Data-driven analysis of biomedical literature suggests broad-spectrum benefits of culinary herbs and spices

DiMB-RE: mining the scientific literature for diet-microbiome associations

OBJECTIVES

To develop a corpus annotated for diet-microbiome associations from the biomedical literature and train natural language processing (NLP) models to identify these associations, thereby improving the understanding of their role in health and disease, and supporting personalized nutrition strategies.

MATERIALS AND METHODS

We constructed DiMB-RE, a comprehensive corpus annotated with 15 entity types (eg, Nutrient, Microorganism) and 13 relation types (eg, increases, improves) capturing diet-microbiome associations. We fine-tuned and evaluated state-of-the-art NLP models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. In addition, we benchmarked 2 generative large language models (GPT-4o-mini and GPT-4o) on a subset of the dataset in zero- and one-shot settings.

RESULTS

DiMB-RE consists of 14 450 entities and 4206 relationships from 165 publications (including 30 full-text Results sections). Fine-tuned NLP models performed reasonably well for named entity recognition (0.800 F1 score), while end-to-end relation extraction performance was modest (0.445 F1). The use of Results section annotations improved relation extraction. The impact of trigger detection was mixed. Generative models showed lower accuracy compared to fine-tuned models.

DISCUSSION

To our knowledge, DiMB-RE is the largest and most diverse corpus focusing on diet-microbiome interactions. Natural language processing models fine-tuned on DiMB-RE exhibit lower performance compared to similar corpora, highlighting the complexity of information extraction in this domain. Misclassified entities, missed triggers, and cross-sentence relations are the major sources of relation extraction errors.

CONCLUSION

DiMB-RE can serve as a benchmark corpus for biomedical literature mining. DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Suppression of the postprandial hyperglycemia in patients with type 2 diabetes by a raw medicinal herb powder is weakened when consumed in ordinary hard gelatin capsules: A randomized crossover clinical trial

INTRODUCTION

Contradictory claims about the efficacy of several medicinal plants to promote glycemic control in patients with type 2 diabetes mellitus (T2DM) have been explained by divergences in the administration form and by extrapolation of data obtained from healthy individuals. It is not known whether the antidiabetic effects of traditional herbal medicines are influenced by gelatin capsules. This randomized crossover trial aimed to evaluate the acute effect of a single dose of raw cinnamon consumed orally either dissolved in water as a beverage or as ordinary hard gelatin capsules on postprandial hyperglycemia (>140 mg/dL; >7.8 mmol/L) in T2DM patients elicited by a nutritionally-balanced meal providing 50 g of complex carbohydrates.

METHODS

Fasting T2DM patients (n = 19) randomly ingested a standardized meal in five experimental sessions, one alone (Control) and the other after prior intake of 3 or 6 g of crude cinnamon in the form of hard gelatin capsules or powder dissolved in water. Blood glucose was measured at fasting and at 0.25, 0.5, 0.75, 1, 1.5 and 2 hours postprandially. After each breakfast, its palatability scores for visual appeal, smell and pleasantness of taste were assessed, as well as the taste intensity sweetness, saltiness, bitterness, sourness and creaminess.

RESULTS

The intake of raw cinnamon dissolved in water, independently of the dose, decreased the meal-induced large glucose spike (peak-rise of +87 mg/dL and Δ1-hour glycemia of +79 mg/dL) and the hyperglycemic blood glucose peak. When cinnamon was taken as capsules, these anti-hyperglycemic effects were lost or significantly diminished. Raw cinnamon intake did not change time-to-peak or the 2-h post-meal glycaemia, but flattened the glycemic curve (lower iAUC) without changing the shape that is typical of T2DM patients.

CONCLUSIONS

This cinnamon's antihyperglycemic action confirms its acarbose-like property to inhibit the activities of the carbohydrate-digesting enzymes α-amylases/α-glucosidases, which is in accordance with its exceptionally high content of raw insoluble fiber. The efficacy of using raw cinnamon as a diabetes treatment strategy seems to require its intake at a specific time before/concomitantly the main hyperglycemic daily meals. Trial registration: Registro Brasileiro de Ensaios Clínicos (ReBEC), number RBR-98tx28b.

FoodAtlas: Automated knowledge extraction of food and chemicals from literature

Automated generation of knowledge graphs that accurately capture published information can help with knowledge organization and access, which have the potential to accelerate discovery and innovation. Here, we present an integrated pipeline to construct a large-scale knowledge graph using large language models in an active learning setting. We apply our pipeline to the association of raw food, ingredients, and chemicals, a domain that lacks such knowledge resources. By using an iterative active learning approach of 4120 manually curated premise-hypothesis pairs as training data for ten consecutive cycles, the entailment model extracted 230,848 food-chemical composition relationships from 155,260 scientific papers, with 106,082 (46.0 %) of them never been reported in any published database. To augment the knowledge incorporated in the knowledge graph, we further incorporated information from 5 external databases and ontology sources. We then applied a link prediction model to identify putative food-chemical relationships that were not part of the constructed knowledge graph. Validation of the 443 hypotheses generated by the link prediction model resulted in 355 new food-chemical relationships, while results show that the model score correlates well (R2 = 0.70) with the probability of a novel finding. This work demonstrates how automated learning from literature at scale can accelerate discovery and support practical applications through reproducible, evidence-based capture of latent interactions of diverse entities, such as food and chemicals.

Computational gastronomy: capturing culinary creativity by making food computable

Cooking, a quintessential creative pursuit, holds profound significance for individuals, communities, and civilizations. Food and cooking transcend mere sensory pleasure to influence nutrition and public health outcomes. Inextricably linked to culinary and cultural heritage, food systems play a pivotal role in sustainability and the survival of life on our planet. Computational Gastronomy is a novel approach for investigating food through a data-driven paradigm. It offers a systematic, rule-based understanding of culinary arts by scrutinizing recipes for taste, nutritional value, health implications, and environmental sustainability. Probing the art of cooking through the lens of computation will open up a new realm of possibilities for culinary creativity. Amidst the ongoing quest for imitating creativity through artificial intelligence, an interesting question would be, 'Can a machine think like a Chef?' Capturing the experience and creativity of a chef in an AI algorithm presents an exciting opportunity for generating a galaxy of hitherto unseen recipes with desirable culinary, flavor, nutrition, health, and carbon footprint profiles.

Curcumin-rich curry consumption and life expectancy: Singapore longitudinal ageing study

The therapeutic potential of curcumin for many diseases are intensively investigated. However, real-world observational data documenting health and longevity effects associated with dietary curcumin in turmeric from consuming curry in food is lacking. A prospective cohort study of 4551 adults aged 55 + assessed curry consumption (never or < once/year, ≥ once/year to < once/month, ≥ once/month to < once/week, ≥ once/week to < daily, ≥ once daily), prevalent health conditions, blood biomarker indexes of atherogenicity, insulin resistance, and inflammation at baseline, and mean (SD) 11.6 (3.8) year follow up of all-cause, CVS and cancer mortality. There were linear positive associations of increasing curry consumption with waist circumference, fasting blood glucose, TyG, AIP, CRI-1, CRI-2, central obesity and diabetes prevalence, and inverse association with eGFR. There were non-linear associations with FEV1/height2 and COPD prevalence, GDS score and depression, MMSE score and cognitive impairment, comorbidity count, serum albumin and haemoglobin, being most favourable with moderate consumption. The levels of NLR, PLR and SII indices of systemic and immune inflammation decreased linearly with curry consumption. Total mortality HR adjusted for baseline co-variables, decreased across curry consumption, 0.68 (95%CI 0.56-0.82), 0.54 (95%CI 0.43-0.69), 0.70 (0.52-0.93), and 0.62 (0.41-0.95), being lowest in the middle categories. Among participants with cardio-metabolic and vascular diseases (CMVD), at least occasional curry consumption was associated with decreased mortality risk by 39%, and increased life expectancy by 1.0 years. Among those without CMVD, the associated life expectancy increase was 1.9 years. Moderate curry consumption may confer meaningful longevity benefits.

Homo medicus: The transition to meat eating increased pathogen pressure and the use of pharmacological plants in Homo

The human lineage transitioned to a more carnivorous niche 2.6 mya and evolved a large body size and slower life history, which likely increased zoonotic pathogen pressure. Evidence for this increase includes increased zoonotic infections in modern hunter-gatherers and bushmeat hunters, exceptionally low stomach pH compared to other primates, and divergence in immune-related genes. These all point to change, and probably intensification, in the infectious disease environment of Homo compared to earlier hominins and other apes. At the same time, the brain, an organ in which immune responses are constrained, began to triple in size. We propose that the combination of increased zoonotic pathogen pressure and the challenges of defending a large brain and body from pathogens in a long-lived mammal, selected for intensification of the plant-based self-medication strategies already in place in apes and other primates. In support, there is evidence of medicinal plant use by hominins in the middle Paleolithic, and all cultures today have sophisticated, plant-based medical systems, add spices to food, and regularly consume psychoactive plant substances that are harmful to helminths and other pathogens. We propose that the computational challenges of discovering effective plant-based treatments, the consequent ability to consume more energy-rich animal foods, and the reduced reliance on energetically-costly immune responses helped select for increased cognitive abilities and unique exchange relationships in Homo. In the story of human evolution, which has long emphasized hunting skills, medical skills had an equal role to play.

Enhanced disease-disease association with information enriched disease representation

OBJECTIVE

Quantification of disease-disease association (DDA) enables the understanding of disease relationships for discovering disease progression and finding comorbidity. For effective DDA strength calculation, there is a need to address the main challenge of integration of various biomedical aspects of DDA is to obtain an information rich disease representation.

MATERIALS AND METHODS

An enhanced and integrated DDA framework is developed that integrates enriched literature-based with concept-based DDA representation. The literature component of the proposed framework uses PubMed abstracts and consists of improved neural network model that classifies DDAs for an enhanced literature-based DDA representation. Similarly, an ontology-based joint multi-source association embedding model is proposed in the ontology component using Disease Ontology (DO), UMLS, claims insurance, clinical notes etc. Results and Discussion: The obtained information rich disease representation is evaluated on different aspects of DDA datasets such as Gene, Variant, Gene Ontology (GO) and a human rated benchmark dataset. The DDA scores calculated using the proposed method achieved a high correlation mainly in gene-based dataset. The quantified scores also shown better correlation of 0.821, when evaluated on human rated 213 disease pairs. In addition, the generated disease representation is proved to have substantial effect on correlation of DDA scores for different categories of disease pairs.

CONCLUSION

The enhanced context and semantic DDA framework provides an enriched disease representation, resulting in high correlated results with different DDA datasets. We have also presented the biological interpretation of disease pairs. The developed framework can also be used for deriving the strength of other biomedical associations.

HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed abstracts

Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays ~ 146,000 studies on HLA reported from diverse locations. Currently, IPD-IMGT/HLA (Robinson et al., Nucleic Acids Research 48:D948-D955, 2019) database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from ~ 28 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 109 countries and 40 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URL http://hla-spread.igib.res.in/ . This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.

RecipeDB: a resource for exploring recipes

Cooking is the act of turning nature into the culture, which has enabled the advent of the omnivorous human diet. The cultural wisdom of processing raw ingredients into delicious dishes is embodied in their cuisines. Recipes thus are the cultural capsules that encode elaborate cooking protocols for evoking sensory satiation as well as providing nourishment. As we stand on the verge of an epidemic of diet-linked disorders, it is eminently important to investigate the culinary correlates of recipes to probe their association with sensory responses as well as consequences for nutrition and health. RecipeDB (https://cosylab.iiitd.edu.in/recipedb) is a structured compilation of recipes, ingredients and nutrition profiles interlinked with flavor profiles and health associations. The repertoire comprises of meticulous integration of 118 171 recipes from cuisines across the globe (6 continents, 26 geocultural regions and 74 countries), cooked using 268 processes (heat, cook, boil, simmer, bake, etc.), by blending over 20 262 diverse ingredients, which are further linked to their flavor molecules (FlavorDB), nutritional profiles (US Department of Agriculture) and empirical records of disease associations obtained from MEDLINE (DietRx). This resource is aimed at facilitating scientific explorations of the culinary space (recipe, ingredient, cooking processes/techniques, dietary styles, etc.) linked to taste (flavor profile) and health (nutrition and disease associations) attributes seeking for divergent applications. Database URL:  https://cosylab.iiitd.edu.in/recipedb.

Intake of Dietary Salicylates from Herbs and Spices among Adult Polish Omnivores and Vegans

There is a growing body of evidence that a diet rich in bioactive compounds from herbs and spices has the ability to reduce the risk of chronic diseases. The consumption of herbs and spices is often overlooked in the studies on food intake. However, measurement of dietary intake of these products, as a source of bioactive compounds, including salicylates, has recently gained much significance. The aims of the study were (i) to assess the intake of herbs and spices at the individual level and (ii) to calculate the dietary salicylates intake from herbs and spices among adult omnivores and vegans. The study group consisted of 270 adults aged 19 to 67 years, including 205 women and 65 men. Among all, 208 individuals were following an omnivorous diet while 62 were vegans. A semi-quantitative food frequency questionnaire (FFQ) was designed to assess the habitual intake of 61 fresh and dried herbs and spices during the preceding three months. The five most frequently eaten herbs among omnivores were parsley, garlic, dill, marjoram and basil, while among vegans they were garlic, parsley, ginger, basil and dill. An average intake of all condiments included in the study was 22.4 ± 18.4 g/day and 25.8 ± 25.9 g/day for both omnivores and vegans, respectively (p = 0.007). Estimated medial salicylates intake was significantly higher among vegans (p = 0.000) and reached 5.82 mg/week vs. 3.13 mg/week for omnivores. Our study confirmed that herbs and spices are important sources of salicylates; however, the type of diet influenced their level in the diet. Vegans consume significantly more total salicylates than omnivores.

Effect of Morning vs. Evening Turmeric Consumption on Urine Oxidative Stress Biomarkers in Obese, Middle-Aged Adults: A Feasibility Study

The circadian rhythm of biological systems is an important consideration in developing health interventions. The immune and oxidative defense systems exhibit circadian periodicity, with an anticipatory increase in activity coincident with the onset of the active period. Spice consumption is associated with enhanced oxidative defense. The objective of this study was to test the feasibility of a protocol, comparing the effects of morning vs. evening consumption of turmeric on urine markers of oxidative stress in obese, middle-aged adults. Using a within-sample design, participants received each of four clock time x treatment administrations, each separated by one week: morning turmeric; evening turmeric; morning control; evening control. Participants prepared for each lab visit by consuming a low-antioxidant diet for two days and fasting for 12 h. Urine was collected in the lab at baseline and one-hour post-meal and at home for the following five hours. The results showed that the processes were successful in executing the protocol and collecting the measurements and that participants understood and adhered to the instructions. The findings also revealed that the spice treatment did not elicit the expected antioxidant effect and that the six-hour post-treatment urine collection period did not detect differences in urine endpoints across treatments. This feasibility study revealed that modifications to the spice treatment and urine sampling timeline are needed before implementing a larger study.

Relative Validity of an Online Herb and Spice Consumption Questionnaire

Culinary herbs and spices contribute bioactives to the diet, which act to reduce systemic inflammation and associated disease. Investigating the health effects of herb/spice consumption is hampered, however, by a scarcity of dietary assessment tools designed to collect herb/spice data. The objective of this study was to determine the relative validity of an online 28-item herb/spices intake questionnaire (HSQ). In randomized order, 62 volunteers residing in Idaho, USA, completed the online Diet History Questionnaire III + the HSQ followed one week later by one of two comparative methods: 7-day food records or three telephone-administered 24-h dietary recalls. Relative validity of the HSQ was tested two ways: (1) by comparing herb/spice intakes between the HSQ and comparator, and (2) by determining the correlation between herb/spice data and Healthy Eating Index 2015 score. The HSQ and both comparators identified black pepper, cinnamon and garlic powder as the three most commonly used herbs/spices. The HSQ captured significantly higher measures of the number and amount of herbs/spices consumed than the comparators. The number of herbs/spices consumed was significantly directly correlated with diet quality for the HSQ. These results support the ability of the HSQ to record general herb/spice use, yet suggest that further validation testing is needed.

Changes in the Content of Phenolic Compounds and Biological Activity in Traditional Mexican Herbal Infusions with Different Drying Methods

Mexican spices are used in the supplementation of the human diet and as medicinal herbs for the particularly high amounts of compounds capable of deactivating free radicals. In addition, these spices can have beneficial effects on chronic, no-transmissible diseases such as type II diabetes and hypertension arterial. The objective of this study is to determine the content of phenolic compounds on the antioxidant activity and inhibitory enzymes of α-amylase, α-glucosidase and angiotensin-converting enzyme in melissa, peppermint, thyme and mint, which are subjected to microwave drying, conventional and freeze-drying to be used as alternative treatments. Spices were evaluated to determine total phenols, flavonoids, tannins, 2,2-Diphenyl-1-picrylhydrazyl (DPPH), (2,2'-azino-bis- (3-ethyl benzothiazolin-6-ammonium sulphonate) (ABTS) and Ferric Reducing/Antioxidant Power (FRAP), enzymatic activity. The investigation showed that conventional drying caused a decrease in antioxidant properties and inhibitory activity, in some species, while remained preserved in microwave drying and freeze-drying. The activity of polyphenol oxides and peroxidase decreases with high temperatures and these increase with the use of cold temperatures. This study aims to determine the extent of optimal drying required to preserve phenolic compounds, and the positive effect on antioxidant activity and enzymatic activity in in vitro models, which will produce benefits for the infusion processing industry and the pharmaceutical industry.

Utilization of text mining as a big data analysis tool for food science and nutrition

Big data analysis has found applications in many industries due to its ability to turn huge amounts of data into insights for informed business and operational decisions. Advanced data mining techniques have been applied in many sectors of supply chains in the food industry. However, the previous work has mainly focused on the analysis of instrument-generated data such as those from hyperspectral imaging, spectroscopy, and biometric receptors. The importance of digital text data in the food and nutrition has only recently gained attention due to advancements in big data analytics. The purpose of this review is to provide an overview of the data sources, computational methods, and applications of text data in the food industry. Text mining techniques such as word-level analysis (e.g., frequency analysis), word association analysis (e.g., network analysis), and advanced techniques (e.g., text classification, text clustering, topic modeling, information retrieval, and sentiment analysis) will be discussed. Applications of text data analysis will be illustrated with respect to food safety and food fraud surveillance, dietary pattern characterization, consumer-opinion mining, new-product development, food knowledge discovery, food supply-chain management, and online food services. The goal is to provide insights for intelligent decision-making to improve food production, food safety, and human nutrition.

The Potential for Plant-Based Diets to Promote Health Among Blacks Living in the United States

Plant-based diets are associated with reduced risks of various chronic diseases in the general population. However, it is unclear how these benefits translate to Blacks living in the United States, who are disproportionately burdened with heart disease, cancer, diabetes, obesity, and chronic kidney disease. The objectives of this study were to: (1) review the general evidence of plant-based diets and health outcomes; (2) discuss how this evidence translates to Blacks following a plant-based diet; and (3) provide recommendations and considerations for future studies in this area. Interestingly, although the evidence supporting plant-based diets in the general population is robust, little research has been done on Blacks specifically. However, the available data suggests that following a plant-based diet may reduce the risk of heart disease and possibly cancer in this population. More research is needed on cardiovascular disease risk factors, cancer subtypes, and other chronic diseases. Further, attention must be given to the unique individual, familial, communal, and environmental needs that Blacks who follow plant-based diets may have. Interventions must be culturally appropriate in order to achieve long-term success, and providing low-cost, flavorful, and nutritious options will be important.

Dietary salicylates in herbs and spices

The aim of this study was to determine dietary salicylate content in selected culinary herbs and spices, using the RP-HPLC method with fluorescence detection. The highest concentrations of salicylates were found in dried basil and cumin, followed by dried oregano and cloves. Our research contributes to the global database of salicylate content in food products.