The Department of Food Science researches the relationship between food production processes, the composition of food and human health through foodomics

Foodomics is a research discipline that examines the entire set of substances present in our food (foodome). The discipline uses advanced analytical platforms to investigate the composition of the food and thus, its nutritional properties and impact on health. The new techniques also provide a detailed picture of food quality and can be used to detect food fraud and to find solutions for other challenges in food production. Research results from foodomics have a direct impact on consumers, the food industry and society.

Picture of a gas chromatography instrument — Gas chromatography-mass spectrometry (GC-MS) instrument. The biggest workhorse in the Foodomics Laboratory for non-targeted analyses of food and bio-fluid samples. Photo: Lene Hundborg Koss.

Although foodomics is a relatively new research discipline, it is developing rapidly, and expectations are high. The hope is that foodomics will be an effective tool to develop healthy foods that are personalised to individual health challenges and prevent food-related diseases and food fraud. The research is also a key player in achieving more sustainable food production and is therefore expected to have a major impact on a circular economy in future.

We need to produce more – without sacrificing food safety

Limited natural resources including water, climate change and continuously decreasing agricultural areas are some of the global problems that challenge food production and supply for a growing population. The UN estimates a 60% rise in food demand as the world’s population reaches 9 billion by 2050. A high standard of living combined with an increasing population places great demands on the Earth’s resources, not least food and clean water, and will require a shift to much more sustainable food production. Food security, food safety and sustainable food production are therefore among the UN’s seventeen Sustainable Development Goals. Foodomics can play a role in achieving these goals.

Picture of the story of Foodomics — Foodomics. Illustration by Søren B. Engelsen and Tim Newlin ©

Foodomics can be used to detect food fraud and misreporting of food content

The quality and safety of food products are primary requirements. Comprehensive and unbiased screening of foodomes during production, from raw ingredients to the final products, is one of the most promising solutions to a global food safety and quality control. This is important as detection of unforeseen deviations in foods, for example extrinsic substances added to adulterate food or deleterious substances derived from production, is only possible using unbiased and untargeted analysis methods. Comprehensive fingerprinting of foodomes facilitates a bird’s-eye view of sustainable food production and its impact on food quality and safety. Foodomics also opens new possibilities to further optimise foods through understanding an impact of food production processes on the final product quality. It plays a key role in personalised nutrition and optimization of diet for groups of populations, for example elderly people.

Foodomics can reveal the impact of circular economy approaches on food quality

Foodomics is an important research discipline for addressing global food challenges in the 21^stcentury. We can use foodomics to examine what impact a new and more sustainable approach to food production will have on society. The development of unbiased, reproducible and rapid foodomics analysis approaches for comprehensive measurements of foodomes can provide an overview of sustainable food production and its impact on food quality, health and the environment. As the world moves towards sustainable food production by maximising reuse of process water and utilisation of waste streams, it is becoming increasingly difficult to detect unforeseen deviations in food production systems using traditional analytical approaches. This is mainly due to the lack of knowledge about persistent contaminants and deleterious substances in food and their origins as well as the lack of optimised standard operating procedures (SOPs) that allow rapid and accurate analysis of foods.

Documentation of foodomics approaches

The Foodomics Laboratory at the Department of Food Science is working to develop and implement foodomics approaches designed to improve our understanding of food, food production and the interaction between food and health. The development of highly standardised and optimised foodomics approaches requires in-depth knowledge of multidisciplinary research, including analytical chemistry, multivariate data analysis (chemometrics), design of experiment (DoE) and metabolomics. We aim to offer ready-to-use solutions – tools and protocols – to our collaborators whose primary expertise is not within foodomics. In addition to researchers at the University of Copenhagen and other institutions around the world, we work closely with the food industry.

Foodomics is a powerful tool in conjunction with other omics studies

Data generated in foodomics studies is often analysed along with data from other omics studies (e.g. genomics, transcriptomics, proteomics, metallomics, phenomics and metabolomics). The integration of foodomics with metabolomics has demonstrated a wide range of uses, including:

Molecular ‘fingerprints’ of food that make it possible to compare the normal state of a given food with a new version of the food and see whether it differs in terms of its nutritional properties and link them with food raw materials and ingredients coming into a food company. This allows early detection of any deviation that may occur during production which could create losses for the company and/or deteriorate food quality or safety
The influence of food processes on foodome, food quality and the nutritional value of food
Reinforcement of food safety
Food authentication and detection of food fraud
Development of healthy food
Reinforcement and development of sustainable food production
Human nutrition. Including how the human body treats nutritionally valuable and bioactive substances and deleterious compounds as well as understanding complex interactions between the foodome and the human gut microbiome

Main research areas at the Foodomics Laboratory

The multidisciplinary character of foodomics requires basic research in many different fields including several areas of chemistry (organic, inorganic and analytical chemistry), biology, physics and mathematics. The Foodomics Laboratory is one of the world’s leading research groups developing, optimising and implementing new methodologies and SOPs for foodomics research.

Development of protocols for sample preparation of biological matrices

In particular, we develop new sample preparation protocols (e.g. metabolite extractions for targeted analysis of few compounds of interest, profiling certain compound classes and untargeted analysis) for different food and food processing-related samples (process water, side streams and waste) as well as biological (e.g. blood, urine, faeces, muscle and adipose tissue) sample matrices to screen using hyphenated analytical platforms such as Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-Mass Spectrometry (LC-MS), and Nuclear Magnetic Resonance Spectrometry (NMR). We continuously invest time and resources for the optimisation of analytical protocols to achieve the highest possible reproducibility, sensitivity and specificity.

Improvement of data acquisition approaches

In addition, we conduct research on improving current data acquisition approaches used in metabolomics, employing NMR and GC-MS, and we are developing new SOPs for more robust, accurate and compatible data generation across laboratories. Our laboratory is one of the first in the world to implement the highly standardised and effective In Vitro Diagnostics (IVDr) methods developed by Bruker (a German manufacturer of NMR equipment and other analytical instruments), which, using 600 MHz proton-NMR spectroscopy, allows the simultaneous quantification of hundreds of metabolites from biological fluids.

Development and improvement of foodomics data pre-processing methods

The Foodomics Laboratory focuses on developing and improving multivariate data analysis-based algorithms to clean complex and raw foodomics and metabolomics datasets from non-sample related artefacts such as signal shifts, noise, baseline drifts and signal overlapping. The algorithm developed for chemical shift alignment in NMR spectroscopy (the Interval Correlation Optimised Shifting algorithm-icoshift is one of the products of our lab. In addition, the lab is conducting research to improve GC-MS and LC-MS data pre-processing methods (retention of time shift alignment, peak deconvolution and identification). One of the recent achievements in this field is the PARADISe software developed for processing the raw GS-MS data using a multi-way deconvolution technique called PARAFAC2. The main aim of these developments is to enable unbiased data conversion from the raw three-dimensional data (samples x retention time x mass spectra) to an informative metabolite table. The latest development of the lab is the SigMa (Signature Mapping) software, which is specifically designed to convert raw one-dimensional proton-NMR data of human bio-fluid samples into an informative metabolite table using set of advanced multivariate data analysis algorithms.

The Foodomics Laboratory is also a world leader in developing, improving and implementing multivariate data analysis algorithms applied in foodomics and metabolomics datasets to extract maximum information out of datasets. The lab is focused on developing and implementing advanced multivariate data analysis methods for solving specific problems in foodomics and metabolomics research.

Mapping of unknown parts of foodomes and metabolomes of biological sample matrices

In addition, our laboratory focuses on mapping unknown parts of the foodomes and metabolomes of biological sample matrices using modern analytical platforms and establishing a comprehensive library (database) of unambiguously identified new compounds. Together with plant scientists from the Department of Plant and Environmental Sciences (PLEN) at The Faculty of Science (SCIENCE), at the University of Copenhagen, we conduct various studies on different plants and plant-based foods to identify new and environmentally friendly biopesticides (saponins), screening of plant food waste products for high-value plant substances, structure elucidation of new plant metabolites using comprehensive 2D NMR experiments and investigation of health promoting plant-derived molecules. Currently, the Foodomics Laboratory is developing a comprehensive mass spectrometry library of unknown plant substances including triterpenoids, saponins, polyphenols, carbohydrates and other primary and secondary metabolites.

Foodomics facilities

The Foodomics Laboratory at the Department of Food Science at the University of Copenhagen is equipped with state-of-the-art analytical instruments that allow both comprehensive and high-throughput analyses. Due to the complex molecular composition of food samples, the analytical platforms must first and foremost be unbiased towards a variety of food sample matrices and molecular classes.

Analytical platforms at the Foodomics Laboratory

Three NMR spectrometers (400 MHz, 500 MHz and 600 MHz from Bruker)
Three GC-MS instruments
High Performance Liquid Chromatography-Ultraviolet/Visible Spectroscopy (HPLC-UV/VIS)
Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES)
Vibrational spectroscopy including Infrared (IR), Near-infrared (NIR) and Raman spectroscopy

These analytical platforms differ in their sensitivity and selectivity towards molecular classes as well as by their high-throughput capacity, but in combination these platforms allow holistic evaluation of molecular perturbations in foods and plants.

Picture of an NMR instrument — The NMR spectroscopy facility at the Foodomics Laboratory. Three high field NMR instruments (600 MHz, 500 MHz, and 400 MHz magnets) are the main platforms for high-throughput analysis of foods, bio-fluids and solid samples. Photo: Bekzod Khakimov

Analytical measurements performed at the Foodomics Laboratory

Profiling of lipoprotein particle distribution in blood samples following the standardised IVDr approach using 600 MHz proton-NMR spectroscopy
Profiling of blood and urine metabolomes following the standardised IVDr approach using 600 MHz proton-NMR spectroscopy
Untargeted high-throughput GC-TOF-MS based metabolome analysis of blood, urine and faecal samples
Short chain fatty acid profiling of blood and faecal samples using single quadrupole GC-MS
Bile acid profiling of blood and faecal samples using single quadrupole GC-MS
Untargeted foodome analysis of beverages (e.g. wine, whisky, beer, juices) using GC-TOF-MS, LC-MS and NMR
Untargeted foodome analysis of cereals using GC-TOF-MS and NMR
Untargeted foodome analysis of fruit, berries, vegetables and nuts using GC-TOF-MS and NMR
Untargeted foodome analysis of plant tissues using GC-TOF-MS and NMR
Metabolite profiling of selected classes of compounds including polyphenols, triterpenoids, fatty acids, amino acids and organic acids from plant and food samples using targeted sample preparation followed by single quadrupole GC-MS, GC-TOF-MS, and NMR
Purification of unknown substances from complex sample matrices using LC-UV/VIS-Automatic Fraction Collector and structure elucidation by means of mass spectrometry and one- and two-dimensional NMR spectroscopy
Rapid spectroscopic measurement (quality control) of plant and food samples using vibrational spectroscopic techniques including Infrared (IR), Near-infrared (NIR) and Raman

Collaborations

The Foodomics Laboratory is the central analytical facility at the Department of Food Science at the University of Copenhagen and closely collaborates with all other sections at UCPH FOOD. It provides qualitative and quantitative foodomics data and helps researchers to design their studies to ensure appropriate experimental design and analysis of mega-variate foodomics datasets using advanced multivariate data analysis methods. The Foodomics Laboratory also works closely with several research groups at the Department of Plant and Environmental Science (KU-PLEN). The laboratory plays a key role in supplying analysis for various research projects at the University of Copenhagen. At PLEN this includes untargeted foodome/metabolome analysis, profiling of agro-economically important plant substances (e.g. saponins) as well as structure elucidation of new plant substances of interest.

In addition, the Foodomics Laboratory collaborates with analytical staff members at the Metabolomics Platforms section at the Copenhagen Plant Science Center (CPSC). The Foodomics Laboratory has one of the largest capacities at the University of Copenhagen for screening the foodome (e.g. plant-based food, beverages, meat and meat products) and the metabolome of biological systems such as blood, urine, muscle tissue, faeces, etc. Therefore, the lab has a central role in several intervention studies conducted together with researchers from the Department of Nutrition, Exercise and Sports (KU-NEXS), as well as with doctors and veterinarians at the Faculty of Health and Medical Sciences (KU-SUND). Studies that are related food and feed production process optimisation are generally conducted in collaboration with the Danish and international food industries, such as Arla Foods, Carlsberg, Unilever and Chr. Hansen.

Collaborations with the food industry and other related industries, including the biotech industry: