This document discusses high-throughput sequencing and metagenomics and its application to analyzing fish microbiomes. It begins by explaining the importance of the fish gut microbiome and then describes how next-generation sequencing techniques allow for more in-depth and accurate analysis of the fish microbiome compared to traditional culturing and Sanger sequencing. Several NGS platforms are presented, and examples are given of how NGS can be applied to study the effect of dietary and environmental factors on the fish gut microbiome. The conclusion states that NGS provides a promising strategy for gaining in-depth knowledge of the fish gut microbiome to improve fish management and future applications.

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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
m.ghanbari@boku.ac.at, www.dlwt.boku.ac.at

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Immune
System
Physiology
Metabolic
Function
Growth
Nutrition
Gut Microbiota
Importance of
Fish Microbiome

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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

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NGS
NGS platforms and Technology

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GS Junior
GS FLX+
The Roche 454 Pyrosequencing

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The Roche 454 Pyrosequencing -Continued
Roche GS FLX++

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The Illumina Genome Analyser

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Developments in next generation sequencing

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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

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Conclusion and Prospectus
A
Promising Strategy
B
In-depth Knowledge of Fish Gut
C
Improve Fish Management
D
The Forthcoming Applications

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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
m.ghanbari@boku.ac.at, www.dlwt.boku.ac.at