UHPLC-MS/MS-Based Nontargeted Metabolomics Analysis Reveals Biomarkers Related to the Freshness of Chilled Chicken

Exploring the effect of part differences on metabolite molecule changes in refrigerated pork: Identifying key metabolite compounds and their conversion pathways

Effect of part differences on metabolite molecule alterations in refrigerated pork was investigated. A metabolomics methodology combined with chemometric analysis was successfully established to identify key compounds and their conversion pathways, including precursors and volatile metabolites, in the Longissimus lumborum as well as the breast and flank stored for 11 days. In total, 12 discriminative precursors were identified using the Short Time-series Expression Miner. In tandem with Random Forest and ANOVA analyses, nine volatile metabolites were identified as key compounds that could be attributed to differences in pork sections. Bidirectional orthogonal partial least squares analysis revealed a potential correlation between these key metabolites and discriminative precursors. Metabolic pathway enrichment analysis demonstrated that the primary metabolic process affected by variations in pork sections is linoleic acid metabolism, which participates in the metabolism of cysteine and glutamic acid to produce methoxy-phenyl-oxime. This study provides valuable insights into the identification of differential metabolites.

In-depth metaproteomics analysis reveals the protein profile and metabolism characteristics in pork during refrigerated storage

Alterations in microbiotas and endogenous enzymes have been implicated in meat deterioration. However, the factors that mediate the interactions between meat quality and microbiome profile were inadequately investigated. In this study, we collected pork samples throughout the refrigeration period and employed metaproteomics to characterize both the pork and microbial proteins. Our findings demonstrated that pork proteins associated with the catabolic process are upregulated during storage compared to the initial stage. Pseudomonas, Clostridium, Goodfellowiella, and Gonapodya contribute to the spoilage process. Notably, we observed an elevated abundance of microbial proteins related to glycolytic enzymes in refrigerated pork, identifying numerous proteins linked to biogenic amine production, thus highlighting their essential role in microbial decay. Further, we reveal that many of these microbial proteins from Pseudomonas are ribosomal proteins, promoting enzyme synthesis by enhancing transcription and translation. This study provides intrinsic insights into the underlying mechanisms by which microorganisms contribute to meat spoilage.

Pseudomonas fragi and Pseudomonas lundensis drove the co-spoilage in chilled pork: Insights from the metabolome

Pseudomonas fragi and Pseudomonas lundensis are key spoilage microorganisms in aerobically stored chilled meat, which had co-spoilage effect on chilled pork. However, the mechanism of co-spoilage interaction of P. fragi and P. lundensis has not been elucidated. The metabolism of nutrients in pork by mixed bacteria may differ from that by single strains. This study applied metabolomics and in vitro metabolite utilization experiment to assess the mechanism of that co-metabolize raw pork during storage. Results showed that co-spoilage group had 104 differential metabolites (histamine, N-methylhydantoin and D-gluconic acid, etc.) and 78 differential metabolites (putrescine, uracil acid and uracil, etc.) compared to P. fragi and P. lundensis group, respectively. These differential metabolites were mainly related to histidine metabolism, arginine biosynthesis, and purine. The co-spoilage effect of P. fragi and P. lundensis was related to the promotion of deamination and decarboxylation of histidine to produce histamine, the promotion of α-ketoglutarate and glutamate-mediated transamination, and the full utilization of the arginine deiminase pathway by the co-culture bacteria in the degradation of arginine to produce putrescine. In vitro experiment, co-cultures of these strains resulted in greater consumption of glucose, higher utilization activity, and promoted deamination and decarboxylation of amino acids. These findings reveal the complex and competitive interactions of co-culture of P. fragi and P. lundensis, providing insight into microbial spoilage mechanisms in chilled pork.

Optimization and Detection of Freshness Biomarkers of Atlantic Salmon Subjected to Different Vacuum Packaging Conditions during Storage at 0 °C by Metabolomics and Molecular Docking

The freshness of Atlantic salmon is influenced mainly by tissue metabolism, which in turn is affected by storage time and conditions. The alterations in taste profiles and nutritional values of salmon when packaged using vacuum methods have not been fully understood, and the factors contributing to these changes require further research. In this work, the extraction method for flavor nutrients from salmon was optimized via the Plackett-Burman (PB) test. A sensitive and rapid targeted metabolomics method for the simultaneous determination of 34 nutrients was successfully established via ultra-performance liquid chromatography-triple quadrupole/linear ion trap composite mass spectrometry (UHPLC-QTRAP/MS), and various nutritional compositions during storage at 0 °C under different vacuum conditions (0 kPa or -90 kPa) for 4 and 8 days were analyzed. Results showed that storage time had a significant effect on salmon metabolism. The total amino acids decreased by 62.95% and 65.89% at 0 kPa and -90 kPa, respectively. Notably, a marked reduction in histidine after 8 days at -90 kPa may have diminished bitterness, while decreased levels of umami-tasting amino acids like glutamine and aspartic acid affected the overall flavor profile. Overall, the packaging conditions at 0 °C and 0 kPa were more suitable for the preservation of most nutrients in salmon. Pathway enrichment analysis revealed that the reduction in substances was mainly related to the alanine, aspartate, and glutamate metabolism pathways. Alanine, inosine, and histidine, whose levels changed significantly, can bind to the typical umami taste receptor TIR1/TIR3 and can be biomarkers to monitor and determine the freshness or spoilage of salmon after 4-8 days of storage. This study revealed the changes in small-molecule nutrients in salmon during storage under different packaging conditions, which provides a reference for the packaging preservation technology of fresh salmon and new ideas for the evaluation of salmon quality and determination of freshness.

Comparative Metabolomic Profiling of Eggs from 3 Diverse Chicken Breeds Using GC-MS Analysis

Eggs, as a crucial source of essential nutrients for consumers, possess a high nutritional value owing to their rich composition of vital components essential for human health. While previous research has extensively investigated genetic factors influencing egg quality, there has been a limited focus on exploring the impact of specific strains, particularly within the African context, on the polar metabolite profile of eggs. In this extensive study, we conducted an untargeted analysis of the chemical composition of both albumen and yolk from 3 distinct strains of hens-Blue Holland, Sasso, and Wassache-raised under identical feeding conditions. Utilizing gas chromatography coupled with mass spectrometry (GC-MS), we meticulously examined amino acids, carbohydrates, fatty acids, and other small polar metabolites. In total, 38 and 44 metabolites were identified in the whites and yolk, respectively, of the 3 studied strains. The application of chemometric analysis revealed notable differences in metabolite profiles with 8 relevant metabolites in each egg part. These metabolites include amino acids (N-α-Acetyl-L-lysine, lysine, L-valine, L-Tryptophan), fatty acids (oleic acid, linoleic acid, palmitic acid and stearic acid), and carbohydrates (d-glucose, maltose, lactose). These findings shed light on strain-specific metabolic nuances within eggs, emphasizing potential nutritional implications. The ensuing discussion delves into the diverse metabolic pathways influenced by the identified metabolites, offering insights that contribute to a broader understanding of egg composition and its significance in tailoring nutritional strategies for diverse populations.

Metabolomics and transcriptomics of embryonic livers reveal hypoxia adaptation of Tibetan chickens

BACKGROUND

Exploring the hypoxia adaptation mechanism of Tibetan chicken is of great significance for revealing the survival law of Tibetan chicken and plateau animal husbandry production. To investigate the hypoxia adaptation of Tibetan chickens (TBCs), an integrative metabolomic-transcriptomic analysis of the liver on day 18 of embryonic development was performed. Dwarf laying chickens (DLCs), a lowland breed, were used as a control.

RESULTS

A total of 1,908 metabolites were identified in both TBCs and DLCs. Energy metabolism and amino acid metabolism related differentially regulated metabolites (DRMs) were significantly enriched under hypoxia. Important metabolic pathways including the TCA cycle and arginine and proline metabolism were screened; PCK1, SUCLA2, and CPS1 were found to be altered under hypoxic conditions. In addition, integrated analysis suggested potential differences in mitochondrial function, which may play a crucial role in the study of chicken oxygen adaptation.

CONCLUSIONS

These results suggest that hypoxia changed the gene expression and metabolic patterns of embryonic liver of TBCs compared to DLCs. Our study provides a basis for uncovering the molecular regulation mechanisms of hypoxia adaptation in TBCs with the potential application of hypoxia adaptation research for other animals living on the Qinghai-Tibet plateau, and may even contribute to the study of diseases caused by hypoxia.

Metabolomic comparison of meat quality and metabolites of geese breast muscle at different ages

The purpose of this study was to distinguish the effect of age on the meat quality and chemical composition of Yangzhou goose breast meat. Nontargeted metabolomics analysis (UHPLC-MS/MS) was used to distinguish the metabolic composition of goose meat at different ages, and Pearson's correlations between differential metabolites and key meat parameters were assessed. Compared with goslings, adult geese had lighter, redder and chewier meat (p < 0.05). Metabolite analysis revealed significant differences in nucleosides, organic acids, amino acids and sugars. Levels of IMP, xanthosine, pretyrosine and l-threonine were significantly higher in older meat (p < 0.05) and positively correlated with meat freshness indicators. However, pyruvic acid, l-cysteine and glucose 6-phosphate were up-regulated in gosling meat (p < 0.05), which were important flavor compounds. These results facilitate the further investigation of changes in goose meat composition and provide biomarkers for determining goose meat quality at different ages.

Multi-Stage Transcriptome Analysis Revealed the Growth Mechanism of Feathers and Hair Follicles during Induction Molting by Fasting in the Late Stage of Egg Laying

Induced molting is a common method to obtain a new life in laying hens, in which periodic changes in feathers are the prominent feature. Nevertheless, its precise molecular mechanism remains unclear. In this study, feather and hair follicle samples were collected during fasting-induced physiological remodeling for hematoxylin-eosin staining, hormone changes and follicle traits, and transcriptome sequencing. Feather shedding was observed in F13 to R25, while newborns were observed in R3 to R32. Triiodothyronine and tetraiodothyronine were significantly elevated during feather shedding. The calcium content was significantly higher, and the ash content was significantly lower after the changeover. The determination of hair follicle traits revealed an increasing trend in pore density and a decrease in pore diameter after the resumption of feeding. According to RNA-seq results, several core genes were identified, including DSP, CDH1, PKP1, and PPCKB, which may have an impact on hair follicle growth. The focus was to discover that starvation may trigger changes in thyroid hormones, which in turn regulate feather molting through thyroid hormone synthesis, calcium signaling, and thyroid hormone signaling pathways. These data provide a valuable resource for the analysis of the molecular mechanisms underlying the cyclical growth of hair follicles in the skin during induced molting.

Untargeted and targeted metabolomics identify metabolite biomarkers for Salmonella enteritidis in chicken meat

Salmonella Enteritidis easily contaminate chicken during slaughtering, processing, transportation, and sales, which seriously endangers human health. This study aimed to identify metabolite biomarkers for Salmonella Enteritidis contamination in chicken meat. UPLC-Q-Orbitrap MS untargeted metabolomics analysis identified 441 and 240 confidently metabolites in positive and negative ion mode, respectively. Thirty metabolites were defined as potential biomarkers for Salmonella enteritidis contamination in chicken meat. UPLC-QQQ-MS based targeted metabolomics was used to quantitatively analyze candidate metabolite biomarkers in Salmonella enteritidis contaminated and fresh chicken samples. A total of 10 candidate metabolite biomarkers were confirmed in the validation set, among which acetylcholine, l-Methionine, l-Proline, l-Valine, and l-Norleucine were identified as biomarkers for Salmonella Enteritidis contamination in chicken. The combined receiver operating characteristic curve analysis of the five biomarkers achieved an AUC of 0.956, indicating their high sensitivity and specificity in predicting Salmonella Enteritidis in raw chicken. In conclusion, the present study identified five metabolite biomarkers for Salmonella enteritidis in raw chicken. These results provide a potential theoretical basis for developing Salmonella Enteritidis detection methods in raw chicken.

Mass spectrometry-based techniques for identification of compounds in milk and meat matrix

Food including milk and meat is often viewed as the mixture of different components such as fat, protein, carbohydrates, moisture and ash, which are estimated using well-established protocols and techniques. However, with the advent of metabolomics, low-molecular weight substances, also known as metabolites, have been recognized as one of the major factors influencing the production, quality and processing. Therefore, different separation and detection techniques have been developed for the rapid, robust and reproducible separation and identification of compounds for efficient control in milk and meat production and supply chain. Mass-spectrometry based techniques such as GC-MS and LC-MS and nuclear magnetic resonance spectroscopy techniques have been proven successful in the detailed food component analysis owing to their associated benefits. Different metabolites extraction protocols, derivatization, spectra generated, data processing followed by data interpretation are the major sequential steps for these analytical techniques. This chapter deals with not only the detailed discussion of these analytical techniques but also sheds light on various applications of these analytical techniques in milk and meat products.

Insight from untargeted metabolomics: Revealing the potential marker compounds changes in refrigerated pork based on random forests machine learning algorithm

Data on changes in non-volatile components and metabolic pathways during pork storage were inadequately investigated. Herein, an untargeted metabolomics coupled with random forests machine learning algorithm was proposed to identify the potential marker compounds and their effects on non-volatile production during pork storage by ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS/MS). A total of 873 differential metabolites were identified based on analysis of variance (ANOVA). Bioinformatics analysis shows that the key metabolic pathways for protein degradation and amino acid transport are amino acid metabolism and nucleotide metabolism. Finally, 40 potential marker compounds were screened using the random forest regression model, innovatively proposing the key role of pentose-related metabolism in pork spoilage. Multiple linear regression analysis revealed that d-xylose, xanthine, and pyruvaldehyde could be key marker compounds related to the freshness of refrigerated pork. Therefore, this study could provide new ideas for the identification of marker compounds in refrigerated pork.

Gas chromatography-mass spectrometry-based untargeted metabolomics analysis reveals circulating biomarkers related to wooden breast myopathy in broilers: a preliminary study

Approaches for the diagnosis of wooden breast (WB) myopathy in live birds are urgently required before applying intervention strategies to reduce occurrence and severity for the poultry industry. The objective of this study was to characterize the serum metabolic profiles in male broilers affected by WB and to identify biomarkers related to this myopathy. Broilers were categorized into normal (CON) and WB groups based on gross scoring and histological evaluation. Gas chromatography-mass spectrometry-based metabolomics, multivariate analysis, and orthogonal partial least squares discriminant analysis revealed a clear separation between CON and WB. A total of 73 significantly different (P < 0.05) metabolites with 17 upregulated and 56 downregulated were identified, which were mainly involved in pathways of alanine, aspartate, and glutamate metabolism, carbohydrate metabolism, and taurine and hypotaurine metabolism. By using the nested cross-validation function of random forest analysis, 9 significantly altered (P < 0.05) metabolites (cerotinic acid, arabitol, phosphoenolpyruvate, terephthalic acid, cis-gondoic acid, N-acetyl-d-glucosamine, 4-hydroxymandelic acid, caffeine, and xanthurenic acid) were identified as biomarkers with an excellent discriminant performance for WB myopathy. Collectively, this study provides new insights for a deeper understanding of the pathogenesis and provides metabolites as biomarkers for diagnostic utilization of WB myopathy.

In Vitro and In Situ Characterization of Psychrotrophic Spoilage Bacteria Recovered from Chilled Chicken

Spoilage bacteria play a remarkable role in the spoilage of chilled chicken. In this paper, a total of 42 isolates belonging to 16 species of four genera were isolated from chilled chicken and displayed different characterizations of psychrotrophic spoilage. Six isolates of J7, J8, Q20, Q23, R1, and R9 with differences in proteolytic capabilities were further characterized for in situ spoilage potential evaluation. Pseudomonas lundensis J8 exhibited the strongest spoilage potential in situ, displaying a fast growth rate, increased pH velocity, high total volatile basic nitrogen, and high peptide content in the chicken samples. The volatile flavor analysis of chicken samples via electronic nose indicated that the content of characteristic odors representing spoilage, including sulfides, organic sulfide, and hydride, increased during storage. Additionally, the principle component and correlation analyses revealed that the spoilage odors produced by different species of bacteria were significantly different and positively correlated with the results of protease activity in vitro. The characteristics of spoilage bacteria in chilled chicken provided a comprehensive insight into microbial assessment during storage.

Indigenous, Yellow-Feathered Chickens Body Measurements, Carcass Traits, and Meat Quality Depending on Marketable Age

Given an increasing trend in slaughter and chilling for the sale of chickens in China, it is important to determine the marketable age of chickens for chilled sales. This study determined the effects of two marketable ages on the body measurements, carcass traits, and meat quality of yellow-feathered chickens. A total of 360 healthy one-day-old male Xueshan chickens were raised in six pens (straw-covered floor, numbered 1 to 6) and treated in the same manner (free access to food and water) until day 100. Sixty chickens from pens numbered 1 to 3 and 4 to 6 were selected to determine the body measurements, carcass traits, and meat quality at two slaughter ages (90 and 100 days), respectively. One hundred-day-old chickens had a higher body slope, cockscomb, keel, shank lengths, and higher live and dressed weights (p < 0.05). The abdomen skin follicle density, a*(redness) and b*(yellowness) values were higher in 100-day-old chickens (p < 0.05), whereas the 90-day-old chickens were characterized by better spotted skin. For the breast muscle, pH, shear force, a*, moisture, and protein and intramuscular fat contents were lower; moreover, L*(lightness) and b* were higher in 90-day-old chickens. In leg muscles, the pH, shear force, L*, b* and collagen content were lower; furthermore, the a* and moisture contents were higher in 90-day-old chickens (p < 0.05). These findings indicate that two marketable ages both have pros and cons, but 90 days chickens perform better on carcass appearance, and producers can adjust the marketable age to meet needs of different consumers. This study provides a unique idea and theoretical reference for breeding and marketing yellow-feathered chickens.

Comparison of chicken breast quality characteristics and metabolites due to different rearing environments and refrigerated storage

The objective of the present study was to compare the breast meat quality and metabolomic characteristics from broilers that were raised in conventional (conventional farm reared-broilers; CB, n = 20) and legally approved animal welfare farms (welfare farm reared-broilers; WB, n = 20) in aerobic cold storage (1, 3, 5, and 7 d). Compared to CB chickens, the WB chickens had a larger floor size as well as lower stocking density, atmospheric ammonia, and nipple-shared chicken counts. The results demonstrated significantly higher pH, L^⁎- and b^⁎-value, and lower shear force in CB compared to WB during cold storage. Using ¹H NMR analysis, 25 compounds were identified in the chicken breast meat. Partial least square-discriminant analysis (PLS-DA) was performed based on the identified metabolites. The content of 15 metabolites (1 di-peptide, 9 free amino acids, 2 glycolytic potential-related products, 2 nucleotide-related products, and 1 organic acid) was significantly different due to the rearing environment (CB vs. WB). Among them, all free amino acids were higher in CB than in WB. Six free amino acids (glycine, isoleucine, leucine, phenylalanine, valine, and β-alanine) had variable importance in projection (VIP) score >1, regardless of the number of cold storage days. Therefore, these compounds in the breast meat may be used as potential markers to determine the rearing environment of broilers. Also, this result might be an indication of stress-related meat quality changes in broilers.

Current State of Metabolomics Research in Meat Quality Analysis and Authentication

In the past decades, as an emerging omic, metabolomics has been widely used in meat science research, showing promise in meat quality analysis and meat authentication. This review first provides a brief overview of the concept, analytical techniques, and analysis workflow of metabolomics. Additionally, the metabolomics research in quality analysis and authentication of meat is comprehensively described. Finally, the limitations, challenges, and future trends of metabolomics application in meat quality analysis and meat authentication are critically discussed. We hope to provide valuable insights for further research in meat quality.

Metabolic Responses of a Model Green Microalga Euglena gracilis to Different Environmental Stresses

Euglena gracilis, a green microalga known as a potential candidate for jet fuel producers and new functional food resources, is highly tolerant to antibiotics, heavy metals, and other environmental stresses. Its cells contain many high-value products, including vitamins, amino acids, pigments, unsaturated fatty acids, and carbohydrate paramylon as metabolites, which change contents in response to various extracellular environments. However, mechanism insights into the cellular metabolic response of Euglena to different toxic chemicals and adverse environmental stresses were very limited. We extensively investigated the changes of cell biomass, pigments, lipids, and paramylon of E. gracilis under several environmental stresses, such as heavy metal CdCl₂, antibiotics paromomycin, and nutrient deprivation. In addition, global metabolomics by Ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was applied to study other metabolites and potential regulatory mechanisms behind the differential accumulation of major high-valued metabolites. This study collects a comprehensive update on the biology of E. gracilis for various metabolic responses to stress conditions, and it will be of great value for Euglena cultivation and high-value [154mm][10mm]Q7metabolite production.

Discovery of Spoilage Markers for Chicken Eggs Using Liquid Chromatography-High Resolution Mass Spectrometry-Based Untargeted and Targeted Foodomics

The current approaches remain insufficient for measuring chicken egg spoilage or present analytical limitations. This study aimed to complement the existing analyses and identify novel markers using liquid chromatography-high resolution mass spectrometry-based foodomics strategies. In the discovery set, comparative untargeted metabolomics was utilized to identify marker candidates in microbially inoculated chicken eggs. Markers were annotated by spectral matching with authentic standards, experimental libraries, or in silico fragmentation. In the validation set, targeted metabolomics was employed to verify the markers in stored chicken eggs from five farms. Statistical differences at a p-value < 0.001 revealed increases in lactic and 3-hydroxybutyric acids and decreases in phosphocholine, LPE(O-18:1), LPC(16:0), and LPC(18:0) in stored eggs. Receiver operating characteristic curve analysis of the six combined markers yielded an AUC of 0.956 and a sensitivity and specificity of ∼90%. Four phospholipids were highlighted as a novel class of spoilage markers. Our findings may contribute to further industrial implementation, benefiting the quality assurance and food safety of poultry egg production.

Characterization of chilled chicken spoilage using an integrated microbiome and metabolomics analysis

Spoilage of chilled chicken can occur as a result of microbial development and consumption of meat nutrients by spoilage bacteria, ultimately resulting in the release of undesired metabolites. Characterizing the profiles of the microbiota and metabolites and clarifying their relationships will contribute to an improved understanding of the mechanism underlying chilled chicken spoilage. In the present study, 16S rRNA gene sequencing and ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS)-based untargeted metabolomics analyses were applied to determine the microbial and metabolic profiles in chicken during chilled storage. The microbial and metabolic datasets were subjected to combined analysis using weighted gene co-expression network analysis (WGCNA) and Spearman's correlation analysis. Brochothrix, Carnobacterium, Photobacterium, Pseudomonas, Acinetobacter, Serratia, Kurthia, Shewanella, and Obesumbacterium genera were identified as the dominant spoilage bacteria in chilled chicken. Ten metabolic pathways, including histidine metabolism and purine metabolism, were identified as potential mechanisms underlying chilled chicken spoilage. Correlation analysis demonstrated that spoilage bacterial genera were highly correlated with spoilage-related metabolites. Taken together, the present study proposed an integrated microbiome and metabolomics approach to investigate the mechanism of chilled chicken spoilage caused by microbial activity. The results obtained by this approach provide a comprehensive insight into changes in the microbial and metabolic profiles of chilled chicken during spoilage.