next generation sequencing of fish microbiome- aquacyprus 2014

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

m.ghanbari@boku.ac.at, 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

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