactis subsp. lactis 70
3.3.4. Functional comparative analysis of pan- and core genomes 73
3.3.5. Comparing abundance of CAZymes among strain 77
3.3.6. Specificity in the genome of strain WFLU12 80
3.3.7. Genes potentially involved in probiotic effects of strain WFLU12 84
3.4. Conclusion 107
3.5. Data access 107
Chapter IV. Dietary probiotics effects of Lactococcus lactis WFLU12 on low-molecular-weight metabolites and growth of olive flounder (Paralichthys olivaceus) 108
4.1. Introduction 109
4.2. Materials and methods 110
4.2.1. Animals and probiotic administration 110
4.2.2. Weight gain and sampling 111
4.2.3. Preparation of intestinal fluid, serum, and pellet for metabolome analysis 111
4.2.4. CE-TOFMS 113
4.2.5. Ratio of metabolite concentration (Probiotic: Control group) 114
4.2.6. Prediction of genes of strain WFLU12 involved in increased metabolites 114
4.2.7. Data analysis and statistics 114
4.3. Results 116
4.3.1. Viability of L. lactis in fish gut 116
4.3.2. Growth measurements 116
4.3.3. The difference in intestinal and serum metabolome between dietary groups 117
4.3.4. Classification of metabolites 123
4.3.5. Comparison of inter-individual metabolic variation of groups 134
4.3.6. Increased metabolites and weight gain 136
4.3.7. Genes of L. lactis WFLU12 involved in increased metabolites 146
4.4. Discussion 152
4.5. Conclusion and perspectives 169
Appendix 170
Reference 216
국문요약 236
Acknowledgements 238
- Degree
- Doctor
- Files in This Item:
-
-
Download
Analysis of whole genome sequence and metabolomic profiles reveals the mode of action of probiotics .pdf
기타 데이터 / 6.57 MB / Adobe PDF
-
Items in Repository are protected by copyright, with all rights reserved, unless otherwise indicated.