next generation sequencing of fish microbiome- aquacyprus 2014
DESCRIPTION
This slides were present in the first international conference of aquaculture in Cyprus-TRANSCRIPT
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 19.05.2014 1
High-Throughput Sequencing and Metagenomics:
Moving Forward in the Culture-Independent Analysis of Fish Microbial Ecology
Mahdi Ghanbari
Konrad J.Domig, Wolfgang Kneifel
BOKU - University of Natural Resources and Life Sciences, Vienna
Department of Food Science and Technology Muthgasse 18, A-1190 Vienna
Phone: +43 1 47654-6750, Fax: +43 1 47654-6751
[email protected], www.dlwt.boku.ac.at
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 2
Immune System
Physiology Metabolic Function
Growth
Nutrition
Gut Microbiota
Importance of
Fish Microbiome
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 3
Culture-Independent
NGS
Cultivation in vitro
• Current knowledge on fish microbiota
• Dubious Sensivity
• Limited fraction
• Qualitative
• 16S rRNA gene amplification (PCR) • Sanger Sequencing Technique
• Cost
• Technical issue
• low coverage
• Definition
• Next-Generation Sequencing • larger number of reads in a single run • In-depth • Faster • Accurate data
Trends and Developments in Fish Gut Analysis
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 4
NGS
NGS platforms and Technology
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 5
GS Junior
GS FLX+
The Roche 454 Pyrosequencing
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 6
The Roche 454 Pyrosequencing -Continued
Roche GS FLX++
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 7
The Illumina Genome Analyser
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 8
Developments in next generation sequencing
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 9
Application of NGS to Fish Microbiology
The Effect of Growth Promoter
The Gut Microbiota in Transgenic Fish
The Influence of Dietary Factors
The Influence of Environmental Conditions
Bacterial Diversity in the Fish Gut
Fish Gut
Microbiome
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 10
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AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 11
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 12
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 13
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari 14
Conclusion and Prospectus
A Promising Strategy
B In-depth Knowledge of Fish Gut
C Improve Fish Management
D The Forthcoming Applications
AquaCyprus 2014, 15-17 May, Girne I High-Throughput Sequencing and Metagenomics I Mahdi Ghanbari
Thank you for your attention!
19.05.2014 15
Mahdi Ghanbari,
BOKU - University of Natural Resources and Life Sciences, Vienna
Department of Food Science and Technology
Muthgasse 18, A-1190 Vienna
Phone: +43 1 47654-6750, Fax: +43 1 47654-6751
[email protected], www.dlwt.boku.ac.at