FDMine: a graph mining approach to predict and evaluate food-drug interactions

Food-drug interactions (FDIs) arise when nutritional dietary consumption regulates biochemical mechanisms involved in drug metabolism. Towards characterizing the nature of food’s influence on pharmacological treatment, it is essential to detect all possible FDIs. In this study, we propose FDMine, a novel systematic framework that models the FDI problem as a homogenous graph. In this graph, all nodes representing drug, food and food composition are referenced as chemical structures. This homogenous representation enables us to take advantage of reported drug-drug interactions for accuracy evaluation, especially when accessible ground truth for FDIs is lacking. Our dataset consists of 788 unique approved small molecule drugs with metabolism-related drug-drug interactions (DDIs) and 320 unique food items, composed of 563 unique compounds with 179 health effects. The potential number of interactions is 87,192 and 92,143 when two different versions of the graph referred to as disjoint and joint graphs are considered, respectively. We defined several similarity subnetworks comprising food-drug similarity (FDS), drug-drug similarity (DDS), and food-food similarity (FFS) networks, based on similarity profiles. A unique part of the graph is the encoding of the food composition as a set of nodes and calculating a content contribution score to re-weight the similarity links. To predict new FDI links, we applied the path category-based (path length 2 and 3) and neighborhood-based similarity-based link prediction algorithms. We calculated the precision@top (top 1%, 2%, and 5%) of the newly predicted links, the area under the receiver operating characteristic curve, and precision-recall curve. We have performed three types of evaluations to benchmark results using different types of interactions. The shortest path-based method has achieved a precision 84%, 60% and 40% for the top 1%, 2% and 5% of FDIs identified, respectively. We validated the top FDIs predicted using FDMine to demonstrate its applicability and we relate therapeutic anti-inflammatory effects of food items informed by FDIs. We hypothesize that the proposed framework can be used to gain new insights on FDIs. FDMine is publicly available to support clinicians and researchers.

Diet of Eastern Imperial Eagle (Aquila heliaca) in Bulgaria: composition, distribution and variation

The Eastern Imperial Eagle (EIE) is a top predator exploiting different prey in different parts of its distribution. In this study, we summarise data collected over a long period of time (for 25 consecutive years), identifying key prey species in the different regions, as well as clarifying seasonal preferences in the eagle’s diet. Most studies on the EIE food composition covering different parts of the species distribution range analyse the breeding season, while data about the winter diet are scarce. To the best of our knowledge, this is the first study detailing the differences in EIE’s dietary preferences between the breeding and the winter periods. We identified 4891 specimens belonging to 196 different taxa, which represents the most comprehensive study considering the diet diversity of this threatened species. Mammals represented the largest proportion of the diet, followed by birds and reptiles. Northern White-breasted Hedgehog was the most common prey, accounting for 25.7% of the total prey caught and 26.75% of the biomass. The European Souslik was the second most important prey with 14.35% participation in the eagle’s diet, but with a 3.75% contribution to the biomass. As we predicted, prey composition and main prey species varied spatially and seasonally. Modelling differences in the EIE diet, we found that the “territory effect” had the strongest impact on the dietary variations. Diet diversity differed significantly between regions (F = 12.6, df = 4, p = 0.01). During the breeding season, eagles fed mainly on Hedgehogs (29.88%), Sousliks (16.85%) and Storks (7.74%), while the winter diet was predominantly small rodents (44.17%) and songbirds (13.96%). We found that top predators, such as EIE, have successfully adapted to a novel food source, which is abundant in the area. The detected flexibility in the diet of the species and its ability to switch to alternative prey, if available, when the primary prey decreased, should be considered when planning species conservation efforts. Investigating the temporal change of the main prey in the eagle’s diet is also crucial for further species conservation measures.

Nutrition by Design: Boosting Selenium Content and Fresh Matter Yields of Salad Greens With Preharvest Light Intensity and Selenium Applications

Selenium (Se) is an essential mineral in multiple human metabolic pathways with immune modulatory effects on viral diseases including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and HIV. Plant-based foods contain Se metabolites with unique functionalities for the human metabolism. In order to assess the value of common salad greens as Se source, we conducted a survey of lettuce commercially grown in 15 locations across the USA and Canada and found a tendency for Se to accumulate higher (up to 10 times) in lettuce grown along the Colorado river basin region, where the highest amount of annual solar radiation of the country is recorded. In the same area, we evaluated the effect of sunlight reduction on the Se content of two species of arugula [Eruca sativa (E. sativa) cv. “Astro” and Diplotaxis tenuifolia (D. tenuifolia) cv. “Sylvetta”]. A 90% light reduction during the 7 days before harvest resulted in over one-third Se decline in D. tenuifolia. The effect of light intensity on yield and Se uptake of arugula microgreens was also examined under indoor controlled conditions. This included high intensity (HI) (160 μ mol−2 s−1 for 12 h/12 h light/dark); low intensity (LI) (70 μ mol m−2 s−1 for 12 h/12 h light/dark); and HI-UVA (12 h light of 160 μ mol m−2 s−1, 2 h UVA of 40 μ mol m−2 s−1, and 10 h dark) treatments in a factorial design with 0, 1, 5, and 10 ppm Se in the growing medium. HI and HI-UVA produced D. tenuifolia plants with 25–100% higher Se content than LI, particularly with the two higher Se doses. The addition of Se produced a marked increase in fresh matter (>35% in E. sativa and >45% in D. tenuifolia). This study (i) identifies evidence to suggest the revision of food composition databases to account for large Se variability, (ii) demonstrates the potential of introducing preharvest Se to optimize microgreen yields, and (iii) provides the controlled environment industry with key information to deliver salad greens with targeted Se contents.

Labelling Assessment of Greek “Quality Label” Prepacked Cheeses as the Basis for a Branded Food Composition Database

A labelling assessment study of Greek prepacked “quality label” cheeses was conducted with a view to provide an overview of the whole category. In total, 158 prepacked products belonging to 19 “quality label” cheeses were identified in the Greek market. Among them, Feta had the highest share followed by Kasseri, Graviera Kritis, Kefalograviera and Ladotyri Mitilinis with 81, 16, 15, 11 and 9 products found in the market, respectively. For the rest of the 14 cheeses, the share was limited, ranging from 1 to 4. All labelling indications, nutritional information, claims and other labelling data were recorded and analysed in relation to their compliance against European food law requirements. The results of the analysis showed that for only 6 of the 19 cheeses, all products fully complied with EU labelling legislation. Among the 14 mandatory labelling requirements, the lowest overall compliance was observed for allergens declaration (65%). The analysis of the nutritional data showed a remarkable variability between cheeses and products. Differences in the nutritional characteristics were more pronounced among soft, semi-hard, hard and whey cheese. The above data were entered into an archival database. Application of global harmonisation and standardisation guidelines and tools lead to the initialisation of a branded food composition database (BFCD), conceptualising a specialised database for “quality label” foods.

Use of Branded Food Composition Databases for the Exploitation of Food Fortification Practices: A Case Study on Vitamin D in the Slovenian Food Supply

Vitamin D deficiency is a worldwide public health concern, which can be addressed with voluntary or mandatory food fortification. The aim of this study was to determine if branded food composition databases can be used to investigate voluntary fortification practices. A case study was conducted using two nationally representative cross-sectional datasets of branded foods in Slovenia, collected in 2017 and 2020, and yearly sales data. Using food labeling data we investigated prevalence of fortification and average vitamin D content, while nutrient profiling was used to investigate overall nutritional quality of the foods. In both datasets, the highest prevalence of vitamin D fortification was observed in meal replacements (78% in 2017; 100% in 2020) and in margarine, corresponding to high market share. Other food categories commonly fortified with vitamin D are breakfast cereals (5% in 2017; 6% in 2020), yogurts and their imitates (5% in 2017; 4% in 2020), and baby foods (18% in both years). The highest declared average content of vitamin D was observed in margarine and foods for specific dietary use (7–8 μg/100g), followed by breakfast cereals (4 μg/100g), while the average content in other foods was below 2 μg/100g. Only minor differences were observed between 2017 and 2020. Major food-category differences were also observed in comparison of the overall nutritional quality of the fortified foods; higher overall nutritional quality was only observed in fortified margarine. Our study showed that branded food composition databases are extremely useful resources for the investigation and monitoring of fortification practices, particularly if sales data can also be used. In the absence of mandatory or recommended fortification in Slovenia, very few manufacturers decide to add vitamin D, and even when this is the case, such products are commonly niche foods with lower market shares. We observed exceptions in imported foods, which can be subject to fortification policies introduced in other countries.

Contribution of fortified margarines and other plant-based fats to micronutrient intake in the Netherlands

Purpose In the Netherlands, margarines and other plant-based fats (fortified fats) are encouraged to be fortified with vitamin A and D, by a covenant between the Ministry of Health and food manufacturers. Frequently, these types of fats are also voluntarily fortified with other micronutrients. The current study investigated the contribution of both encouraged as well as voluntary fortification of fortified fats on the micronutrient intakes in the Netherlands. Methods Data of the Dutch National Food Consumption Survey (2012–2016; N = 4, 314; 1–79 year.) and the Dutch Food Composition Database (NEVO version 2016) were used to estimate micronutrient intakes. Statistical Program to Assess Dietary Exposure (SPADE) was used to calculate habitual intakes and compared to dietary reference values, separate for users and non-users of fortified fats. Results Of the Dutch population, 84% could be considered as user of fortified fats. Users consumed mostly 1 fortified fat a day, and these fats contributed especially to the total micronutrient intake of the encouraged fortified micronutrients (vitamins D and A; 44% and 29%, respectively). The voluntary fortification also contributed to total micronutrient intakes: between 7 and 32%. Vitamin D and A intakes were up to almost double among users compared to non-users. Intakes were higher among users for almost all micronutrients voluntarily added to fats. Higher habitual intakes resulted into higher risks of excessive vitamin A-intakes among boys and adult women users. Conclusion Consumption of fortified fats in the Netherlands resulted into higher vitamin A and D-intakes among users, compared to non-users of these products.

Changes in the feeding behavior and habitat use of the desert hedgehog Paraechinus aethiopicus (Ehrenberg 1832, Eulipotyphla: Erinaceidae), in Saudi Arabia

Due to the urbanization and human invasion of the natural environments, great changes have been occurred on the food composition and feeding ecology of several animals especially those are sharing human his habitat in fields, wadis and gardens. The desert hedgehogs Paraechinus aethiopicus populations inhabiting different localities in Saudi Arabia were studied by using stomach contents analysis between February 2015 and October 2019. Precise analysis of stomach contents of 55 hedgehogs showed that the food of P. aethiopicus is highly diverse and highly influenced with effect of human on the environment including cooked rice, insects, plant materials, eggshells, worms, garbage and remnants of mammals and birds. Diet composition showed seasonal variations that are apparently associated with changes in the availability of different food items. The present results clearly showed that P. aethiopicus is an omnivorous mammal, capable of adapting to a great variety of dietary compositions in the study sites.

Nutrigenetics and nutrigenomics: A brief review with future prospects

Individual’s genetic makeup best describes the properties regarding its growth and development. It is stored and passed on to generations and is in dynamic equilibrium with the environmental and other non-living factors. The most predominant environmental stimuli are diet/nutrition. Diet/nutrition interacts and modulates varying underlying molecular mechanisms central to various physiological functions basically at three different levels: genome, proteome, and metabolome. Advances in genomic studies are paving the way to the development of scientific insights into nutritional sciences. Nutrigenetics and nutrigenomics are closely associated but two different areas of nutritional research. Both the fields involved the study of the implication between nutrition, metabolism, and genetic mechanism. The primary goal is to pinpoint nutrient-dependent health characteristics and nutrition dependent diseases. Another important area connected to these sciences concerns food composition and performance of quality assessment by studying proteomics and metabolic pathways. Nutrigenomics explains how the nutrients influences or effects the expression of the, while the response of different gene variants to nutrients or different dietary components is called Nutrigenetics. A personalized based diet can help us to know the right nutrient to take or avoid those who may potentially harm overall health. The goals are intended to alter or decrease the impact of hostile dietary changes that have occurred in since past in the developed world and more recently in the developing countries.

Effect of Tamarillo Fortification and Fermentation Process on Physicochemical Properties and Nutrient and Volatiles Content of Yoghurt

Bright-red Laird’s Large tamarillo is a unique and under-utilised fruit that is a dietary source of carotenoids, vitamins C and E, and dietary fibre. The effects of the addition of freeze-dried tamarillo powder (5–15%) to milk and yoghurt starter either before (PRE) or after (POS) fermentation on physicochemical properties were examined. Using LC-MS and GG-MS, nutrient and volatile contents of tamarillo yoghurt were also examined. The addition of tamarillo prior to fermentation was associated with a more yellow colour and higher concentrations of tocopherol compared to when tamarillo was added after fermentation. Higher elastic modulus, PUFAs, pro-vitamin A content, and vitamin C retention were observed for POS than PRE. All tamarillo yoghurts showed improvement in syneresis, lower lactose content, and higher concentrations of antioxidant vitamins than the commercial premium-assorted fruits yoghurt from New Zealand Food Composition Data. Yoghurt fortified with tamarillo powder offers the potential for the development of a high-value nutritional product that could be a good source of vitamin C and a source of vitamin E and β-carotene, and maintain the volatiles that give tamarillo its distinctive flavour.

Temporal Change in Iron Content of Vegetables and Legumes in Australia: A Scoping Review

Studies in UK and US have reported a temporal decline in the iron content of plant-based foods. Limited research on this topic has been conducted in Australia. The aim of this scoping review was to provide a comprehensive evaluation on the temporal change in iron content of Australian vegetables and legumes from 1900 onward. A systematic search of electronic databases, websites, backward reference searching, and Australian food composition tables was conducted. A total of 34 articles and six versions of Australian food composition databases published between 1930s to 2021, were included in this review. Overall, iron content of vegetables and legumes were assessed at limited time points and geographical origin, cultivars, sampling and analytical techniques varied across studies. The majority of vegetables had similar iron content between two or more timepoints but decreases of 30–50% were noted for sweet corn, red-skinned potatoes, cauliflower and green beans while increases of 150–300% were seen for Hass avocadoes, mushrooms and silverbeet. More pronounced reductions in iron content were observed for legumes, with higher and more variable values reported pre-2000 compared to recent years. Due to limited data and variations in sampling and analytical techniques, no definitive conclusions could be established. As plant-based diets are becoming more popular, consistent monitoring of the nutrient composition of staple plant-based foods is strongly recommended.