Nutri-informatics: a new kid on the block?

Abstract

From an epistemological point of view, nutritional physiology has been developed, like other factual sciences such as physics, from a purely descriptive to a mechanismic-explanatory scientific discipline. Nowadays, nutritional physiology has entered the molecular stage. Based on this micro-reductionism, molecular targets (e.g., transcription factors) of energy intake, certain nutrients (e.g., zinc) and selected plant bioactives (e.g., flavonoids) have been identified. Although these results are impressive, molecular approaches in nutritional physiology are limited by nature since the molecular targets of nutrients seem to have no ontic priority to understand the nutritional phenotype of an organism. Here we define, to the best of our knowledge, for the first time Nutri-informatics as a new bioinformatics discipline integrating large-scale data sets from nutritional studies into a stringent nutritional systems biology context. We suggest that Nutri-informatics, as an emerging field, may bridge the gap between nutritional biochemistry, nutritional physiology and metabolism to understand the interactions between an organism and its environment.Keywords Micro-reductionism Á Nutrigenomics Á Nutritional systems biology Á Nutri-informatics Based on a view from history of science, it is interesting to note that factual sciences such as physics, biology and psychology have developed through the stages of statics, kinematics and dynamics (Bunge 2004). For nutritional physiology (Fig. 1), a similar trend from a purely descriptive to mechanismic 1 -explanatory scientific discipline can be recognized (Strohle and Doring 2010). For example, in the stages of statics (''What is there?'') and kinematics (''How does it change?''), nutritional physiologists identified the essentials components of our diet and answered the question, how the status of nutrients may change as function of intake. On this basis, robust dietary recommendations were made for many nutrients. In the stage of dynamics (''Why does it change?''), the physiological and biochemical functions of the nutrients were unraveled. During the last two decades, nutritional physiology has entered a molecular stage (''What is the molecular mechanism?''). This kind of micro-reductionism has contributed to a deeper understanding of nutritional processes. For example, pioneering work on vitamin A as transcription factor ligands has been published for more than 20 years (Chambon 1996). More recently, by applying gene chip technology, we and others have identified molecular targets differentially regulated by dietary restriction (Giller et al. 2013), vitamins (Fischer et al. 2001, trace elements (Fischer et al. 2001;tom Dieck et al. 2003), and plant bioactives (Boomgaarden et al. 2010). Notably, dietary factors do not only regulate gene expression on the mRNA, but also on the micro-RNA level (Boesch-Saadatmandi et al. 2011;Gaedicke et al. 2008).

Zinc proteome interaction network as a model to identify nutrient-affected pathways in human pathologies

“…Interactome models have been increasingly used, especially proteinprotein interaction (PPI) networks which provide an abstraction of the complex relationships among different molecular components-spanning from nutrients and their metabolites to diet-modulated transcription factors (Nguyen et al 2011). Nutritional systems biology has a tremendous potential to provide comprehensive predictions of nutrient dyshomeostasis in biological processes (Doring and Rimbach 2014). Zinc, being involved in such a large number of protein activities, is an ideal micronutrient to be studied in an integrated framework.…”

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

“…The term ‘nutri-informatics’ describes approaches to understand the interactions between an organism and its nutritional environment via bioinformatics-based integration of nutrition study data sets ( 1 ). Nutri-informatics aims to computationally integrate and analyze nutrition study data sets in order to disentangle the interactions between an organism and its nutritional environment.…”

Mechanistic Network Models in Safety and Toxicity Evaluation of Nutraceuticals

“…Furthermore, even small differences in experimental design can have large impacts on the expression of a particular gene or protein, which can lead to discrepancies in the results obtained in different studies (Doring and Rimbach, 2014). Omics technologies such as transcriptomics can generate a vast amount of information, but it is challenging to extract the relevant biological information from these data in a direct manner.…”