Postprandial plasma and whole blood amino acids are largely indicative of dietary amino acids in adult dogs consuming diets with increasing whole pulse ingredient inclusion.

BACKGROUND: Pulse ingredients often replace grains in grain-free dog diets due to their high protein content. However, research to ascertain the benefit of this modification is limited. OBJECTIVE: To correlate food compounds in one corn-inclusive control diet (Ctl) and three grain-free diets with increasing inclusions of whole pulses (up to 45%; Pulse15, Pulse30, Pulse45), formulated to meet similar macro and micronutrient targets with postprandial amino acids (AA) in healthy dogs over 20-weeks. METHODS: Diets were analyzed for biochemical compounds using tandem-MS. Twenty-eight outdoor-housed, healthy, adult Siberian Huskies were allocated to diet and meal responses took place at baseline and weeks 2, 4, 8, 16 and 20 with samples collected at fasted and 15, 30, 60, 90, 120 and 180 minutes after meal presentation. Blood AAs were analyzed by UPLC and differences across week, treatment and time post-meal were analyzed in SAS Studio. Partial least squares regression was performed in SAS Studio using biochemical compounds in the diet as predictor variables and blood AAs as response variables. RESULTS: In plasma, Pulse45 had ∼32% greater postprandial Asn compared to Pulse15, and Ctl had ∼34% greater postprandial Leu and ∼35% greater Pro compared to Pulse15 (P < 0.05). In whole blood, Pulse30 had ∼23% greater postprandial Lys compared to Ctl, and Ctl had ∼21% greater postprandial Met and ∼18% greater Pro compared to Pulse45 and Pulse30, respectively (P < 0.05). Several phospholipids were correlated with postprandial AAs. Compounds in the 'urea cycle' and 'glycine and serine metabolism' were more enriched (P < 0.05) in plasma and whole blood, respectively. CONCLUSIONS: In macro and micronutrient balanced canine diets that differ in their inclusion of corn- versus pulse-derived ingredients, postprandial changes in circulating AAs are largely indicative of the dietary AAs. This helps further our understanding of AA metabolism in healthy dogs fed grain-free diets.

Multi Omics Applications in Biological Systems.

Traditional methodologies often fall short in addressing the complexity of biological systems. In this regard, system biology omics have brought invaluable tools for conducting comprehensive analysis. Current sequencing capabilities have revolutionized genetics and genomics studies, as well as the characterization of transcriptional profiling and dynamics of several species and sample types. Biological systems experience complex biochemical processes involving thousands of molecules. These processes occur at different levels that can be studied using mass spectrometry-based (MS-based) analysis, enabling high-throughput proteomics, glycoproteomics, glycomics, metabolomics, and lipidomics analysis. Here, we present the most up-to-date techniques utilized in the completion of omics analysis. Additionally, we include some interesting examples of the applicability of multi omics to a variety of biological systems.

Untargeted foodomics for authenticating the organic farming of water spinach (Ipomoea aquatica).

This study aimed to conduct a comprehensive analysis of the primary and secondary metabolites of water spinach (Ipomoea aquatica) using hydrophilic interaction liquid chromatography coupled with Orbitrap high-resolution mass spectrometry (HILIC-Orbitrap-HRMS). Certified samples from two cultivars, Green stem water spinach (G) and White stem water spinach (W) cultivated using organic and conventional farming methods, were collected from the Hong Kong market. Multivariate analysis was used to differentiate water spinach of different cultivars and farming methods. We identified 12 metabolites to distinguish between G and W, 26 metabolites to identify G from organic farming and 8 metabolites to identify W from organic farming. Then, two metabolites, isorhamnetin and jasmonic acid, have been proposed to serve as biomarkers for organic farming (in both G and W). Our foodomics findings provide useful tools for improving the crop performance of water spinach under abiotic/biotic stressesand authentication of organic produce.

Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider.

Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.

Microwave-Assisted Extraction/UHPLC-Q-Orbitrap-MS-Based Lipidomic Workflow for Comprehensive Study of Lipids in Soft Cheese.

In this work, Microwave-Assisted Extraction (MAE) was proposed as an alternative and environmentally friendly technique in lipidomics to study the lipid fingerprint of soft cheeses, such as mozzarella. For method development, a first step concerning an evaluation of extraction solvents was carried out via testing three different mixtures, including methanol/ethyl acetate, isopropanol/ethyl acetate, and ethanol/ethyl acetate, at a 1:2 v/v ratio. The latter was chosen as a solvent mixture for subsequent method optimization. MAE conditions, in terms of solvent volume, time, and temperature, were explored to define their effects on extraction capability through a full factorial experimental design. The best compromise to extract more lipids at the same time was obtained with 24 mL g-1 for solvent-to-solid ratio, 65 °C for temperature, and 18 min for time. Lipid analyses were conducted by UHPLC-Q-Orbitrap-MS associated with multivariate statistics. The developed lipidomic workflow allowed for the extraction of over 400 lipids grouped into 18 different subclasses. The results confirmed that MAE is a suitable technique for lipid extraction in the omics approach with high efficiency, even using low-cost and less toxic solvents. Moreover, a comprehensive structure characterization of extracted lipids, in terms of fatty acid composition and regiochemistry, was carried out.

Untargeted metabolomics and machine learning unveil quality and authenticity interactions in grated Parmigiano Reggiano PDO cheese.

The chemical composition of Parmigiano Reggiano (PR) hard cheese can be significantly affected by different factors across the dairy supply chain, including ripening, altimetric zone, and rind inclusion levels in grated hard cheeses. The present study proposes an untargeted metabolomics approach combined with machine learning chemometrics to evaluate the combined effect of these three critical parameters. Specifically, ripening was found to exert a pivotal role in defining the signature of PR cheeses, with amino acids and lipid derivatives that exhibited their role as key discriminant compounds. In parallel, a random forest classifier was used to predict the rind inclusion levels (> 18%) in grated cheeses and to authenticate the specific effect of altimetry dairy production, achieving a high prediction ability in both model performances (i.e., ∼60% and > 90%, respectively). Overall, these results open a novel perspective to identifying quality and authenticity markers metabolites in cheese.

MS based foodomics: An edge tool integrated metabolomics and proteomics for food science.

Foodomics has become a popular methodology in food science studies. Mass spectrometry (MS) based metabolomics and proteomics analysis played indispensable roles in foodomics research. So far, several methodologies have been developed to detect the metabolites and proteins in diets and consumers, including sample preparation, MS data acquisition, annotation and interpretation. Moreover, multiomics analysis integrated metabolomics and proteomics have received considerable attentions in the field of food safety and nutrition, because of more comprehensive and deeply. In this context, we intended to review the emerging strategies and their applications in MS-based foodomics, as well as future challenges and trends. The principle and application of multiomics were also discussed, such as the optimization of data acquisition, development of analysis algorithm and exploration of systems biology.

mini-MED: study protocol for a randomized, multi-intervention, semi-controlled feeding trial of a Mediterranean-amplified vs. habitual Western dietary pattern for the evaluation of food-specific compounds and cardiometabolic health.

BACKGROUND: Diet is among the most influential lifestyle factors impacting chronic disease risk. Nutrimetabolomics, the application of metabolomics to nutrition research, allows for the detection of food-specific compounds (FSCs) that can be used to connect dietary patterns, such as a Mediterranean-style (MED) diet, to health. This validation study is based upon analyses from a controlled feeding MED intervention, where our team identified FSCs from eight foods that can be detected in biospecimens after consumption and may therefore serve as food intake biomarkers. METHODS: Individuals with overweight/obesity who do not habitually consume a MED dietary pattern will complete a 16-week randomized, multi-intervention, semi-controlled feeding study of isocaloric dietary interventions: (1) MED-amplified dietary pattern, containing 500 kcal/day from eight MED target foods: avocado, basil, cherry, chickpea, oat, red bell pepper, walnut, and a protein source (alternating between salmon or unprocessed, lean beef), and (2) habitual/Western dietary pattern, containing 500 kcal/day from six non-MED target foods: cheesecake, chocolate frozen yogurt, refined grain bread, sour cream, white potato, and unprocessed, lean beef. After a 2-week washout, participants complete four, 4-week intervention periods, with biospecimen sampling and outcome assessments at baseline and at intervention weeks 4, 8, 12, and 16. The primary outcome is change in the relative abundance of FSCs from the eight MED target foods in participant biospecimens from baseline to the end of each intervention period. Secondary outcomes include mean change in cardiometabolic health indicators, inflammatory markers, and adipokines. Exploratory outcomes include change in diversity and community composition of the gut microbiota. DISCUSSION: Our stepwise strategy, beginning with identification of FSCs in whole diets and biospecimens, followed by relating these to health indicators will lead to improved methodology for assessment of dietary patterns and a better understanding of the relationship between food and health. This study will serve as a first step toward validating candidate food intake biomarkers and allow for assessment of relationships with cardiometabolic health. The identification of food intake biomarkers is critical to future research and has implications spanning health promotion and disease prevention for many chronic conditions. TRIAL REGISTRATION: Registered at ClinicalTrials.gov: NCT05500976 ; Date of registration: August 15, 2022.

Multiple and Optimal Screening Subset: a method selecting global characteristic congeners for robust foodomics analysis.

Metabolomics and foodomics shed light on the molecular processes within living organisms and the complex food composition by leveraging sophisticated analytical techniques to systematically analyze the vast array of molecular features. The traditional feature-picking method often results in arbitrary selections of the model, feature ranking, and cut-off, which may lead to suboptimal results. Thus, a Multiple and Optimal Screening Subset (MOSS) approach was developed in this study to achieve a balance between a minimal number of predictors and high predictive accuracy during statistical model setup. The MOSS approach compares five commonly used models in the context of food matrix analysis, specifically bourbons. These models include Student's t-test, receiver operating characteristic curve, partial least squares-discriminant analysis (PLS-DA), random forests, and support vector machines. The approach employs cross-validation to identify promising subset feature candidates that contribute to food characteristic classification. It then determines the optimal subset size by comparing it to the corresponding top-ranked features. Finally, it selects the optimal feature subset by traversing all possible feature candidate combinations. By utilizing MOSS approach to analyze 1406 mass spectral features from a collection of 122 bourbon samples, we were able to generate a subset of features for bourbon age prediction with 88% accuracy. Additionally, MOSS increased the area under the curve performance of sweetness prediction to 0.898 with only four predictors compared with the top-ranked four features at 0.681 based on the PLS-DA model. Overall, we demonstrated that MOSS provides an efficient and effective approach for selecting optimal features compared with other frequently utilized methods.

Milk and Its Derivatives as Sources of Components and Microorganisms with Health-Promoting Properties: Probiotics and Bioactive Peptides.

Milk is a source of many valuable nutrients, including minerals, vitamins and proteins, with an important role in adult health. Milk and dairy products naturally containing or with added probiotics have healthy functional food properties. Indeed, probiotic microorganisms, which beneficially affect the host by improving the intestinal microbial balance, are recognized to affect the immune response and other important biological functions. In addition to macronutrients and micronutrients, biologically active peptides (BPAs) have been identified within the amino acid sequences of native milk proteins; hydrolytic reactions, such as those catalyzed by digestive enzymes, result in their release. BPAs directly influence numerous biological pathways evoking behavioral, gastrointestinal, hormonal, immunological, neurological, and nutritional responses. The addition of BPAs to food products or application in drug development could improve consumer health and provide therapeutic strategies for the treatment or prevention of diseases. Herein, we review the scientific literature on probiotics, BPAs in milk and dairy products, with special attention to milk from minor species (buffalo, sheep, camel, yak, donkey, etc.); safety assessment will be also taken into consideration. Finally, recent advances in foodomics to unveil the probiotic role in human health and discover novel active peptide sequences will also be provided.

Changes in Plasma, Urine, and Fecal Metabolome after 16 Weeks of Consuming Dairy With Different Food Matrixes - A Randomized Controlled Trial.

SCOPE: Understanding the mode-of-action by which fermented dairy consumption influences health is of interest. The aim of this study is to elucidate the impact of the chemical-physical properties of the dairy matrix and postbiotic effects on the metabolomics response to fermented dairy consumption. METHODS AND RESULTS: Hundred males (Body Mass Index (BMI) 28.0-45.0 kg m-2, waist circumference ≥ 102 cm) are included in the study. During a 16-week intervention, the study subjects are instructed to consume 400 g per day of either 1) milk, 2) yogurt, 3) heat-treated yogurt, or 4) chemically acidified milk as part of their habitual diet. Nuclear Magnetic Resonance (NMR)-based metabolomics is conducted on plasma, urine, and fecal samples collected before and after the intervention. Both consumption of acidified milk and heat-treated yogurt resulted in changes in the fecal metabolome including decreases in the level of amino acids (leucine, valine, and threonine), and the branched-chain fatty acid (BCFA) isobutyrate that indicated an altered protein putrefaction, and proteolytic metabolism in the gut. In the plasma metabolome, an increased citrate is found for yogurt consumption. No difference in the urine metabolome is found. CONCLUSIONS: Our metabolomics analyses indicate that consumption of heat-treated yogurt and acidified milk exerted similar effects on the metabolic activity in the gut as yogurt consumption.

New Implications of Metabolites and Free Fatty Acids in Quality Control of Crossbred Wagyu Beef during Wet Aging Cold Storage.

Efficient cold-chain delivery is essential for maintaining a sustainable global food supply. This study used metabolomic analysis to examine meat quality changes during the "wet aging" of crossbred Wagyu beef during cold storage. The longissimus thoracic (Loin) and adductor muscles (Round) of hybrid Wagyu beef, a cross between the Japanese Black and Holstein-Friesian breeds, were packaged in vacuum film and refrigerated for up to 40 days. Sensory evaluation indicated an increase in the umami and kokumi taste owing to wet aging. Comprehensive analysis using gas chromatography-mass spectrometry identified metabolite changes during wet aging. In the Loin, 94 metabolites increased, and 24 decreased; in the Round, 91 increased and 18 decreased. Metabolites contributing to the umami taste of the meat showed different profiles during wet aging. Glutamic acid increased in a cold storage-dependent manner, whereas creatinine and inosinic acid degraded rapidly even during cold storage. In terms of lipids, wet aging led to an increase in free fatty acids. In particular, linoleic acid, a polyunsaturated fatty acid, increased significantly among the free fatty acids. These results provide new insight into the effects of wet aging on Wagyu-type beef, emphasizing the role of free amino acids, organic acids, and free fatty acids generated during cold storage.

Maillard reaction products and metabolite profile of plant-based meat burgers compared with traditional meat burgers and cooking-induced alterations.

We are undergoing a food transformation with the introduction of plant-based meat analogues, but little is known about their chemical characteristics. This study aimed to elucidate the Maillard reactions in plant-based meat burger alternatives (PBMBA). For this purpose, NMR-based metabolomics and targeted MS analysis of Maillard and dehydroalanine pathway markers were conducted on six PBMBA prototypes with different proportions of high-moisture protein extrudates, low-moisture extrudates and pea protein on a commercial PBMBA and on a meat burger before and after cooking. Results revealed that higher levels of Maillard reaction markers were present in PBMBAs in the uncooked state, with lower levels formed during cooking compared with conventional meat. The metabolite profile disclosed that the distinct pattern of the Maillard reaction could be attributed to different substrate availability, but data also revealed that pre-processing of the plant protein affects the presence of Maillard reaction products in PBMBAs.

Development and validation of a classification model for boar taint detection in pork fat samples.

This study aims to characterize a complete volatile organic compound profile of pork neck fat for boar taint prediction. The objectives are to identify specific compounds related to boar taint and to develop a classification model. In addition to the well-known androstenone, skatole and indole, 10 other features were found to be discriminant according to untargeted volatolomic analyses were conducted on 129 samples using HS-SPME-GC×GC-TOFMS. To select the odor-positive samples among the 129 analyzed, the selection was made by combining human nose evaluations with the skatole and androstenone concentrations determined using UHPLC-MS/MS. A comparison of the data of the two populations was performed and a statistical model analysis was built on 70 samples out of the total of 129 samples fully positive or fully negative through these two orthogonal methods for tainted prediction. Then, the model was applied to the 59 remaining samples. Finally, 7 samples were classified as tainted.

Utilizing fish wastewater in aquaponic systems to enhance anti-inflammatory and antioxidant bioactive compounds in Sarcodia suae.

Aquaculture wastewater, rich in organic nutrients, is an essential environmental factor. When applied to seaweed cultivation systems, this wastewater holds the potential to notably increase the growth rate and carbon capture of Sarcodia suae. Sarcodia suae has the potential to be a healthy food due to its various biological activities; however, its chemical composition has yet to be completely defined. In this study, we applied a UHPLC-HRMS-based foodomics strategy to determine and classify possible bioactive metabolites in S. suae. From pooled seaweed samples (S. suae cultured in filtered running, FR, aquaponic recirculation, AR systems), we identified 179 and 146 compounds in POS and NEG modes, respectively. These compounds were then classified based on their structures using the Classyfire classification. Results show that S. suae in AR exhibited higher growth performance, and ten upregulated metabolites were determined. We also validated the anti-inflammatory and antioxidative bioactivities of some selected compounds. Our study provided important insights into the potential use of fish wastewater in aquaponic systems to profile and produce bioactive compounds in S. suae comprehensively. This has significant implications for the development of sustainable food and the promotion of environmental health.

Capillary electromigration methods for food analysis and Foodomics: Advances and applications in the period March 2021 to March 2023.

This work presents a revision of the main applications of capillary electromigration (CE) methods in food analysis and Foodomics. Papers that were published during the period March 2021 to March 2023 are included. The work shows the multiple CE methods that have been developed and applied to analyze different types of molecules in foods and beverages. Namely, CE methods have been applied to analyze amino acids, biogenic amines, heterocyclic amines, peptides, proteins, phenols, polyphenols, pigments, lipids, carbohydrates, vitamins, DNAs, contaminants, toxins, pesticides, additives, residues, small organic and inorganic compounds, and other minor compounds. In addition, new CE procedures to perform chiral separation and for evaluating the effects of food processing as well as the last developments of microchip CE and new applications in Foodomics will be also discussed. The new procedures of CE to investigate food quality and safety, nutritional value, storage, and bioactivity are also included in the present review work.

'Nine Steaming Nine Sun-drying' processing enhanced properties of Polygonatum kingianum against inflammation, oxidative stress and hyperglycemia.

BACKGROUND: Polygonatum kingianum Coll. & Hemsl (PK), a prominent medicine and food homology plant, has been consumed as a decoction from boiling water for thousands of years. 'Nine Steaming Nine Sun-drying' processing has been considered an effective method for enriching tonic properties, but studies investigating such impacts on PK and underlying mechanisms are extremely rare. RESULTS: We first demonstrated substantial improvements in the anti-oxidative, anti-inflammatory and anti-hyperglycemia effects of the Nine Steaming Nine Sun-drying processed PK water extracts compared with crude PK in cell models (i.e., HepG2 and Raw 264.7 cells). We then integrated foodomics and network pharmacology analysis to uncover the key compounds responsible for the improved benefits. A total of 551 metabolites of PK extracts were identified, including polyphenols, flavonoids, alkaloids, and organic acids. During processing, 204 metabolites were enhanced, and 32 metabolites were recognized as key constituents of processed PK responsible for the improved health-promoting activities, which may affect PI3K-Akt-, MAPK-, and HIF-1 pathways. We further confirmed the high affinity between identified key constituents of processed PK and their predicted acting targets using molecular docking. CONCLUSION: Our results provide novel insights into bioactive compounds of processed PK, elaborating the rationality of processing from the perspective of tonic effects. Consuming processed PK could be an efficacious strategy to combat the high prevalence of metabolic diseases that currently affect millions of people worldwide. © 2023 Society of Chemical Industry.

Fingerprinting and profiling in metabolomics of biosamples.

This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.

The effect of common duckweed (Lemna minor L.) extract on the shelf-life of beef burgers stored in modified atmosphere packs: A metabolomics approach.

The impact of duckweed extracts (DEs) on the shelf-life of packaged beef burgers was evaluated through classical assays and untargeted metabolomics. Beef burgers were formulated with an antioxidants-free control (CON), 1 g/kg sodium ascorbate (ASC), and increasing levels of a DEs, namely 1 (DE1), 5 (DE5), and 10 (DE10) g/kg, packaged under modified atmosphere and stored at 4 °C for 19 days. The DEs, abundant in phytochemicals, determined no issues with the hygienic status of the product. DEs modulated the redox status, being ineffective in preserving linolenic acid from peroxidation. However, the oxidation marker 2-nonenoic acid was down-accumulated in the DE10 sample following 19 days of storage, recording a lower glutathione:glutathione disulfide ratio. The accumulation of adipate semialdehyde revealed the inefficiency of DEs in coping with protein oxidation, while DEs prevented the accumulation of biogenic amines. Therefore, this work suggests a potential pro-oxidant role of the formulated DEs.

Oilomics: An important branch of foodomics dealing with oil science and technology.

Oil is one of three nutritious elements. The application of omics techniques in the field of oil science and technology is attracted increasing attention. Oilomics, which emerged as an important branch of foodomics, has been widely used in various aspects of oil science and technology. However, there are currently no articles systematically reviewing the application of oilomics. This paper aims to provide a critical overview of the advantages and value of oilomics technology compared to traditional techniques in various aspects of oil science and technology, including oil nutrition, oil processing, oil quality, safety, and traceability. Moreover, this article intends to review major issues in oilomics and give a comprehensive, critical overview of the current state of the art, future challenges and trends in oilomics, with a view to promoting the optimal application and development of oilomics technology in oil science and technology.