The Rising Role of Foodomics

Ten years since its official definition, foodomics continues to expand the scientific knowledge of food and nutrition while resolving many analytical challenges along the way. LCGC Europe spoke to Alejandro Cifuentes from the Institute of Food Science Research, in Madrid, Spain, about his current foodomics research projects, the overall state of the field, and the future of foodomics.

Q. Foodomics has evolved in terms of knowledge and technology since the term was coined in 2009. What is foodomics and why is it important?

A: Foodomics was defined for the first time by our research group in 2009 as “a new discipline that studies the food and nutrition domains through the application and integration of advanced ‘omics’ technologies to improve consumer’s well-being, health, and knowledge” (1). Foodomics has subsequently been applied by many laboratories and numerous papers have been published in the literature (2–15). Basically, we believe that foodomics, even in its current early stages, can provide new answers to many crucial questions that need to be solved in food science and nutrition.

Q. Could you give a general overview of the field with regards to major research areas, the chromatographic techniques used, and the analytical challenges that have been overcome during this decade?

A: The major research areas of foodomics include investigations on food safety, food quality, food traceability, and food bioactivity. As you can deduce, the number of research areas where foodomics can play a role is therefore huge. Any food-related research in which an “omics” methodology is applied may be considered a part of foodomics. Apart from miniaturization, there are two other major analytical developments that have had a clear influence on the evolution of foodomics in the past ten years.

The first is related to the new and fast sequencing methods that are categorized together under the common umbrella of next-generation sequencing (NGS), which is having a crucial impact on genomics and transcriptomics applications. The second is the manufacture of high resolution mass spectrometers with improved features and capabilities that are becoming available at more affordable prices, and which are significantly contributing to the progression of foodomics in general, and metabolomics and proteomics in particular.

In foodomics, we develop transcriptomics, proteomics, and metabolomics approaches to study the safety, quality, and traceability of foods, or to investigate how foods (including functional ingredients) interact with our genome and the subsequent modifications that these interactions can generate at the proteome and metabolome level.

The chromatographic techniques used in foodomics are those typically used in proteomics and metabolomics, such as liquid chromatography (LC), ultrahigh‑performance liquid chromatography (UHPLC), nano-LC, gas chromatography (GC), or capillary electrophoresis (CE) hyphenated to high-resolution mass spectrometry (HRMS).

With these techniques we are able to obtain massive amounts of information at different expression levels, such as proteins and metabolites.

In addition, we have developed many comprehensive two‑dimensional liquid chromatography tandem mass spectrometry (LC×LC–MS/MS) methods for metabolomics profiling of different natural compounds in complex matrices (7,8). Logically, an important additional step in all these procedures is the use of adequate sample preparation techniques (6). One of the main analytical challenges that we had to overcome was the development of the three different “omics” strategies used in foodomics: transcriptomic-, proteomic-, and metabolomic methods.

Considering that practically all “omics” laboratories around the world may work in just one of these “omics” disciplines, the amount of work we had to face was really challenging! Collaboration with other groups and laboratories was, of course, essential to meet these challenges. For example, we always need collaborations for in vivo experiments because we do not have the necessary infrastructure in our institute. As a result, in our publications we usually have co-authors from other institutions and countries.

Q. Data management is a huge part of any “omics” field and is often cited as a bottleneck in research. Is this true for foodomics? And if so, what is being done to solve this issue?

A: Data handling is a global problem for any discipline that generates huge amounts of data and foodomics is no exception. This bottleneck prevents the integration of data from the different “omic” levels making it impossible to obtain the biological meaning from the data generated in a straightforward way. At the moment there is no bioinformatic tool that can put together and handle the data that we generate from transcriptomics, proteomics, and metabolomics experiments simultaneously.

Other typical problems are the difficult data storage, the slow processing time, the improvement needed by metabolomic databases, the suitable mining of massive datasets, and the need for harmonized and standardized methods to generate and analyze data, among many others. Fortunately, there are many groups all around the world working on these problems and trying to solve them.

Q. How has data that can be obtained at present translated to useful dietary or medical information?

A: After several years working in foodomics, we have obtained useful information about the antiproliferative effect of several extracts from natural sources and food by-products. For example, we have found a very interesting and active extract obtained from rosemary using a green extraction process that has demonstrated an impressive antiproliferative activity against different in vitro and in vivo models of colon cancer together with low toxicity.

The biological mechanisms of this activity were found and explained via foodomics. This was one of the first works published in which the three “omics” levels were simultaneously interrogated (9). This is the first step to understanding and demonstrating scientifically the health impact of a given food or dietary ingredient before providing any dietary or medical recommendation. I will discuss other aspects of this research in more detail later.

Although foodomics is a new discipline and still in its early stages, the discipline is expected to help to overcome the controversial messages that consumers are continuously receiving from the food industries and the regulatory agencies about the benefits and risks of different foods.

Q. From an analytical perspective what challenges do scientists involved in foodomics face?

A: As foodomics uses advanced analytical instruments and “omics” approaches, the challenges to be faced are the common ones for any laboratory working with these technologies. Thus, for transcriptomics we must evaluate if the cost linked to a transcriptomic study using microarrays compensates (or not) for the option to do the same study using NGS of all the transcripts-something unthinkable a few years ago.

Regarding proteomics studies, we are now moving from the classical procedures, such as using two‑dimensional electrophoresis, (isoelectric focusing followed by size separation), imaging comparison, tryptic hydrolysis, and matrix‑assisted laser desorption–ionization (MALDI) MS/MS of peptides, to very powerful strategies using isotopic derivatization of enzymatically hydrolyzed proteins followed by nano-LC–HRMS analysis for identification and quantitation of all the proteins (and samples) in a single run.

In metabolomics the challenges remain linked to getting a picture as wide as possible of the metabolome of any biological system. This means putting together several metabolomics platforms, such as LC–HRMS plus GC–HRMS and CE–HRMS, to reduce the bias induced by the sample preparation step as much as possible, and to manage the development of metabolomics databases. Of course, all of them share the same analytical constraints related to speed, sensitivity, and resolution. There will always be a desire to improve these factors in any analytical instrument.

Q. You recently published two papers using a multianalytical platform based on pressurized liquid extraction (PLE), in vitro assays, and liquid chromatography/gas chromatography coupled to high-resolution mass spectrometry to investigate food by-products valorization. Why were you investigating food by-products valorization, what was novel about your approach, and what were your main findings?

A: One unique aspect of the group involved in publishing these two papers is the capability of integrating different areas of expertise and backgrounds (3,4). One co-author has expertise in the development of new green processes to get valuable extracts from different raw materials that, ultimately, can increase the viability and economic interest of the whole study. Another important aspect of these studies is sustainable development, which is an important goal of our group as we enter a new “green food era”. In view of the potential of Colombian food by-products as a promising source of bioactive phytochemicals, a multianalytical platform based on separation techniques coupled to HRMS was presented as part of an integrated valorization strategy for these by-products and includes PLE using green solvents and different in vitro evaluations of their bioactivity.

Thus, a comprehensive phytochemical profiling analysis of the compounds extracted from goldenberries calyx (using an optimized PLE process) was performed by LC and GC coupled to quadrupole time-of-flight tandem mass spectrometry (QTOF-MS/MS), applying new and integrated identification approaches for the confident identification and structural elucidation of the bioactive phytochemicals from the HRMS data.

Q. Could this “multianalytical” technique be adapted for other applications?

A: The proposed strategy could be readily implemented in many other applications, such as the complete characterization of preparations with health-promoting effects intended to be used as functional foods or in traditional medicines. And, of course, for revalorization of any food by-products by obtaining from them bioactive compounds with added value via, for example, some specific bioactivity.

Q. You mentioned earlier a metabolomics study you published last year to investigate metabolomic changes in cells in response to rosemary diterpene exposure (2). What was the aim of this research, and what were your main findings?A: Rosemary diterpenes have demonstrated diverse biological activities, such as anticancer and anti-inflammatory properties, as well as other beneficial effects against neurological and metabolic disorders. In particular, carnosic acid (CA), carnosol (CS), and rosmanol (RS) diterpenes have shown interesting results on anticancer activity.

However, little was known about the toxic effects of rosemary diterpenes at the concentrations needed to exert their antiproliferative effect on cancer cells. In the mentioned work, CA, CS, and RS exhibited a concentration‑dependent effect on cell viability of two human colon cancer cell lines (HT-29 and HCT116) after 24 h exposure. The HT-29 cell line was more resistant to the inhibitory effect of the three diterpenes than the HCT116 cell line. Among the three diterpenes, RS exerted the strongest effect in both cell lines. To investigate the hepatotoxicity of CA, CS, and RS, undifferentiated and differentiated HepaRG cells were exposed to increasing concentrations of the diterpenes (from 10 mM to 100 mM). Differentiated cells were found to be more resistant to the toxic activity of the three diterpenes than undifferentiated HepaRG, probably related to a higher detoxifying function of differentiated HepaRG cells compared with the undifferentiated cells.

The metabolic profiles of differentiated HepaRG cells in response to CA, CS, and RS were examined to determine biochemical alterations and deepen the study of the effects of rosemary phenolic diterpenes at the molecular level. A multiplatform metabolomics study based on liquid and gas chromatography hyphenated to HRMS was used and revealed that rosemary diterpenes exerted different effects when HepaRG cells were treated with the same concentration of each diterpene. RS revealed a greater metabolome alteration followed by CS and CA, in agreement with their observed cytotoxicity. In this work, we demonstrated the usefulness of metabolomics combined with cell lines for toxicity studies because it provides valuable information about early events in the metabolic profiles of cells after the treatment with the investigated compounds. Interestingly, this new analytical method reduces the use of animals classically used in toxicology studies.

Q. Are there any other recent research projects that you think demonstrate the value of foodomics?

A: We have recently founded the first Joint Research Center for Green Foodomics Research in Beijing together with the Chinese Academy of Agricultural Sciences (CAAS), and in a year a major reference work on comprehensive foodomics (10 books and more than 150 book chapters) will be published (10).

The 65,000 results obtained in Google using the search term “foodomics” may be regarded as additional proof of the interest generated by foodomics among research institutions, agencies, food industries, regulatory laboratories, scientific instrumentation manufacturers, and consumers.

In this regard, we are in collaboration with several Latin American universities to work together on foodomics for food waste and food by-product revalorization, mainly through different stays, exchanges, courses, or roundtables. This interaction with students, teachers, and local people is probably one of the most rewarding experiences that one may have in science.

Q. What are you currently working on?

A: Amongst the different bioactivities studied related to the consumption of health-promoting food components, their possible neuroprotective effect is gaining importance because of the huge negative impact that neurodegenerative diseases have in society. However, to date, the mechanisms through which the neuroprotective activities would be exerted are largely unknown. In this regard, foodomics might be a very useful tool to discover the neuroprotective effects of dietary terpenes at a molecular level.

The main aim of the new project in which we are working is to study the neuroprotective activity of terpenes and terpenoids from natural extracts, such as microalgae, seaweeds, and food-related by-products from olive oil and orange juice production, carrying out a systematic study of different chemical structures combined with in vitro and in vivo Alzheimer’s disease models and a foodomics study of their activity. The selection of this family of compounds is based on previously published reports highlighting the possible neuroprotective effect of some terpenoids, although, up to now, there still exists a lot of missing information on how they may exert this activity. This project proposal also includes the development of a new methodology for the valorization of by-products and fractions based on the concept of biorefinery and zero‑waste philosophy.

Q. What is the future of foodomics?

A: In the future of food science, the first demand will still be to guarantee food safety. The global movement of food and related raw materials will increase in the next few years and it will bring about an increasing number of contamination episodes worldwide. In addition, many food products containing multiple and processed ingredients shipped from all over the world will share common storage spaces and production lines, which will make it even more complicated to face food safety episodes. As a result, ensuring the safety, quality, and traceability of food will be even more complicated and important than now. It will require the development of new, more advanced, and more powerful analytical strategies as proposed by foodomics.

Foodomics can also help to investigate and solve other crucial topics in food science and nutrition, such as establishing the global role and functions of the gut microbiome; obtaining sound scientific evidence that supports or refutes the beneficial claims of functional foods and constituents; establishing analytical methods to guarantee food safety, origin, traceability, and quality, including the discovery of biomarkers to detect unsafe products, the understanding of the stress adaptation responses of foodborne pathogens, or the early detection of food safety problems; and understanding the molecular basis of biological processes with agronomic and economic relevance, such as the interaction between crops and their pathogens, as well as physicochemical changes that take place during fruit ripening.

We are still far from solving many of the aforementioned challenges. This is why we need to keep working, probably for a number of years, before getting the necessary perspective (and knowledge) on these complex and fundamental topics.

Q. How do you see foodomics becoming more commonly used in practice?

A: Food industries and regulatory agencies have traditionally not been particularly interested in any new approaches that may require more investment or effort.

We are not proposing to use foodomics as a sledgehammer to crack a nut. The problem is that there are many questions that need to be solved and clarified in food science and nutrition. These issues are much bigger and more crucial to our health than a nut, and, you can be sure, to address them you really need to have the right approach, investment, and knowledge. For example, traditional targeted analytical approaches are the ones typically used by food industries and regulatory agencies, and they are useful to detect known allergens in foods, no doubt. However, the use of foodomics-in this case based on proteomics approaches-might be essential to obtain the complete de novo sequencing and identification of
new previously unknown food allergens.

In addition, the use of foodomics‑based systems, biology combined with data mining, interpretation, and integration, might be a key tool to discover the molecular mechanisms beneath food allergies at a physiological level. For example, you can also think about the new possibilities for foodomics related to safety and bioactivity of new compounds from food by-products or waste revalorization, or how to elucidate the complexity of the food digestome or the food microbiome, to mention a few. I fully expect foodomics to lead food science and nutrition research into a new era.

References

1. A. Cifuentes, J. Chromatogr. A1216, 7109 (2009).
2. T. Acunha et al., Anal. Chim. Acta1037(1), 40–151 (2018).
3. D. Ballesteros-Vivas et al., J. Chromatogr. A1584, 155–164 (2019).
4. D. Ballesteros-Vivas et al., J. Chromatogr. A1584, 144–154 (2019).
5. A. Cifuentes, Ed., Special issue on Foodomics and Modern Food Analysis in TrAC-Trends in Analytical Chemistry96, 1–212 (2017).
6. T. Martinovic, M.G. Šrajer, and D. Josic, Electrophoresis39, 1527–1542 (2018).
7. L. Montero, M. Herrero, E. Ibáñez, and A. Cifuentes, J. Chromatogr. A1313, 275–284 (2013).
8. L. Montero, V. Sáez, D. von Baer, A. Cifuentes, and M. Herrero, J. Chromatogr. A1536, 205–215 (2018).
9. C. Ibáñez, A. Valdés, V. García-Cañas, C. Simó, M. Celebier, L. Rocamora, A. Gómez, M. Herrero, M. Castro, A. Segura-Carretero, E. Ibáñez, J.A. Ferragut, and A. Cifuentes, J. Chromatogr. A1248, 139–153 (2012).
10. A. Cifuentes, Ed., Major References Work on Comprehensive Foodomics (Elsevier, To be published in 2021).
11. A. Cifuentes, Ed., Foodomics. Advanced Mass Spectrometry in Modern Food Science and Nutrition (John Wiley & Sons, Hoboken, New Jersey, USA. 2013). (The first book published on foodomics)
12. M. Herrero et al., Mass Spec. Rev.31, 49–69 (2012).
13. T Skov, A.H. Honoré, H.M. Jensen, T Næs, and S.B. Engelsen, TrAC Trends in Analytical Chemistry60, 71–79 (2014).
14. P. Ferranti, Curr. Opin. Food Sci.22, 102 (2018).
15. A. Bordoni and F. Capozzi, Current Opinion in Food Science4, 124–128 (2015).

Alejandro Cifuentes is a Professor at the National Research Council of Spain (CSIC) in Madrid, Spain, and Head of the Laboratory of Foodomics and Director of the Metabolomics Platform (International Excellence Campus CSIC + University Autonoma of Madrid). He is the Founding Director of the Institute of Food Science Research and Deputy Director of the Institute of Industrial Fermentations, both belonging to CSIC. Alejandro’s activities include advanced analytical method development for foodomics, food quality, and safety, as well as the isolation and characterization of natural bioactive compounds and their effect on human health.