Advanced genomics in food industry

Yalun Arifin
Food Business Technology department
School of Applied STEM
Prasetiya Mulya University
18 October 2018

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The presentation

• Introduction: synthetic biology and systems

biology
• Genomics application in food production and
safety

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Our challenges today

• Food security
• Environmental degradation
• Energy crisis
• Global warming
• Health issues (cancer, infectious diseases,
degenerative diseases)

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21st century: Age of Biotechnology
• Biotechnology: the use of living systems and organisms to develop or make
products, or "any technological application that uses biological systems, living
organisms or derivatives thereof, to make or modify products or processes for
specific use" (UN Convention on Biological Diversity, Art. 2).
• Rapid advancements in the biotechnology for medical and pharmaceutical
applications, securing food supply, and chemical industry.

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Biotechnology milestone in 21st century

• 2001: Imatinib, the 1st gene targeted drug for cancer treatment, receives FDA
approval
• 2002: Rice, the 1st crop genome sequenced. The transgenic rootworm-resistant
corn obtains FDA approval
• 2003: Human genome project is completed
• 2004: UN FAO endorses biotech crops
• 2005: Genographic project (study of historical human migration pattern based
on DNA samples) is started
• 2006: Recombinant vaccine Gardasil® for HPV
• 2007: FDA approves the H5N1 vaccine for avian flu

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Biotechnology milestone in 21st century

• 2009: Global biotech crop land usage reaches 130 million hectares
• 2010:1st synthetically design organism by Craig Venter Lab
• 2011: >350 species genomes have been sequenced
• 2012: The 1st man with a nervous system-controlled bionic leg
• 2013: CRISPR-Csc9, powerful tool for DNA editing
• 2014: The 1st bionic eyes
• 2016: Syn 3.0, synthetic microbe with only 473 genes.

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Modern strategies in Biotechnology

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Systems Biology
• Integrative approach in Biology
• Systemic approach in analyzing the interconnections and the
functional interrelationships among cells and their components,
organisms, and the environments.
• Aim: Systems level understanding of biological phenomena

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Systems Biology

Lee SY, Lee DY, Kim TY. 2005.

Systems biotechnology for
strain improvement. Trends in
Biotechnology 23(7):349-358.

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Systems biology: genomics

• Genome sequencing
• Assembly
• Annotation
• Sequencing pipelines and databases

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The presentation

• Introduction: Metabolic engineering, synthetic

biology, systems biology
• Genomics application in food production and
safety

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Genomics for obtaining superior
strain
Case: cocoa tree genomics
• Among the 20 Theobroma species,
only one, T. cacao is currently used
as raw material
• Major cocoa types: Foresteros and
Criollo, Trinitaro (hybrid)
• Phylogenetic study and DNA
fingerprinting  identified superior
strain

Similar case: oil palm tree genomics 

applied for the plant tissue culture

Singh et.al (2013), Oil palm genome sequence

reveals divergence of interfertile species in Old and 12
New worlds, Nature, 500, 335–339
Precision food safety

Whole genome sequencing for identifying and

surveillance of pathogenic microorganism in
food
Examples: Listeria and Salmonella

Salmonella

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 Precision food safety

Metagenomics  the study of genetic material

recovered directly from environmental samples
For example:
• 16S metagenomics is used for surveillance of pathogenic
bacteria. Also to characterize the microbiota of various foods

Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, et al. (2015) Use of 16S rRNA Gene for Identification of a Broad
Range of Clinically Relevant Bacterial Pathogens. PLOS ONE 10(2): e0117617. https://doi.org/10.1371/journal.pone.0117617 14
Ted Agres (2018) Food Genomics Is Going Global. https://www.foodqualityandsafety.com/article/food-genomics-global/?singlepage=1
Thank you

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