Application of metabolomics for revealing the interventional effects of functional foods on metabolic diseases

Data on the cytotoxicity of chlorogenic acid in 3D cultures of HT-29 cells

Functional foods, beyond basic nutrition, offer health benefits to consumers thanks to the presence of bioactive compounds such as some phytochemicals [1,2]. Today, these foods are of particular interest in biomedical research due to their chemopreventive potential, as they have been shown to induce various biological effects on tumor cells, including the ability to inhibit cell proliferation, induce apoptosis, arrest cell cycle progression, and increase reactive oxygen species [3,4]. Multiple studies have confirmed the relationship between diet and the onset and progression of colorectal cancer (CRC), a malignant neoplasm that arises in the lining of the colon and/or rectum. Therefore, finding foods that can intervene in the carcinogenesis process is an important avenue of research [5,6]. Chlorogenic acid (CGA) is one of the most abundant phenolic compounds in coffee and is also found in fruits and vegetables. Scientific evidence suggests that CGA has chemopreventive potential on CRC cells [7], [8], [9]. For example, in previous studies conducted by our research group, green and roasted coffee extracts were characterized, and this compound was identified as the most abundant [7]. In addition, it was found to significantly decrease cell viability, reduce migration capacity, cause DNA fragmentation, and induce the production of reactive oxygen species in colorectal adenocarcinoma cells cultured in monolayer and treated with different doses of CGA. Furthermore, the mechanism underlying this biological activity has been related to CGA's ability to modulate the Wnt- /β-catenin pathway, which is implicated in the development and progression of CRC [7,10,11]. This paper presents data on the cytotoxic response of CGA treatments on HT-29 cells cultured in a 3D model. To this end, morphological changes in cell spheroids, propidium iodide and DiOC6 uptake, quantification of reactive oxygen species (ROS) production, phosphatidylserine exposure, and cell cycle progression were evaluated by flow cytometry.

LC-MS based metabolomics analysis of okara fermented by Bacillus subtilis DC-15: Insights into nutritional and functional profile

Recent studies emphasize the improved nutritional and functional status of fermented okara; however, little is known about the metabolite change during fermentation and how it alters metabolic pathways. A metabolomics approach based on untargeted LC-MS reveals metabolic changes in okara fermented by Bacillus subtilis DC-15. We identified 761 differential metabolites, with the highest abundances found in amino acids, dipeptides, fatty acids, small molecule sugars, and vitamins. Moreover, these identified metabolites were mapped to their respective biosynthesis pathways in order to gain a better understanding of the biochemical reactions triggered by fermentation. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, 485 metabolites were enriched to metabolism-related pathways. They include 37 carbohydrate metabolites, 79 amino acid metabolites, and 22 lipid metabolites. As a result of okara fermentation, we observed a gradual enrichment of metabolites and stabilization of the compounds.

Antioxidant capacity and cytotoxic effect of an optimized extract of isabella grape (Vitis labrusca) on breast cancer cells

The phenolic profile of Isabella grape (Vitis labrusca) offers beneficial properties to human health and makes it a functional food product. In order to better understand the phenolic compounds found in this grape variety and the biological effect they induce on breast cancer cells, an ultrasound-assisted extraction was carried out. During the extraction of polyphenols from Isabella grapes organically grown in Antioquia (Colombia), parameters such as frequency (33 kHz and 40 kHz), time and solvent were optimized to finally obtain a crude extract with antioxidant properties (Oxygen Radical Absorbance Capacity, ORAC: 293.22 ± 34.73 μmol of Trolox/g of sample), associated with a total polyphenol content (TPC) of 43.14 ± 5.00 mg GAE/g sample and a total anthocyanin content composed of 17.69 ± 2.59 mg of malvidin-3-glucoside/100 g of sample. MCF-7 breast cancer cells were treated with different concentrations of the optimized extract, and results show a decrease in cell viability related to mitochondrial membrane depolarization, ROS increase, and chromatin condensation. To determine the possible death induction mechanism, molecular docking was simulated to predict the molecular interactions between the most abundant phenolic compounds in Isabella grape and the main apoptosis-related proteins. The results obtained from in silico and in vitro experiments were consistent with each other, suggesting that the phenolic compounds found in Isabella grape can be considered potential adjuvant chemopreventive agents for the treatment of breast cancer.

Untargeted GC-MS and FT-NIR study of the effect of 14 processing methods on the volatile components of Polygonatum kingianum

Introduction

Polygonatum kingianum is a traditional medicinal plant, and processing has significantly impacts its quality.

Methods

Therefore, untargeted gas chromatography-mass spectrometry (GC-MS) and Fourier transform-near-infrared spectroscopy (FT-NIR) were used to analyze the 14 processing methods commonly used in the Chinese market.It is dedicated to analyzing the causes of major volatile metabolite changes and identifying signature volatile components for each processing method.

Results

The untargeted GC-MS technique identified a total of 333 metabolites. The relative content accounted for sugars (43%), acids (20%), amino acids (18%), nucleotides (6%), and esters (3%). The multiple steaming and roasting samples contained more sugars, nucleotides, esters and flavonoids but fewer amino acids. The sugars are predominantly monosaccharides or small molecular sugars, mainly due to polysaccharides depolymerization. The heat treatment reduces the amino acid content significantly, and the multiple steaming and roasting methods are not conducive to accumulating amino acids. The multiple steaming and roasting samples showed significant differences, as seen from principal component analysis (PCA) and hierarchical cluster analysis (HCA) based on GC-MS and FT-NIR. The partial least squares discriminant analysis (PLS-DA) based on FT-NIR can achieve 96.43% identification rate for the processed samples.

Discussion

This study can provide some references and options for consumers, producers, and researchers.

Processing technologies, phytochemistry, bioactivities and applications of black ginseng-a novel manufactured ginseng product: A comprehensive review

Black ginseng is a novel manufactured ginseng product, and the application of black ginseng products in market is increasing in recent years. Black ginseng is prepared by steaming and fermentation, but not as mature as processing red ginseng. Therefore, complete proposals for preparation techniques are firstly presented. Additionally, there are also abundant chemical components in black ginseng, including ginsenosides, polysaccharides, amino acids, polyphenols, flavonoids, etc. Among them, ginsenosides, polysaccharides and phenolic compounds are the main ingredients, making health benefits of black ginseng stronger than other ginseng products. Therefore, black ginseng as a functional food has come to the market in various forms, such as candies, tea, porridge, soup, etc. The improvement in nutrition, flavor, and safety has exhibited a broad prospect for black ginseng products in food industry. Accordingly, preparation technologies, phytochemistry, health benefits and application of black ginseng are comprehensively evaluated.

Ganoderma lucidum: Novel Insight into Hepatoprotective Potential with Mechanisms of Action

Ganoderma lucidum (G. lucidum) has been widely used for its health benefits as an edible and traditional medicinal mushroom for thousands of years in Asian countries. It is currently used as a nutraceutical and functional food owing to its major bioactive compounds, polysaccharides and triterpenoids. G. lucidum exhibits a broad range of hepatoprotective impacts in various liver disorders, such as hepatic cancer, nonalcoholic fatty liver disease (NAFLD), alcohol-induced liver disease, hepatitis B, hepatic fibrosis, and liver injury induced by carbon tetrachloride (CCl4) and α-amanitin. G. lucidum protects the liver through a broad range of mechanisms that include the modulation of liver Phase I and II enzymes, the suppression of β-glucuronidase, antifibrotic and antiviral actions, the regulation of the production of nitric oxide (NO), the maintenance of hepatocellular calcium homeostasis, immunomodulatory activity, and scavenging free radicals. G. lucidum could signify an encouraging approach for the management of various chronic hepatopathies, and its potential mechanisms make it a distinctive agent when used alone or with other drugs and applied as a functional food, nutraceutical supplement, or adjuvant to modern medicine. This review summarizes the hepatoprotective properties of G. lucidum with its various mechanisms of action on different liver ailments. Biologically active substances derived from G. lucidum are still being studied for their potential benefits in treating different liver ailments.

Comparative phytochemical analysis of Ferula assa-foetida with Ferula jaeschkeana and commercial oleo-gum resins using GC-MS and UHPLC-PDA-QTOF-IMS

Ferula assa-foetida is an important species of the genus Ferula, best known for its oleo-gum resin, mainly used as a flavoring agent. Ferula jaeschkeana is another Himalayan medicinal plant of this genus, known for its contraceptive effect but not used in food applications. This study aimed to do a detailed phytochemical analysis of F. assa-foetida growing under controlled conditions in India using GC-MS/headspace and UHPLC-PDA-QTOF-IMS. Further, a comparative analysis of F. assa-foetida was performed with F. jaeschkeana (collected from its natural habitat) and commercial samples of F. assa-foetida oleo-gum resin (collected from the local market). UHPLC-QTOF-IMS profiling of F. assa-foetida led to the identification of foetisulfide C, assafoetidnol A, gumosin, flabellilobin (A/B), and foetisulfide A. In total, 141 metabolites were identified, including vitamins, nucleosides, sulfur compounds, flavonoids, sugars derivatives, and others, using METLIN database. Serine, arginine, asparagine, isoleucine, and phenylalanine were major amino acids quantified among the samples for the nutritional aspect. Characteristic sulfurous compounds (n-propyl-sec-butyl disulfide, trans-propenyl-sec-butyl disulfide, cis-propenyl-sec-butyl disulfide, and bis[1-(methylthio)propyl] disulfide) were identified in all samples except F. jaeschkeana. PCA and cluster analysis showed a significant difference in the volatile constituents of rhizomes of both species. Metabolomics studies also revealed the association of sesquiterpenoid and triterpenoid biosynthesis, phenylpropanoid, flavon, and flavanol biosynthesis. The current study demonstrates, "why only F. assa-foetida is used in culinary applications instead of F. jaeschkeana"?

Metabolomics during the spontaneous fermentation in cocoa (Theobroma cacao L.): An exploraty review

Spontaneous fermentation is a process that depends on substrates' physical characteristics, crop variety, and postharvest practices; it induces variations in the metabolites that are responsible for the taste, aroma, and quality. Metabolomics makes it possible to detect key metabolites using chemometrics and makes it possible to establish patterns or identify biomarker behaviors under certain conditions at a given time. Therefore, sensitive and highly efficient analytical techniques allow for studying the metabolomic fingerprint changes during fermentation; which identify and quantify metabolites related to taste and aroma formation of an adequate processing time. This review shows that studying metabolomics in spontaneous fermentation permits the characterization of spontaneous fermentation in different stages. Also, it demonstrates the possibility of modulating the quality of cocoa by improving the spontaneous fermentation time (because of volatile aromatic compounds formation), thus standardizing the process to obtain attributes and quality that will later impact the chocolate quality.

Quantitative metabolome analysis of boiled chicken egg yolk

Boiling has important effects on the texture of chicken eggs, but its effects on egg nutrients have not been systematically investigated. In this study, changes in the metabolites of egg yolks boiled under different heating intensities were quantified and compared by metabolomic analysis. A total of 797 metabolites were identified, and the abundance of 162 metabolites changed significantly after boiling. The significant reduction of L-lysine and D-fructose suggested that Maillard reactions occurred in over-boiled egg yolks. Egg yolk endogenous enzymes might induce a partial hydrolysis of proteins and phospholipids during the warm-up period of boiling, as the abundance of dipeptides, lysophospholipids, and free fatty acids was significantly increased in boiled egg yolks. Boiling increased the detectable abundance of fat-soluble vitamins, riboflavin, and biotin, possibly by altering the complex structure of protein-lipid-lipophilic compounds or denaturing vitamin-binding proteins. The results of metabolomic analyses provide important information for understanding the nutritional changes of egg yolk boiled under different heating intensities.

Integrative analyses of widely targeted metabolomic profiling and derivatization-based LC-MS/MS reveals metabolic changes of Zingiberis Rhizoma and its processed products

Zingiberis Rhizoma (ZR) has nutritional value and application potentiality, while Zingiberis Rhizoma Praeparatum (ZRP) and Carbonised Ginger (CG) are two main processed products of ZR based on different methods. Here, we performed a widely targeted metabolomics method with Sequential Windowed Acquisition of all Theoretical fragment ions (SWATH) mode to analyze differential metabolites in ZR, ZRP and CG. Additionally, the chemical derivatization was applied to characterize different submetabolomes and improve the separation effect and MS response of metabolites. In total, 369 metabolites were identified and divided into 14 categories, 104 of which were differential metabolites. Our results suggest that carbohydrates, nucleotides, organic acids, vitamins, lipids, indoles, alkaloids, and terpenes contributed to a downward trend after processing, but the maximum content of flavanones, phenylpropanes and polyphenols appeared in ZRP, and that of alcohols appeared in CG. These findings serve as promising perspectives for developing functional food in ZR, ZRP and CG.

The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota

In the present study, we assembled and analyzed the mitogenomes of two Ramaria species. The assembled mitogenomes of Ramaria cfr. rubripermanens and R. rubella were circularized, with sizes of 126,497 bp and 143,271 bp, respectively. Comparative mitogenome analysis showed that intron region contributed the most (contribution rate, 43.74%) to the size variations of Ramaria mitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the two Ramaria mitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) in Phallomycetidae mitogenomes varied. We detected large-scale gene rearrangements between Phallomycetidae mitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes of R. cfr. rubripermanens and R. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events in Phallomycetidae mitogenomes during the evolution, and the mitogenomes of R. rubella contained a novel intron P44. Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. This study served as the first report on mitogenomes from the genus Ramaria, which provides a basis for understanding the evolution, genetics, and taxonomy of this important fungal group.

A Study on Glycyrrhiza glabra-Fortified Bread: Predicted Glycemic Index and Bioactive Component

Bread is one of the highest-selling food products throughout the world. Lots of demand arose from the bread producers by the consumers to convert the traditional bread into functional food. In this study, normal bread was converted to functional herbal bread by infusing it with extracts of Glycyrrhiza glabra. The functional components of the Glycyrrhiza glabra were analyzed by liquid chromatography-mass spectroscopy (LCMS). The antioxidant study revealed that the extract has high antioxidant potency. The present study also investigated the antidiabetic potency of the extract. Bread is fortified with various percentages of Glycyrrhiza glabra, such as 2, 4, and 6. The fortified bread was analyzed for various sensory and taste parameters. Biochemical assays such as the in vitro digestibility test and glycaemic index suggest that fortified bread reduces the glycaemic index. From the study, it was inferred that 6% of infused bread was found to have high potency as a functional food when compared to 2 and 4%. From the above study, it was suggested that fortified bread reduces the glycaemic index and is best suited for diabetic people and diet watchers.

Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function

Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.

DNAzyme-based biosensors for mercury (Ⅱ) detection: Rational construction, advances and perspectives

Mercury contamination is one of the most severe issues in society due to its threats to public health and the ecological system. However, traditional methods for mercury ion detection are still limited by their time-consuming procedures, requirement of expensive instruments, and low selectivity. In recent decades, tremendous progress has been made in the development of functional nucleic acid-based, especially DNAzyme sensors for mercury (Ⅱ) (Hg²⁺) determination, including RNA-cleaving DNAzymes and G-quadruplex-based DNAzymes in particular. Researchers have heavily studied the construction of Hg²⁺ sensors, mainly originating from in vitro selection-derived DNAzymes, by incorporating T-Hg²⁺-T recognition moieties in existing DNAzyme scaffolds, and interfacing Hg²⁺-sensitive sequences with nanomaterials. In the last case, the employment of materials (as quenchers, signal transducers and DNA immobilizers) enriches the application scenarios of current Hg²⁺-DNAzymes, due to a combination of their functions. We summarize a broad range of sensing approaches, including optical, electrochemical, and other sensing methods, and compare their features. This review elaborates on the rational design strategies for engineering DNAzymes to selectively sense Hg²⁺, critically discusses their properties in different application scenarios, and summarizes recent advances in this field. Additionally, current progress, challenges and future perspectives are also discussed. This minireview provides deeper insights into the chemistry of these functional nucleic acids when working with Hg²⁺, explains the design ideas of DNAzyme-sensors in each platform, and reveals potential opportunities in developing more advanced DNAzyme sensors for the highly selective and sensitive recognition of Hg²⁺. ENVIRONMENTAL IMPLICATION: Mercury is one of the most toxic metallic contaminants due to its high toxicity, non-biodegradability, and serious human health risks when accumulated in the body. In the recent decade, intensive studies have focused on exploring mercury sensors by combining DNAzymes with various sensing methods, paving a promising avenue to gain ultra-high sensitivity and selectivity. However, so far, no review has introduced the recent advances on DNAzyme-based sensors for mercury detection in a critical way. In this review, we comprehensively summarized the studies on DNAzyme-based sensors for mercury detection using various sensing techniques including optical, electrochemical and other sensing methods.

Metabolomics as a valid analytical technique in environmental exposure research: application and progress

BACKGROUND

In recent years, studies have shown that exposure to environmental pollutants (e.g., radiation, heavy metal substances, air pollutants, organic pollutants) is a leading cause of human non-communicable diseases. The key to disease prevention is to clarify the harmful mechanisms and toxic effects of environmental pollutants on the body. Metabolomics is a high-sensitivity, high-throughput omics technology that can obtain detailed metabolite information of an organism. It is a crucial tool for gaining a comprehensive understanding of the pathway network regulation mechanism of the organism. Its application is widespread in many research fields such as environmental exposure assessment, medicine, systems biology, and biomarker discovery.

AIM OF REVIEW

Recent findings show that metabolomics can be used to obtain molecular snapshots of organisms after environmental exposure, to help understand the interaction between environmental exposure and organisms, and to identify potential biomarkers and biological mechanisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review focuses on the application of metabolomics to understand the biological effects of radiation, heavy metals, air pollution, and persistent organic pollutants exposure, and examines some potential biomarkers and toxicity mechanisms.

Recent Advances in Utilizing Omics Approach to Identify the Bioactive Peptides and Ripening Metabolism in Plant-based Food

Abstract:

Bioactive peptides with potential health benefits and metabolic functionality have been identified from plant-based food. The aim of this perspective is to report the recent progress in the research of plant-derived bioactive peptides using the combination of omics technologies and bioinformatics tools. Studies examining bioactive peptides with identified amino acid sequences and well-characterized biological functionalities are highlighted. Various software, webtools and workflows for analyzing and interpreting the biological data acquired from different omics approaches are discussed. The emerging evidence from the integration of proteomics and metabolomics data with advanced laboratory analytical methods supports more potential applications in the envisioned development of nutraceutical and therapeutic products. Notwithstanding, much works are mandatory to resolve those lied-ahead challenges before realizing the proposed applications of plant peptides.

The Acute Effect of a Novel Miso-Type Sauce, Enhanced with a Carotenoid-Rich Extract from Fruit By-Products, on Postprandial Biomarkers of Oxidative Stress and Inflammation

Several fruit by-products may exert a beneficial role on oxidative stress and inflammation modulation, providing essential bioactive components, such as polyphenols and carotenoids. Recently, the potential bioactivity of miso has been reported. The aim of this dietary intervention−clinical study was to evaluate the acute effect of a novel, functional miso-type sauce based on legumes, on postprandial biomarkers of oxidative stress and inflammation. In this randomized, cross-over design, intervention−clinical trial, 14 healthy volunteers, aged 20−30 years old, consumed a rice meal rich in fat and carbohydrates (258 g), containing a legume-based sauce. After a 1-week washout period, the same subjects consumed the same meal, containing the novel fermented miso-type sauce, enhanced with 50% carotenoid-rich, fruit peel extract. Differences in postprandial total plasma antioxidant capacity according to the FRAP method, serum lipids, glucose, uric acid levels, and antithrombotic activity in platelet-rich plasma were evaluated before, 30 min, 1.5 h, and 3 h after consumption. The results showed that, in comparison to the control group, consumption of the novel sauce resulted in a significantly increased total plasma antioxidant capacity 3 h after consumption (p < 0.05). In addition, we observed a significant attenuation of triglycerides concentration increase in the last 1.5 h in the functional group (p < 0.05). A significant decrease in serum aggregation was found at 30 min and 3 h after functional sauce intake in comparison with the baseline (p < 0.05). Finally, LDL-cholesterol concentrations were significantly reduced 3 h after the functional meal consumption, in comparison with baseline values (p < 0.05). The remaining biomarkers did not show statistically significant differences (p > 0.05). Further investigation is needed in order to validate the current results.

Triterpenoid ursolic acid drives metabolic rewiring and epigenetic reprogramming in treatment/prevention of human prostate cancer

Ursolic acid (UA) is a triterpenoid phytochemical with a strong anticancer effect. The metabolic rewiring, epigenetic reprogramming, and chemopreventive effect of UA in prostate cancer (PCa) remain unknown. Herein, we investigated the efficacy of UA in PCa xenograft, and its biological effects on cellular metabolism, DNA methylation, and transcriptomic using multi-omics approaches. The metabolomics was quantified by liquid-chromatography-mass spectrometry (LC-MS) while epigenomic CpG methylation in parallel with transcriptomic gene expression was studied by next-generation sequencing technologies. UA administration attenuated the growth of transplanted human VCaP-Luc cells in immunodeficient mice. UA regulated several cellular metabolites and metabolism-related signaling pathways including S-adenosylmethionine (SAM), methionine, glucose 6-phosphate, CDP-choline, phosphatidylcholine biosynthesis, glycolysis, and nucleotide sugars metabolism. RNA-seq analyses revealed UA regulated several signaling pathways, including CXCR4 signaling, cancer metastasis signaling, and NRF2-mediated oxidative stress response. Epigenetic reprogramming study with DNA Methyl-seq uncovered a list of differentially methylated regions (DMRs) associated with UA treatment. Transcriptome-DNA methylome correlative analysis uncovered a list of genes, of which changes in gene expression correlated with the promoter CpG methylation status. Altogether, our results suggest that UA regulates metabolic rewiring of metabolism including SAM potentially driving epigenetic CpG methylation reprogramming, and transcriptomic signaling resulting in the overall anticancer chemopreventive effect.

Metabolomics-based evidence of the hypoglycemic effect and alleviation of diabetic complications by Ficus racemosa fruit in diabetic mice

The hypoglycemic and metabolic effects of Ficus racemosa fruit were studied in diabetic mice, and its potential mechanisms of hypoglycemic activity and its alleviation of diabetic complications were explored using...