Bioinformatics and data knowledge: the new frontiers for nutrition and foods

Machine learning models to predict micronutrient profile in food after processing

The information on nutritional profile of cooked foods is important to both food manufacturers and consumers, and a major challenge to obtaining precise information is the inherent variation in composition across biological samples of any given raw ingredient. The ideal solution would address precision and generability, but the current solutions are limited in their capabilities; analytical methods are too costly to scale, retention-factor based methods are scalable but approximate, and kinetic models are bespoke to a food and nutrient. We provide an alternate solution that predicts the micronutrient profile in cooked food from the raw food composition, and for multiple foods. The prediction model is trained on an existing food composition dataset and has a 31% lower error on average (across all foods, processes and nutrients) than predictions obtained using the baseline method of retention-factors. Our results argue that data scaling and transformation prior to training the models is important to mitigate any yield bias. This study demonstrates the potential of machine learning methods over current solutions, and additionally provides guidance for the future generation of food composition data, specifically for sampling approach, data quality checks, and data representation standards.

Personalized Nutrition and -Omics

With change in global concern toward food quality over food quantity, consumer concern and choice of healthy food has become a matter of prime importance. It gave rise to concept of “personalized or precision nutrition”. The theory behind personalization of nutrition is supported by multiple factors including advances in food analytics, nutrition based diseases and public health programs, increasing use of information technology in nutrition science, concept of gene-diet interaction and growing consumer capacity or concern by better and healthy foods. The advances in “omics” tools and related analytical techniques have resulted into tremendous scope of their application in nutrition science. As a consequence, a better understanding of underlying interaction between diet and individual is expected with addressing of key challenges for successful implementation of this science. In this chapter, the above aspects are discussed to get an insight into driving factors for increasing concern in personalized nutrition.

Analysis of Domains in Selected Plant and Animal Food Proteins - Precursors of Biologically Active Peptides - In Silico Approach

In silico methods are useful tool in protein structure-functional relationships analysis. BIOPEP and InterPro databases were applied to analyze the presence of bioactive fragments in the domains occurring in the sequences representing the major groups of proteins. Domains found in the proteins analyzed had mostly transporting (bovine β-lactoglobulin), immunoglobulin-like (chicken connectin), alpha-amylase inhibitor (a/β-wheat gliadin), calcium binding (chicken myosin) functions, or allowed straightly to assign the protein to an appropriate superfamily (bovine casein). It confirmed the thesis about the existence of the functional relations between the structure (sequence) and the domains with identified conformation. Amongst the domains present in the protein sequences we revealed the presence of fragments with the activities: antihypertensive, opioid, dipeptidylpeptidase IV inhibitors, immunomodulating, and neuropeptides. In the chicken connectin within the immunoglobulin-like domain we found immunomodulating fragments. InterPro analysis did not reveal the existence of any domains in a soybean globulin. It can be explained by the lack of the key structure information helpful in the defining the structure-function relationships. As the number of information in the applied databases will continue to increase we can expect to find stronger relationships between bioactivity of fragments encrypted in proteins and the functionality of domains. This might allow in the future to find evolutionary similarity between different origin food proteins - sources of bioactive peptides.

Polyphasic characterization of the lactic acid bacteria in kefir

The lactic acid bacteria of kefir were isolated and characterized using phenotypical, biochemical, and genotypical methods. Polyphasic analyses of results permitted the identification of the microflora to the strain level. The genus Lactobacillus was represented by the species Lb. kefir and Lb. kefiranofaciens. Both subspecies of Lactococcus lactis (lactis and cremoris) were isolated. Leuconostoc mesenteroides subsp. cremoris was also found. The kefir studied contained few species of lactic acid bacteria but showed a high number of different strains. We found that the polyphasic analysis approach increases the confidence in strain determination. It helped confirm strain groupings and it showed that it could have an impact on the phylogeny of the strains.

Nutrigenomics: The Impact of Biomics Technology on Nutrition Research

The interaction between the human body and nutrition is an extremely complex process involving multi-organ physiology with molecular mechanisms on all levels of regulation (genes, gene expression, proteins, metabolites). Only with the recent technology push have nutritional scientists been able to address this complexity. Both the challenges and promises that are offered by the merge of 'biomics' technologies and mechanistic nutrition research are huge, but will eventually evolve in a new nutrition research concept: nutritional systems biology. This review describes the principles and technologies involved in this merge. Using nutrition research examples, including gene expression modulation by carbohydrates and fatty acids, this review discusses applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, and systems biology. Furthermore, reference is made to gene polymorphisms that underlie individual differences in nutrient utilization, resulting in, e.g., different susceptibility to develop obesity.

Functional Foods: A Survey of Health Claims, Pros and Cons, and Current Legislation

Functional foods stand for a new category of remarkably promising foods bearing properties (i.e., low cholesterol, antioxidant, anti-aging, anticancer, etc.) that have already rendered them quite appealing. There are many classes offunctionalfoods (pro- and pre-biotics, dietary fiber, low fat, etc.), and their definition is occasionally confused with that of nutraceuticals and novel foods. Consumers' main skepticism regarding functional foods resides in the veracity of health claims and in the low and often inadequate control of their claimed properties. Legislation concerning this matter is progressing at an extremely low pace and currently only Japan, the U.K., U.S.A., and Scandinavian countries have managed to make notable progress. Moreover, the labeling of functional foods is far from informative, providing scanty information about nutritional value, storage, and cooking recipes. It is anticipated that technological advances in the food industry, in conjunction with extensive clinical trials and governmental control, will eventually guarantee the credibility of health claims and ensure consumers' confidence in functional foods.

Genome data mining of lactic acid bacteria: the impact of bioinformatics

Lactic acid bacteria (LAB) have been widely used in food fermentations and, more recently, as probiotics in health-promoting food products. Genome sequencing and functional genomics studies of a variety of LAB are now rapidly providing insights into their diversity and evolution and revealing the molecular basis for important traits such as flavor formation, sugar metabolism, stress response, adaptation and interactions. Bioinformatics plays a key role in handling, integrating and analyzing the flood of 'omics' data being generated. Reconstruction of metabolic potential using bioinformatics tools and databases, followed by targeted experimental verification and exploration of the metabolic and regulatory network properties, are the present challenges that should lead to improved exploitation of these versatile food bacteria.

Towards a systems biology understanding of human health: Interplay between genotype, environment and nutrition

Sequencing of the human genome has opened the door to the most exciting new era for the holistic system description of human health. It is now possible to study the underlying mechanisms of human health in relation to diet and other environmental factors such as drugs and toxic pollutants. Technological advances make it feasible to envisage that in the future personalized drug treatment and dietary advice and possibly tailored food products can be used for promoting optimal health on an individual basis, in relation to genotype and lifestyle. Life-Science research has in the past very much focused on diseases and how to reestablish human health after illness. Today, the role of food and nutrition in human health and especially prevention of illness is gaining recognition. Diseases of modern civilization, such as diabetes, heart disease and cancer have been shown to be effected by dietary patterns. The risk of disease is often associated with genetic polymorphisms, but the effect is dependent on dietary intake and nutritional status. To understand the link between diet and health, nutritional-research must cover a broad range of areas, from the molecular level to whole body studies. Therefore it provides an excellent example of integrative biology requiring a systems biology approach. The current state and implications of systems biology in the understanding of human health are reviewed. It becomes clear that a complete mechanistic description of the human organism is not yet possible. However, recent advances in systems biology provide a trajectory for future research in order to improve health of individuals and populations. Disease prevention through personalized nutrition will become more important as the obvious avenue of research in life sciences and more focus will need to be put upon those natural ways of disease prevention. In particular, the new discipline of nutrigenomics, which investigates how nutrients interact with humans, taking predetermined genetic factors into account, will mediate new insights into human health that will finally have significant positive impact on our quality of life.

Determinants of nutritional behaviour: a multitude of levers for successful intervention?

Nutritional behaviour is framed by biological, anthropological, economic, psychological, socio-cultural, and home economics related determinants and it is shaped by the individual situation. From a public health point of view, the outcome is often unsatisfactory, because it is associated with preventable cases of various diseases. This situation evoked the founding of the German Association for Nutritional Behaviour (Arbeitsgemeinschaft Ernährungsverhalten, AGEV) which celebrated its 25th anniversary within the scope of the 10th Food Choice Conference in the summer of 2002 with a plenary session on 'Sensible policies for nutrition and life-style intervention'. One might assume that the many determinants of nutritional behaviour provide a whole set of means to intervene into people's food choices. But closer deliberations make clear that there are two important aspects that tend to hinder dietary changes: on the one hand, nutritional behaviour is characterized by many conflicts of its related determinants. In order to cope with them, people develop individual guiding strategies for food choice situations which are quite stable as soon as they proved their suitability. On the other hand, any dietary modification leads to certain gains (like increased health), but losses, as well (like decreased palatability). Thus, a sustainable change can only be expected, if its gains are evaluated higher than its losses. These aspects need to be carefully considered when designing nutrition and life-style related intervention concepts.

Impact of nutrition behaviour research on nutrition programmes and nutrition policy

Development of a society is interrelated with research. Innovation in food and nutritional sciences enable citizens to live in conditions of food security. Current dietary goals can be reached by understanding the biopsychosocial background of human nutrition behaviour. Examples of diffusion of such findings into practice are presented with emphasis on Germany and the activities of AGEV (the Working Association of Nutritional Behaviour), which was founded 25 years ago. Nutrition behaviour research should strengthen the focus on practical applications of its findings, since the prevalence of nutrition-related problems, like obesity in children and the estrangement on food and nutrition, is increasing.

Transcending reductionism in nutrition research

The reductionist approach has traditionally been and continues today as the dominant approach in nutrition research. This means that parts of diet rather than the whole, or single food components rather than food habits, are studied. Even though much progress has been made with this approach, the relationship between diet and health is not yet fully understood. With the recognition about the whole being more than the sum of its parts, the limitations on the applicability of the reductionist approach, and the growing knowledge about parts of diet, another epistemological approach, such as holism, and new research strategies, such as transdisciplinarity, are needed to reveal more about the relationship between diet and health.