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Foodomics-Use of Integrated Omics in Nutrition, Food Technology and Biotechnology

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Djuro Josic at University of Rijeka
Djuro Josic
Jasminka Giacometti at University of Rijeka
Jasminka Giacometti
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Open AccessEditorial
Data Mining in Genomics & Proteomics
Josic and Giacometti, J Data Mining Genomics Proteomics 2013, 4:2
http://dx.doi.org/10.4172/2153-0602.1000e106
Volume 4 • Issue 2 • 1000e106
J Data Mining Genomics Proteomics
ISSN: 2153-0602 JDMGP, an open access journal
Introduction
Aer rather slow beginning, the “omics” methods are gaining in
importance for process development and validation in food technology
and biotechnology as well as corresponding quality control of starting
materials and nal products [1]. is methodology is increasingly used
for analyses of food composition and quality, food authentication,
safety assessment of genetically modied food, identication of food
allergens, presence of toxins, analysis of the physiological activity
of food proteins and peptides, and the inuence of the production
process on the chemical, physicochemical and biological properties of
food proteins [2], and a specic term “foodomics” was also recently
coined. e number of papers dealing with use of omics methods in
food processing and nutrition has also rapidly increased, especially
on the eld of food of animal origin [3]. Advances in whole genome
sequencing of plants that are important for human nutrition have
also removed the major obstacle for the use of foodomic, especially
proteomic methods for food of plant origin [1]. Furthermore, organic
food of both plant and animal origin plays an increasingly important
role in the food market, therefore foodomic methods are used for the
identication and quality assurance of organic food, and discovery
of potential fake organic products [4]. Similar to the organic food,
the traditional fermented food is again gaining in popularity. In this
kind of food of both animal and plant origin such as meat, milk and
milk products, wine, beer and other fermented products, changes of
the proteome of the substrate (e.g. sausages, fermented milk products
and grape juice) and in the starter culture microorganisms (e.g. milk
bacteria, bacterial and mixed microora in fermented meat product,
and yeasts in both wine and beer) as well as their interaction play a
crucial role in the quality of the nal products [4]. Fermentation also
means enzymatic digestion of food components, and accumulation of
small molecules in the nal product. ese molecules are frequently
responsible for specic avor of original fermented food and can be
used as markers for its originality and identity [5]. On the other hand,
in production of both organic and traditional fermented food, thermal
and other steps for microbial inactivation and inactivation of toxins
and allergens are frequently avoided. It is the reason that this kind
of food can get a serious safety risk, especially if contaminated raw
materials are used or improperly prepared.
Foodomics-Towards the Integrated Omics in Food
Science
At this moment, foodomics constitute one of the most relevant
and fast developing areas in food science. Slowly, but constantly, the
formerly fully independent worlds of the experts in food technology
and microbiology, nutrition, genomics, proteomics (together with
glycomics, phosphoproteomics and other methods dealing with
posttranslational modication of proteins) and metabolomics have
started to interact. e aim of this cooperation is to ameliorate the
food quality and safety, and to prevent food adulteration. e rights of
consumers and genuine food processors in terms of food adulteration
and fraudulent or deceptive practices in food processing are set out in
the European Union regulations regarding food safety and traceability.
is system was developed in order to: (i) encourage diverse
agricultural production; (ii) protect product names from misuse and
imitation; (iii) help consumers by giving them information concerning
the specic character of the product [6]. e potential use of foodomics
in their development pathway for food production, assessing the safety,
originality and quality is shown in gure 1.
As soon as the above mentioned collaboration was intensied,
it clearly emerged that the integration of all foodomics disciplines
will represent a more suitable tool than each discipline by itself, e.g.,
proteomics or genomics alone. e result was an intensive collaboration
between the experts on dierent elds of food science and nutrition
and omics experts. e use of foodomics enabled, or at least facilitated
the answers to the questions that are crucial for food safety, quality,
traceability and its protection against adulteration. ese points are:
(i) geographical origin (ii) handling (iii) quality and originality of the
starting material (iv) use of genetically modied food and/or transgenic
microbial cultures (v) use of antibiotics, fungicides and herbicides
during animal and crop cultivation (vi) microbial contamination
during the production process, handling and storage [7].
*Corresponding author: Djuro Josic, Warren Alpert Medical School, Brown
University, Providence, USA, E-mail: djuro_josic@brown.edu
Received March 01, 2013; Accepted March 04, 2013; Published March 11, 2013
Citation: Josic D, Giacometti J (2013) Foodomics-Use of Integrated Omics
in Nutrition, Food Technology and Biotechnology. J Data Mining Genomics
Proteomics 4: e106. doi:10.4172/2153-0602.1000e106
Copyright: © 2013 Josic D, et al. This is an open-access article distributed under
the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and
source are credited.
Foodomics-Use of Integrated Omics in Nutrition, Food Technology and
Biotechnology
Djuro Josic1,2* and Jasminka Giacometti2
1Warren Alpert Medical School, Brown University, Providence, USA
2Department of Biotechnology, University of Rijeka, Rijeka, Croatia
Quality control
Quality control
Microbial control
In process control
Raw material
(plant or animal origin)
Food processing
Final products
Cleaning and sanitation
Production process,food safety and quality
Microbial and biological safety
Production steps
Analysis of food components
Safety
Batch-to-batch variations
Detection of resistent microorganisma
Proteomics - microbial proteomics
Proteomics
Proteomics
Proteomics
Protein interactions
Protein interactions
Protein changes
Protein changes
Protein changes
Contaminants
Contaminants
Contaminants
Figure 1: Use of foodomics in the development pathway for food production,
and assessing food safety, originality and quality [7].
Citation: Josic D, Giacometti J (2013) Foodomics-Use of Integrated Omics in Nutrition, Food Technology and Biotechnology. J Data Mining Genomics
Proteomics 4: e106. doi:10.4172/2153-0602.1000e106
Page 2 of 3
Volume 4 • Issue 2 • 1000e106
J Data Mining Genomics Proteomics
ISSN: 2153-0602 JDMGP, an open access journal
High-throughput Methods
Both the sampling and the high-throughput sample preparation are
the rst critical point in foodomic analyses. ey are critical for both
exact and very fast analytical work. Optimization of sample preparation,
extraction and parallel chromatographic separation of extracts before
further analysis by use of robotics is the rst step on the way for fast and
exact omics food analyses. e use of miniaturized columns packed
with bulk supports or containing monoliths for parallel separation
of 96 samples was already introduced [8]. Dierent chromatographic
supports can be used for stepwise separation of complex biological
mixtures before further proteomic and metabolomic analyses.
Already three years ago, we emphasized that most proteomic
analyses of food components are based on protein separation
by gel electrophoresis [7]. In proteomic analysis of food, the 2D
electrophoresis is still the most used method for protein separation
before their identication by LC-MS/MS [1]. Although this method
provides very high resolution and eective separation of very similar
components, it is time-consuming and the use of robotics for high-
throughput sampling is dicult. e use of gel-free proteomics enables
the sample preparation and high-throughput analysis of samples, as
well as integration of other parallel omics methods, e.g., determination
of metabolites in the same analytical run. For quantitative analyses, gel-
free, label-free methods with application of the corresponding soware
will be introduced. New soware can be used for direct comparison of
samples at both protein (proteomics), peptide and other low molecular
weight components (peptidomic, metabolomic) level in order to
determine dierently expressed components on the further way of
determination of possible candidates and validation of (bio) marker
candidates [7].
Development of Methods for Determination of Food
Quality and Originality
In order to determine the discrimination of fresh versus frozen
meat (http://www.spiegel.de/spiegel/print/d-81562346.html, Der
Spiegel online), several foodomic methods can be used such as
DNA based techniques, spectroscopy (including the NMR), sensory
methods and bio imaging. Omics methods are also gaining importance
for determination of the used antibiotics in meat production, use
of growth promoter abuse by metabolomic or proteomic methods
[1,7], adulteration of raw materials in production of high-value food
[9,10], and in order to determine the speed of the spoilage of raw
material [11]. It was already demonstrated that previous, very eective
methods for food analysis and detection of adulterations can be further
optimized by introduction of new, rapid and more sensitive methods
at the higher level of the present state-of-the art [9,12]. Important
contribution will be the application of so-called “activomics”. It is
the method that is following the change of enzyme activities in target
samples (e.g., dierent proteases or kinases) by use of MALDI-TOF
mass spectrometry. In combination with other methods, activomics
can explore the changes in the food during storage (e.g., freezing, or
freezing/thawing) as well as during the production process, or changes
caused by microbial contamination.
Russo et al. [12] demonstrated that the adulteration by replacement
of bualo by bovine milk can be detected by analyses of post-translation
modications, in this case, casein phosphopeptides. Introduction of
this methodology will be also be very useful for (phospho) proteomic
and genomic meat analysis [13].
With few exceptions, glycomic and phosphoproteomic analyses in
foodomics are now limited to milk [7]. Analyses of changes of post-
translational modications, primarly glycosylation and phosporylation
will be applied in order to determine the quality and originality of the
starting materials following the changes during food fermentation,
as well as typical pattern related to food adulterations. Additional
information will be gained by parallel investigation of phospholipids’
changes [14].
Imaging mass spectrometry is further method for determination
of the distribution of small molecules and small and middle sized
proteins in complex biological samples. is method was mostly used
in medicine for discovery of disease biomarkers [15] which can be
adapted for use in food analysis.
e eld of foodomic disciplines is a rapidly evolving scenario
lled with the technological innovations (high-throughput sample
preparation, optimized LC and MS instruments), bioinformatics tools
(e.g., in direction of the label-free quantitative MS analysis) and other
practical issues in this eld. e coordination of the collaboration of all
participating groups will nally result in an integration of all applied
omic disciplines converging to the eld of foodomics and it will
represent more suitable tool than each discipline alone in providing
the answers that are addressed above.
References
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optimization of processing and quality control of food of animal origin. Food
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Citation: Josic D, Giacometti J (2013) Foodomics-Use of Integrated Omics in Nutrition, Food Technology and Biotechnology. J Data Mining Genomics
Proteomics 4: e106. doi:10.4172/2153-0602.1000e106
Page 3 of 3
Volume 4 • Issue 2 • 1000e106
J Data Mining Genomics Proteomics
ISSN: 2153-0602 JDMGP, an open access journal
14. Wang Y, Zhang H (2011) Tracking phospholipid proling of muscle from
Ctenopharuyngodon idellus during storage by shotgun lipidomics. J Agric Food
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sections down to cellular level, multiscale imaging of phospholipids by MALDI
mass spectrometry. Mol Cell Proteomics 10.
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  • Jul 2012
The revolution of 'omic' sciences has introduced integrated high-throughput approaches to address the understanding of the biochemical systems and of their dynamic evolution. In the field of food research, 'omics' are depicting a comprehensive view which largely overcomes the merely descriptive approaches of the early proteomic and metabolomic era. Thus, the recently born 'foodomics' is to be intended as a global perspective of knowledge about foods, which covers the assessment of their composition, the effects of (bio)technological processes for their production, their modifications over time and the impact that food consumption has on human health. Food proteomics and metabolomics, along with their derived 'omic' branches such as peptidomics, lipidomics and glycomics, are still evolving technologies capable of tackling the nature and the transformations of foods. In the development of the advanced 'omic' platforms, because of their potential to profile complex mixtures of biomolecules, mass spectrometry techniques have assumed an unquestionable role. Because proteins are central molecules in all biological systems, proteomic platforms are pivotal among the 'foodomic' tools, as the proteomes and related peptidomes provide biomolecular subsets mostly informative about the history of a food product. Similarly, food interactomics and metabonomics aim to study the dynamics that occur in foodstuff. The ultimate aim of foodomics is the production of high-quality and safe food products for improving human health and well-being. In this review we critically present the recent research outcomes in the field of food sciences that have been achieved through the contribution of the 'omic' methodologies relying on mass spectrometry.
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Detection of buffalo mozzarella adulteration by an ultra-high performance liquid chromatography tandem mass spectrometry methodology
Article
Full-text available
  • Nov 2012
  • J MASS SPECTROM
Over the past years, LC–MS-based approaches have gained a growing interest in food analysis by using different platforms and methodologies. In particular, enhanced selectivity and sensitivity of multiple reaction monitoring (MRM) scan function offer powerful capabilities in detecting and quantifying specific analytes within complex mixtures such as food matrices. The MRM approach, traditionally applied in biomedical research, is particularly suitable for the detection of food adulteration and for the verification of authenticity to assure food safety and quality, both recognized as top priorities by the European Union Commission. Increasingly stringent legislation ensure products safety along every step ‘from farm to fork’, especially for traditional foods designed with the Protected Designation of Origin certification. Therefore, there is a growing demand of new methodologies for defining food authenticity in order to preserve their unique traits against frauds. In this work, an ultra performance liquid chromatopgraphy-electrospray ionization-tandem mass spectrometry (MS/MS) methodology based on MRM has been developed for the sensitive and selective detection of buffalo mozzarella adulteration. The targeted quantitative analysis was performed by monitoring specific transitions of the phosphorylated β-casein f33-48 peptide, identified as a novel species-specific proteotypic marker. The high sensitivity of MRM-based MS and the wide dynamic range of triple quadrupole spectrometers have proved to be a valuable tool for the analysis of food matrices such as dairy products, thus offering new opportunities for monitoring food quality and adulterations. Copyright
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High-throughput fractionation of human plasma for fast enrichment of low- and high-abundance proteins
Article
Full-text available
  • May 2012
Background: Fast, cost-effective and reproducible isolation of IgM from plasma is invaluable to the study of IgM and subsequent understanding of the human immune system. Additionally, vast amounts of information regarding human physiology and disease can be derived from analysis of the low abundance proteome of the plasma. In this study, methods were optimized for both the high-throughput isolation of IgM from human plasma, and the high-throughput isolation and fractionation of low abundance plasma proteins. Materials and methods: To optimize the chromatographic isolation of IgM from human plasma, many variables were examined including chromatography resin, mobile phases, and order of chromatographic separations. Purification of IgM was achieved most successfully through isolation of immunoglobulin from human plasma using Protein A chromatography with a specific resin followed by subsequent fractionation using QA strong anion exchange chromatography. Through these optimization experiments, an additional method was established to prepare plasma for analysis of low abundance proteins. This method involved chromatographic depletion of high-abundance plasma proteins and reduction of plasma proteome complexity through further chromatographic fractionation. Results: Purification of IgM was achieved with high purity as confirmed by SDS-PAGE and IgM-specific immunoblot. Isolation and fractionation of low abundance protein was also performed successfully, as confirmed by SDS-PAGE and mass spectrometry analysis followed by label-free quantitative spectral analysis. Discussion: The level of purity of the isolated IgM allows for further IgM-specific analysis of plasma samples. The developed fractionation scheme can be used for high throughput screening of human plasma in order to identify low and high abundance proteins as potential prognostic and diagnostic disease biomarkers.
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We Are What We Eat: Food Safety and Proteomics
Article
Full-text available
  • Jan 2012
  • J PROTEOME RES
In this review, we lead the reader through the evolution of proteomics application to the study of quality control in production processes of foods (including food of plant origin and transgenic plants in particular, but also meat, wine and beer, and milk) and food safety (screening for foodborne pathogens). These topics are attracting a great deal of attention, especially in recent years, when the international community has become increasingly aware of the central role of food quality and safety and their influence on the health of end-consumers. Early proteomics studies in the field of food research were mainly aimed at performing exploratory analyses of food (bovine, swine, chicken, or lamb meat, but also transgenic food such as genetically modified maize, for example) and beverages (wine), with the goal of improving the quality of the end-products. Recently, developments in the field of proteomics have also allowed the study of safety issues, as the technical advantages of sensitive techniques such as mass spectrometry have guaranteed a faster and improved individuation of food contaminating pathogens with unprecedented sensitivity and specificity.
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Recent technological advances for the determination of food authenticity
Article
  • Jul 2006
  • TRENDS FOOD SCI TECH
The relative potential of various technologies for the confirmation of food authenticity and quality are discussed. Techniques that have found new applications in the field of quality assurance since 2001 are discussed in terms of their potential ease of application in an industrial setting. The use of specific techniques with chemometric analysis for the classification of food samples based on quality attributes is also included in this review. The techniques discussed are spectroscopy (UV, NIR, MIR, visible, Raman), isotopic analysis, chromatography, electronic nose, polymerase chain reaction, enzyme-linked immunosorbent assay and thermal analysis.
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Flavor precursor development in Cheddar cheese due to lactococcal starters and the presence and lysis of Lactobacillus helveticus
Article
  • Apr 2007
  • INT DAIRY J
The rapid release of intracellular enzymes due to autolysis of lactic acid bacteria in the cheese matrix has been shown to accelerate cheese ripening. The objective of this work was to investigate the evolution of the flavour precursors, individual free amino acids (FAAs), free fatty acids (FFAs) and volatile compounds that contribute to the sensory profiles of cheeses at 2, 6 and 8 months of ripening in Cheddar cheese manufactured using starter systems which varied with respect to their autolytic properties. Starter system A contained a blend of two commercial Lactococcus lactis strains (223 and 227) which had a low level of autolysis. System B was identical to A but also included a highly autolytic strain of Lactobacillus helveticus (DPC4571). System C contained only strain DPC4571. Levels of all individual FAAs were elevated in cheeses B and C relative to A after 2 months of ripening. By 8 months of ripening the main FAA were glutamate, leucine, lysine, serine, proline and valine. Levels of C6:0, C8:0, C12:0 and C18:0 fatty acids did not vary greatly over ripening, while levels of C4:0, C10:0, C14:0, C16:0 and C18:1 were elevated in cheeses B and C. Principal component analysis of the headspace volatiles separated cheese A from cheeses B and C. Cheeses B and C had highest levels of dimethyl disulphide, carbon sulphide, heptanal, dimethyl sulphide, ethyl butanoate, 2-butanone, and 2-methyl butanal and were described as having a ‘caramel’ odour and ‘sweet’, ‘acidic’ and ‘musty’ flavour. Cheese A had highest levels of 2-butanol, 2-pentanone, 2-heptanone, 1-hexanol and heptanal and was described as having a ‘sweaty/ sour’ odour and ‘soapy’, ‘bitter’ and ‘mouldy’ flavour. The results highlight the impact of starter lactococci on flavour precursor development and the positive effect of Lb. helveticus and the lysis of this strain on enhancing levels of substrate and flavour precursors early during ripening resulting in early flavour development.
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Present and Future Challenges in Food Analysis: Foodomics
Article
  • Sep 2012
  • ANAL CHEM
The state-of-the-art of food analysis at the beginning of the 21st century is presented in this work, together with its major applications, current limitations, and present and foreseen challenges.
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Tracking Phospholipid Profiling of Muscle from Ctennopharyngodon idellus during Storage by Shotgun Lipidomics
Article
  • Oct 2011
  • J AGR FOOD CHEM
This paper aims to study phospholipid (PL) profiling of muscle from Ctenopharyngodon idellus during room-temperature storage for 72 h by direct-infusion electrospray ionization tandem mass spectrometry (ESI-MS/MS). Five classes of PLs, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylserine (PS), and sphingomyelin (SM), were analyzed. At least 110 molecular species of PLs were identified, including 32 species of PC, 34 species of PE, 24 species of PS, 18 species of PI, and 2 species of SM. The result showed that oxidation and hydrolysis are the two main causes for the deterioration of PLs in fish muscle during storage. Most content of PL molecular species increased and then decreased gradually. However, some special PE molecular species with former low abundance, such as PE 32:1, PE 34:2, and PE 34:1, emerged during the storage in quantity. It indicated that those PE molecular species may come from the microbe bred in the muscle. This phenomenon was found and discussed for the first time. The possible relevance between the emergence of these special PE molecular species and the freshness of the fish muscle during storage will be investigated in further studies.
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