Gerard Klein Essink and Dr. Robert D. Hall04.28.11
The conclusion to a three part series, this third and final article examines the application of metabolomics in the raw material production process.
As previously detailed, metabolomics has been developed as a new high-throughput analytical chemistry platform for the deep analysis of the biochemical composition of biological materials. The technology takes many forms and there are no real limits to the biological fields of application. Already metabolomics has been used in the medical industry for disease monitoring and the discovery of infection biomarkers, as well as microbial fermentation industry in the production of beer and high value chemicals. But perhaps the widest field of application has been in the area of the plant sciences.
Many uses for the technology have been found—in fundamental research for enhancing our understanding of how plants function—but primarily in applied plant science and nutritional science, where metabolomics is being used to help different industries improve plant-based products. One main area of application is using the technologies to advance knowledge of the biochemical composition of our crop-based foods and how we might improve this through targeted breeding and production/processing strategies.
Below are listed a small number of the many areas of metabolomics applications in the crop and food industries of relevance to food and nutritional quality.
Metabolomics and Fresh Produce: Fruits
Major fruit crops such as melon, citrus and grape (fresh and wine varieties) as well as some minor crops such as raspberry, strawberry and cranberry have already been subjected to metabolomics analyses. Through these approaches the influence of aspects such as fruit ripening, cultivation conditions, storage and shelf-life has been investigated and biochemical changes defined.
For example, metabolomics of melons revealed the three dimensional nature of fruit ripening in these large fruits (top to bottom/inside to outside). Analyses of strawberry ripening revealed the huge complexity of the process, which leads to a global reprogramming of the biochemical composition of the fruit within just a few days. The transition from green to white to red-ripe fruits is accompanied by dramatic changes (both in negative and positive senses) in a wide range of biochemical pathways enabling the conversion of an astringent hard tissue into the soft and fragrant one we like to eat. Never before have we had such a detailed insight into such complex processes.
Metabolomics and Fresh Produce: Vegetables
Potato and tomato are two of the world’s top four most important vegetable crops. Both are eaten in a wide variety of forms, either cooked (tomato and potato) or fresh (tomato). Both are also cultivated and eaten in most of the world’s countries where they often represent a significant component of the daily diet. In tomato research, metabolomics is already being used extensively to help identify which components are linked to key quality traits such as taste and flavor and how these are influenced by variety and cultivation conditions.
Results have already revealed the complexity of taste and how different varieties/fruit types differ biochemically. Through metabolomics approaches, combined with detailed sensory (taste panel) tests, biostatistical analyses of the complex data obtained is allowing us to slowly build up a picture of the molecular basis of tomato taste and how this influences consumer preference. With this knowledge we shall gain a better hold on how, in future, we can specifically tailor breeding programmes to improve tomato fruit quality and taste.
In potato, scientists have utilized metabolomics technologies to assess compositional differences in existing cultivars in relation to consumer quality. For example, the levels of key amino acids isoleucine, tyrosine and phenylalanine were found to be higher in certain cultivars under certain growth conditions. This is of considerable relevance as these amino acids have been associated with post cooking blackening, bruising as well as flavor after cooking. Seasonality has also been shown to greatly influence the biochemical profile of potato tubers, irrespective of variety.
Metabolomics and Processed Produce: Coffee and Tomato
Tomatoes are eaten in many cooked forms, often after undergoing extensive processing (for canning and the production of tomato puree). The influence of such processes on the biochemical composition is generally poorly understood and food processors often have few indicators as to how production might be improved in order to yield better quality products. Metabolomics analyses of the entire tomato puree production process have revealed several steps that heavily influence the final composition of the canned product. One step in particular was shown to result in extensive loss of antioxidants and this step should therefore become a main target in any strategy to improve the procedure. This could then lead to the production of a more nutritious/healthier product that also has an extended shelf life.
Coffee is another product that always undergoes extensive processing before ingestion. Metabolomics is being used in this vein to help understand the biochemical changes that occur between the farm and the factory where the beans eventually end roasting. Results have demonstrated that both strongly influence final bean quality and taste perception.
Where to Go From Here
While the technology is still under development, there are clearly many areas where the metabolomics is becoming firmly established. The small number of examples given in these articles emphasize the broad applicability of the approach. Huge amounts of data are being generated of relevance to crop and food applications, but only time will truly tell how important this information is and how readily it can be translated into biologically-relevant knowledge.
A current technological limitation is that while fantastic improvements in analytical equipment mean that we can now detect many more potentially important plant compounds than was ever possible before, we still do not know what most of them are or how they are synthesized by the plant. However, once we can successfully pair such individual compounds to key food or nutritional quality traits we can then use this to focus our efforts specifically on the identification of these biologically-relevant metabolites. In so doing, we shall continue to expand our knowledge of quality and nutrition/health related components in our food, which will lead to more targeted strategies for food quality improvement for the diets of both Western and developing countries—through targeted crop breeding approaches as well as the improved treatment of the harvested products.
*Acknowledgement: Both GKL and RDH kindly acknowledge financial support for this paper from the EU Framework VI project “Metabolomics for Plants, Health and OutReach,” or META-PHOR (No. FOOD-CT-2006-036296).
October 2006 marked the beginning of an EU-funded project called META-PHOR tasked with the following purpose: "To generate knowledge on those metabolites in our food which determine key characteristics such as nutritional value, quality and health by developing the advanced tools required for their detection. This knowledge will facilitate better monitoring of the food production chain and will create new opportunities for targeted strategies for breeding, storage and processing.”
This project united the activities of most of the main research groups in Europe dedicated to technology development and overcoming some of the main bottlenecks experienced with this new approach. Next to biochemical analyses, much emphasis was also placed on developing statistics, bioinformatics and software tools that are essential for success.
META-PHOR focused on three crops—broccoli, melon and rice (a vegetable, a grain and a fruit crop, each with their own technological challenges, see Table 1). However, the goals were to develop generic approaches applicable to all crops that would facilitate new strategies for food quality improvement, biofortification and nutrigenomics issues. Key chemical components linked to taste, flavor, nutritional value, etc., have been characterised and we now have a better understanding as to how metabolomics approaches can better be applied in an industrial context.
Table 1. A summary of the key groups of metabolites present in the crops chosen, which are linked to nutrition, health promoting effects and quality.
GC-MS: Gas Chromatography-Mass Spectrometry; NMR: Nuclear Magnetic Resonance; LC-MS: Liquid Chromatography-Mass Spectrometry; FT-MS: Fourier Transform-Ion Cyclotron-Mass Spectrometry; LC-ICP-MS: Liquid Chromatography-Inductively Coupled Plasma-Mass Spectrometry.
Gerard Klein Essink, MSc, is managing director of Bridge2Food in The Netherlands, and Dr. Robert D. Hall is managing director of Centre for BioSystems Genomics CBSG2012, Plant Research International, also in The Netherlands.
As previously detailed, metabolomics has been developed as a new high-throughput analytical chemistry platform for the deep analysis of the biochemical composition of biological materials. The technology takes many forms and there are no real limits to the biological fields of application. Already metabolomics has been used in the medical industry for disease monitoring and the discovery of infection biomarkers, as well as microbial fermentation industry in the production of beer and high value chemicals. But perhaps the widest field of application has been in the area of the plant sciences.
Many uses for the technology have been found—in fundamental research for enhancing our understanding of how plants function—but primarily in applied plant science and nutritional science, where metabolomics is being used to help different industries improve plant-based products. One main area of application is using the technologies to advance knowledge of the biochemical composition of our crop-based foods and how we might improve this through targeted breeding and production/processing strategies.
Below are listed a small number of the many areas of metabolomics applications in the crop and food industries of relevance to food and nutritional quality.
Metabolomics and Fresh Produce: Fruits
Major fruit crops such as melon, citrus and grape (fresh and wine varieties) as well as some minor crops such as raspberry, strawberry and cranberry have already been subjected to metabolomics analyses. Through these approaches the influence of aspects such as fruit ripening, cultivation conditions, storage and shelf-life has been investigated and biochemical changes defined.
For example, metabolomics of melons revealed the three dimensional nature of fruit ripening in these large fruits (top to bottom/inside to outside). Analyses of strawberry ripening revealed the huge complexity of the process, which leads to a global reprogramming of the biochemical composition of the fruit within just a few days. The transition from green to white to red-ripe fruits is accompanied by dramatic changes (both in negative and positive senses) in a wide range of biochemical pathways enabling the conversion of an astringent hard tissue into the soft and fragrant one we like to eat. Never before have we had such a detailed insight into such complex processes.
Metabolomics and Fresh Produce: Vegetables
Potato and tomato are two of the world’s top four most important vegetable crops. Both are eaten in a wide variety of forms, either cooked (tomato and potato) or fresh (tomato). Both are also cultivated and eaten in most of the world’s countries where they often represent a significant component of the daily diet. In tomato research, metabolomics is already being used extensively to help identify which components are linked to key quality traits such as taste and flavor and how these are influenced by variety and cultivation conditions.
Results have already revealed the complexity of taste and how different varieties/fruit types differ biochemically. Through metabolomics approaches, combined with detailed sensory (taste panel) tests, biostatistical analyses of the complex data obtained is allowing us to slowly build up a picture of the molecular basis of tomato taste and how this influences consumer preference. With this knowledge we shall gain a better hold on how, in future, we can specifically tailor breeding programmes to improve tomato fruit quality and taste.
In potato, scientists have utilized metabolomics technologies to assess compositional differences in existing cultivars in relation to consumer quality. For example, the levels of key amino acids isoleucine, tyrosine and phenylalanine were found to be higher in certain cultivars under certain growth conditions. This is of considerable relevance as these amino acids have been associated with post cooking blackening, bruising as well as flavor after cooking. Seasonality has also been shown to greatly influence the biochemical profile of potato tubers, irrespective of variety.
Metabolomics and Processed Produce: Coffee and Tomato
Tomatoes are eaten in many cooked forms, often after undergoing extensive processing (for canning and the production of tomato puree). The influence of such processes on the biochemical composition is generally poorly understood and food processors often have few indicators as to how production might be improved in order to yield better quality products. Metabolomics analyses of the entire tomato puree production process have revealed several steps that heavily influence the final composition of the canned product. One step in particular was shown to result in extensive loss of antioxidants and this step should therefore become a main target in any strategy to improve the procedure. This could then lead to the production of a more nutritious/healthier product that also has an extended shelf life.
Coffee is another product that always undergoes extensive processing before ingestion. Metabolomics is being used in this vein to help understand the biochemical changes that occur between the farm and the factory where the beans eventually end roasting. Results have demonstrated that both strongly influence final bean quality and taste perception.
Where to Go From Here
While the technology is still under development, there are clearly many areas where the metabolomics is becoming firmly established. The small number of examples given in these articles emphasize the broad applicability of the approach. Huge amounts of data are being generated of relevance to crop and food applications, but only time will truly tell how important this information is and how readily it can be translated into biologically-relevant knowledge.
A current technological limitation is that while fantastic improvements in analytical equipment mean that we can now detect many more potentially important plant compounds than was ever possible before, we still do not know what most of them are or how they are synthesized by the plant. However, once we can successfully pair such individual compounds to key food or nutritional quality traits we can then use this to focus our efforts specifically on the identification of these biologically-relevant metabolites. In so doing, we shall continue to expand our knowledge of quality and nutrition/health related components in our food, which will lead to more targeted strategies for food quality improvement for the diets of both Western and developing countries—through targeted crop breeding approaches as well as the improved treatment of the harvested products.
*Acknowledgement: Both GKL and RDH kindly acknowledge financial support for this paper from the EU Framework VI project “Metabolomics for Plants, Health and OutReach,” or META-PHOR (No. FOOD-CT-2006-036296).
October 2006 marked the beginning of an EU-funded project called META-PHOR tasked with the following purpose: "To generate knowledge on those metabolites in our food which determine key characteristics such as nutritional value, quality and health by developing the advanced tools required for their detection. This knowledge will facilitate better monitoring of the food production chain and will create new opportunities for targeted strategies for breeding, storage and processing.”
This project united the activities of most of the main research groups in Europe dedicated to technology development and overcoming some of the main bottlenecks experienced with this new approach. Next to biochemical analyses, much emphasis was also placed on developing statistics, bioinformatics and software tools that are essential for success.
META-PHOR focused on three crops—broccoli, melon and rice (a vegetable, a grain and a fruit crop, each with their own technological challenges, see Table 1). However, the goals were to develop generic approaches applicable to all crops that would facilitate new strategies for food quality improvement, biofortification and nutrigenomics issues. Key chemical components linked to taste, flavor, nutritional value, etc., have been characterised and we now have a better understanding as to how metabolomics approaches can better be applied in an industrial context.
Table 1. A summary of the key groups of metabolites present in the crops chosen, which are linked to nutrition, health promoting effects and quality.
| Crop | Key Phytonutrients | Relevance | Profiling technology |
| Broccoli |
Phytosterols Glucosinolates Flavonoids Vitamins Folate |
Health applications Potentially anti-cancer Antioxidants/Health Nutritional value Health benefits |
GC-MS / NMR LC-MS / FT-MS / NMR LC-MS / FT-MS / NMR LC-PDA-MS NMR / LC-MS |
| Melon |
Isoprenoids Flavonoids Sugars Volatiles |
Antioxidants/Quality Antioxidants/Health Flavor/Taste Fragrance |
LC-PDA-MS LC-MS / FT-MS / NMR LC-MS / GC-MS GC-MS |
| Rice |
Micronutrients Volatiles Vitamins |
Nutritional value Quality/market value Nutritional value |
LC-ICP-MS GC-MS LCMS / GCMS |
GC-MS: Gas Chromatography-Mass Spectrometry; NMR: Nuclear Magnetic Resonance; LC-MS: Liquid Chromatography-Mass Spectrometry; FT-MS: Fourier Transform-Ion Cyclotron-Mass Spectrometry; LC-ICP-MS: Liquid Chromatography-Inductively Coupled Plasma-Mass Spectrometry.
Gerard Klein Essink, MSc, is managing director of Bridge2Food in The Netherlands, and Dr. Robert D. Hall is managing director of Centre for BioSystems Genomics CBSG2012, Plant Research International, also in The Netherlands.
