Comparative metabolomics of Japanese Black cattle beef and other meats using gas chromatography-mass spectrometry

- Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality

Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.

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.

Gas chromatography-mass spectrometry-based quantitative method using tert-butyldimethylsilyl derivatization for plasma levels of free amino acids and related metabolites in Japanese Black cattle

The quantification of amino acid and related metabolite levels is important for evaluating amino acid metabolism and function in animals. However, a useful quantitative method is not enough. In this study, we developed and validated tert-butyldimethylsilyl derivatization method using gas chromatography-mass spectrometry to quantify plasma levels of free amino acids and related metabolites in Japanese Black cattle. Of the 51 metabolites examined, 24, including 20 amino acids, one amine, and three keto acids, could be quantified. Compared with the trimethylsilyl derivatization method using gas chromatography-mass spectrometry, which has been used for untargeted metabolomic analysis, the present method had higher analytical reliability. This method is advantageous for assessing branched-chain amino acid (BCAA) metabolism because it enables the quantification of not only BCAA levels (valine, leucine, and isoleucine) but also their bioactive metabolite keto acid levels (2-ketoisovaleric acid, 2-ketoisocaproic acid, and 2-keto-3-methylvaleric acid) in the plasma. In addition, this method can quantify the plasma levels of not only tryptophan but also its bioactive metabolites kynurenine and serotonin. These results suggest that this quantitative method has the potential to further our understanding of amino acid metabolic processes and their functions in Japanese Black cattle.

Rapid analysis of meat floss origin using a supervised machine learning-based electronic nose towards food authentication

Authentication of meat floss origin has been highly critical for its consumers due to existing potential risks of having allergic diseases or religion perspective related to pork-containing foods. Herein, we developed and assessed a compact portable electronic nose (e-nose) comprising gas sensor array and supervised machine learning with a window time slicing method to sniff and to classify different meat floss products. We evaluated four different supervised learning methods for data classification (i.e., linear discriminant analysis (LDA), quadratic discriminant analysis (QDA), k-nearest neighbors (k-NN), and random forest (RF)). Among them, an LDA model equipped with five-window-extracted feature yielded the highest accuracy values of >99% for both validation and testing data in discriminating beef, chicken, and pork flosses. The obtained e-nose results were correlated and confirmed with the spectral data from Fourier-transform infrared (FTIR) spectroscopy and gas chromatography-mass spectrometry (GC-MS) measurements. We found that beef and chicken had similar compound groups (i.e., hydrocarbons and alcohol). Meanwhile, aldehyde compounds (e.g., dodecanal and 9-octadecanal) were found to be dominant in pork products. Based on its performance evaluation, the developed e-nose system shows promising results in food authenticity testing, which paves the way for ubiquitously detecting deception and food fraud attempts.

Metabolomic profiling of postmortem aged muscle in Japanese Brown beef cattle revealed an interbreed difference from Japanese Black beef

OBJECTIVE

Japanese Brown (JBR) cattle, especially the Kochi (Tosa) pedigree (JBRT), is a local breed of moderately marbled beef. Despite the increasing demand, the interbreed differences in muscle metabolites from the highly marbled Japanese Black (JBL) beef remain poorly understood. We aimed to determine flavor-related metabolites and postmortem metabolisms characteristic to JBRT beef in comparison with JBL beef.

METHODS

Lean portions of the longissimus thoracis (loin) muscle from four JBRT cattle were collected at 0, 1, and 14 d postmortem. The muscle metabolomic profiles were analyzed using capillary electrophoresis time-of-flight mass spectrometry. The difference in postmortem metabolisms and aged muscle metabolites were analyzed by statistical and bioinformatic analyses between JBRT (n = 12) and JBL cattle (n = 6).

RESULTS

A total of 240 metabolite annotations were obtained from the detected signals of the JBRT muscle samples. Principal component analysis separated the beef samples into three different aging point groups. According to metabolite set enrichment analysis, postmortem metabolic changes were associated with the metabolism of pyrimidine, nicotinate and nicotinamide, purine, pyruvate, thiamine, amino sugar, and fatty acid; citric acid cycle; and pentose phosphate pathway as well as various amino acids and mitochondrial fatty acid metabolism. The aged JBRT beef showed higher ultimate pH and lower lactate content than aged JBL beef, suggesting the lower glycolytic activity in postmortem JBRT muscle. JBRT beef was distinguished from JBL beef by significantly different compounds, including choline, amino acids, uridine monophosphate, inosine 5'-monophosphate, fructose 1,6-diphosphate, and betaine, suggesting interbreed differences in the accumulation of nucleotide monophosphate, glutathione metabolism, and phospholipid metabolism.

CONCLUSION

Glycolysis, purine metabolism, fatty acid catabolism, and protein degradation were the most common pathways in beef during postmortem aging. The differentially expressed metabolites and the relevant metabolisms in JBRT beef may contribute to the development of a characteristic flavor.

Candidate Genes and Gene Networks Change with Age in Japanese Black Cattle by Blood Transcriptome Analysis

Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To this end, we used the blood transcriptomes of Japanese black cattle at different ages as the study subjects and screened 1055, 345, and 1058 differential expressed genes (DEGs) in the calf vs. adult, adult vs. old, and calf vs. old comparison groups, respectively. The weighted co-expression network consisted of 1731 genes. Finally, blue, brown, and yellow age-specific modules were obtained, in which genes were enriched in signaling pathways related to growth and development and immune metabolic dysfunction, respectively. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 20 of the highest connectivity genes were chosen as potential hub genes. Finally, we identified 495, 244, and 1007 genes by exon-wide selection signature (EWSS) analysis of different comparison groups. Combining the results of hub genes, we found that VWF, PARVB, PRKCA, and TGFB1I1 could be used as candidate genes for growth and development stages of beef cattle. CORO2B and SDK1 could be used as candidate marker genes associated with aging. In conclusion, by comparing the blood transcriptome of calves, adult cattle, and old cattle, the candidate genes related to immunity and metabolism affected by age were identified, and the gene co-expression network of different age stages was constructed. It provides a data basis for exploring the growth, development, and aging of beef cattle.

Transcriptomics and Lipid Metabolomics Analysis of Subcutaneous, Visceral, and Abdominal Adipose Tissues of Beef Cattle

Fat deposition traits are influenced by genetics and environment, which affect meat quality, growth rate, and energy metabolism of domestic animals. However, at present, the molecular mechanism of fat deposition is not entirely understood in beef cattle. Therefore, the current study conducted transcriptomics and lipid metabolomics analysis of subcutaneous, visceral, and abdominal adipose tissue (SAT, VAT, and AAT) of Huaxi cattle to investigate the differences among these adipose tissues and systematically explore how candidate genes interact with metabolites to affect fat deposition. These results demonstrated that compared with SAT, the gene expression patterns and metabolite contents of VAT and AAT were more consistent. Particularly, SCD expression, monounsaturated fatty acid (MUFA) and triglyceride (TG) content were higher in SAT, whereas PCK1 expression and the contents of saturated fatty acid (SFA), diacylglycerol (DG), and lysoglycerophosphocholine (LPC) were higher in VAT. Notably, in contrast to PCK1, 10 candidates including SCD, ELOVL6, ACACA, and FABP7 were identified to affect fat deposition through positively regulating MUFA and TG, and negatively regulating SFA, DG, and LPC. These findings uncovered novel gene resources and offered a theoretical basis for future investigation of fat deposition in beef cattle.

Metabolomics Characterize the Differential Metabolic Markers between Bama Xiang Pig and Debao Pig to Identify Pork

The Bama Xiang pig (BM) is a unique pig species in Guangxi Province, China. Compared to other breeds of domestic pig, such as the Debao pig (DB), it is smaller in size, better in meat quality, resistant to rough feeding and strong in stress resistance. These unique advantages of Bama Xiang pigs make them of great edible value and scientific research value. However, the differences in muscle metabolites between Bama Xiang pigs (BM) and Debao pigs (DB) are largely unexplored. Here, we identified 214 differential metabolites between these two pig breeds by LC-MS. Forty-one such metabolites are enriched into metabolic pathways, and these metabolites correspond to 11 metabolic pathways with significant differences. In Bama pigs, the abundance of various metabolites such as creatine, citric acid, L-valine and hypoxanthine is significantly higher than in Debao pigs, while the abundance of other metabolites, such as carnosine, is significantly lower. Among these, we propose six differential metabolites: L-proline, citric acid, ribose 1-phosphate, L-valine, creatine, and L-arginine, as well as four potential differential metabolites (without the KEGG pathway), alanyl-histidine, inosine 2'-phosphate, oleoylcarnitine, and histidinyl hydroxyproline, as features for evaluating the meat quality of Bama pigs and for differentiating pork from Bama pigs and Debao pigs. This study provides a proof-of-concept example of distinguishing pork from different pig breeds at the metabolite level and sheds light on elucidating the biological processes underlying meat quality differences. Our pork metabolites data are also of great value to the genomics breeding community in meat quality improvement.

1H NMR Metabolic Profiling and Meat Quality in Three Beef Cattle Breeds from Northeastern Thailand

The increasing need for effective analytical tools to evaluate beef quality has prompted the development of new procedures to improve the animal sector's performance. In this study, three beef breeds-Thai native (TN), crossbred Brahman × Thai native (BT), and crossbred Charolais × Brahman (CB)-were compared in terms of their physicochemical and metabolic profiles. The findings demonstrated that TN beef was lighter and tougher than other beef. Beef odor was stronger in BT. In addition, CB beef was the most tender and had the highest intramuscular fat content. Twenty-one different metabolites were found overall through NMR and chemometric approaches. The primary factors contributing to the difference in OPLS-DA loading plots were acetylcholine, valine, adenine, leucine, phosphocreatine, β-hydroxypyruvate, ethanol, adenosine diphosphate, creatine, acetylcholine, and lactate. The multivariate analysis indicated that these metabolites in beef cattle breeds could be distinguished using NMR spectroscopy. The results of this study provide valuable information on the quality and meat metabolites of different breeds. This could help in the development of a more accurate assessment of the quality of beef in future research.

Blood Transcriptome Analysis of Beef Cow with Different Parity Revealed Candidate Genes and Gene Networks Regulating the Postpartum Diseases

Maternal parity is an important physiological factor influencing beef cow reproductive performance. However, there are few studies on the influence of different calving periods on early growth and postpartum diseases. Here, we conducted blood transcriptomic analysis on cows of different parities for gene discovery. We used Short Time Series Expression Miner (STEM) analysis to determine gene expression levels in cows of various parities and divided multiple parities into three main periods (nulliparous, primiparous, and multiparous) for subsequent analysis. Furthermore, the top 15,000 genes with the lowest median absolute deviation (MAD) were used to build a co-expression network using weighted correlation network analysis (WGCNA), and six independent modules were identified. Combing with Exon Wide Selection Signature (EWSS) and protein-protein interaction (PPI) analysis revealed that TPCN2, KIF22, MICAL3, RUNX2, PDE4A, TESK2, GPM6A, POLR1A, and KLHL6 involved in early growth and postpartum diseases. The GO and KEGG enrichment showed that the Parathyroid hormone synthesis, secretion, and action pathway and stem cell differentiation function-related pathways were enriched. Collectively, our study revealed candidate genes and gene networks regulating the early growth and postpartum diseases and provided new insights into the potential mechanism of reproduction advantages of different parity selection.

Application of Mass Spectrometry for Determining the Geographic Production Area of Wagyu Beef

Japanese Black cattle (Japanese Wagyu) beef is attracting attention for its aroma and marbling, and its handling is increasing worldwide. Here, we focused on the origin discrimination of Wagyu beef and analyzed the nutritional components of Japanese Wagyu (produced in multiple prefectures of Japan), Hybrid Wagyu (a cross between Angus and Wagyu cattle born in Australia and transported to Japan), and Australian Wagyu beef using mass spectrometry (MS). Triple-quadrupole liquid chromatography–MS was used to clarify the molecular species of lipids in Wagyu beef. Fourteen classes of lipids were separated, and 128 different triacylglycerides (TGs) were detected. A simple comparative analysis of these TGs using high-performance liquid chromatography revealed significantly higher levels of triolein (C18:1/C18:1/C18:1; abbreviated OOO) and C18:1/C18:1/C16:1 (OOPo) in Japanese Wagyu. Wagyu elements beef were comprehensively analyzed using inductively coupled plasma (ICP)–MS and ICP–optical emission spectrometry. We found significant differences in the rubidium, cesium, and lithium levels of Japanese and Australian Wagyu beef. On comparing metabolites using gas chromatography–MS, we identified significant differences in the levels of amino acids and other components of the Japanese and Australian Wagyu beef. These results suggest the possibility of determining the origin of Wagyu cattle breeds using MS and genetic discrimination.

The successful use of -omic technologies to achieve the 'One Health' concept in meat producing animals

Human health and wellbeing are closely linked to healthy domestic animals, a vital wildlife, and an intact ecosystem. This holistic concept is referred to as 'One Health'. In this review, we provide an overview of the potential and the challenges for the use of modern -omics technologies, especially transcriptomics and proteomics, to implement the 'One Health' idea for food-producing animals. These high-throughput studies offer opportunities to find new potential molecular biomarkers to monitor animal health, detect pharmacological interventions and evaluate the wellbeing of farm animals in modern intensive livestock systems.

Applications of Omics Technology for Livestock Selection and Improvement

Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals’ actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.

Production of Hydroxy Fatty Acids, Precursors of γ-Hexalactone, Contributes to the Characteristic Sweet Aroma of Beef

Aroma is an essential factor for meat quality. The meat of Japanese Black cattle exhibits fine marbling and a rich and sweet aroma with a characteristic lactone composition. The mechanism of lactone formation associated with beef aroma has not been elucidated. In this study, we examined the precursors of γ-hexalactone, an indicator of the sweet aroma of beef and identified the mechanism underlying γ-hexalactone production. A low-temperature vacuum system was used to prepare beef tallow from Japanese Black cattle and Holstein cattle. The odor components were identified using headspace–gas chromatography. The analysis revealed that γ-hexalactone, γ-dodecalactone, δ-tetradecalactone, and δ-hexadecalactone were present as sweet aroma components of beef tallow prepared from marbling and muscle. Since we previously reported that γ-hexalactone formation correlates with linoleic acid content in beef, we analyzed ten oxidized fatty acids derived from linoleic acid by liquid chromatography–triple quadrupole mass spectrometry and detected two hydroxy-octadecadienoic acids (9S-HODE and 13S-HODE) in beef tallow. Significant differences in arachidonic acid 15-lipoxygenase and cyclooxygenase protein expression levels among subcutaneous fat, intramuscular fat, and muscle tissue were observed. Our results suggest that the combination of linoleic acid and the expression of lipid oxidase derived from beef muscle and intramuscular fat produce hydroxy fatty acids that result in a sweet aroma.

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

UHPLC-QTOF/MS-based comparative metabolomics in pectoralis major of fast- and slow-growing chickens at market ages

The molecular regulatory mechanism underlying meat quality between different chicken genotypes remains elusive. This study aimed to identify the differences in metabolites and pathways in pectoralis major (breast muscle) between a commercial fast-growing chicken genotype (Cobb500) and a slow-growing Chinese native chicken genotype (Beijing-You chickens, BYC) at market ages respectively based on ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry (UHPLC-QTOF/MS). Eighteen metabolites were identified as potential biomarkers between BYC and Cobb500 at market ages. Among them, L-cysteine exhibited a higher relative intensity in BYC compared with Cobb500 and was enriched into 10 potential flavor-associated KEGG pathways. In addition, the glycerophospholipid metabolism pathway was found to be associated with chicken meat flavor and the accumulation of sn-glycerol 3-phosphate and acetylcholine was more predominant in BYC than that in Cobb500, which were catalyzed by glycerophosphocholine phosphodiesterase (GPCPD1, EC:3.1.4.2), choline O-acetyltransferase (CHAT, EC:2.3.1.6), and acetylcholinesterase (ACHE, EC:3.1.1.7). Overall, the present study provided some metabolites and pathways for further investigating the roles of the differences in meat flavor quality in breast muscle between Cobb500 and BYC at market ages.

Effects of different feeding regimes on muscle metabolism and its association with meat quality of Tibetan sheep

This study aimed to explore the effects of different feeding regimes on muscle metabolism and its association with meat quality of Tibetan sheep through correlation analysis of meat quality and differential metabolites using untargeted and targeted metabolomics. The untargeted metabolome was detected by UHPLC-QTOF-MS, and the targeted metabolome was detected by UHPLC-QQQ-MS (amino acids) and GC-MS (fatty acids). Based on the researched results, the nutritional quality of meat, including the content of protein and fat and the edible quality of meat, including tenderness, water holding capacity (WHC), texture, and flavor of Tibetan sheep were superior in the stall-feeding group (GBZ) than in the traditional grazing group (CBZ). In the GBZ group, the key upregulated metabolites and metabolic pathways were dominated by essential amino acids (EAAs) and amino acid metabolism as well as the key downregulated metabolites and metabolic pathways were dominated by polyunsaturated fatty acids (PUFA) and lipid metabolism. Correlation analysis showed that there was a significant correlation between the results of untargeted metabolomics and some phenotypic data, including shear force, cooking loss, drip loss, chewiness, elasticity, flavor, and the content of protein and fat. Taken together, stall-feeding would be appropriate for the production of Tibetan mutton, offering better mouthfeel and higher nutrition by altering the muscle metabolism and increasing the beneficial compound deposition in the muscle.

Muscle and Serum Metabolomics for Different Chicken Breeds under Commercial Conditions by GC-MS

Globally, village chicken is popular and is known as a premium meat with a higher price. Food fraud can occur by selling other chicken breeds at a premium price in local markets. This study aimed to distinguish local village chicken from other chicken breeds available in the market, namely, colored broiler (Hubbard), broiler (Cobb), and spent laying hen (Dekalb) in pectoralis major and serum under commercial conditions using an untargeted metabolomics approach. Both pectoralis major and serum were analyzed using gas chromatography-mass spectrometry (GC-MS). The principal component analysis (PCA) results distinguished four different chicken breeds into three main groups for pectoralis major and serum. A total of 30 and 40 characteristic metabolites were identified for pectoralis major and serum, respectively. The four chicken breeds were characterized by the abundance of metabolites such as amino acids (L-glutamic acid, L-threonine, L-serine, L-leucine), organic acids (L-lactic acid, succinic acid, 3-hydroxybutyric acid), sugars (D-allose, D-glucose), sugar alcohols (myo-inositol), and fatty acids (linoleic acid). Our results suggest that an untargeted metabolomics approach using GC-MS and PCA could discriminate chicken breeds for pectoralis major and serum under commercial conditions. In this study, village chicken could only be distinguished from colored broiler (Hubbard) by serum samples.

Gene Expression Analysis Provides New Insights into the Mechanism of Intramuscular Fat Formation in Japanese Black Cattle

Japanese Black cattle (Japanese Wagyu) have a unique phenotype in which ectopic intramuscular fat accumulates in skeletal muscle, producing finely marbled beef. However, the mechanism of intramuscular fat formation in Japanese Black cattle remains unclear. To investigate the key genes involved in intramuscular fat accumulation, we comprehensively analyzed mRNA levels in subcutaneous and intramuscular fat tissues using RNA sequence (RNA-seq) analysis, which detected 27,606 genes. We identified eight key genes, namely carboxypeptidase E, tenascin C, transgelin, collagen type IV alpha 5 (COL4A5), cysteine and glycine-rich protein 2, PDZ, and LIM domain 3, phosphatase 1 regulatory inhibitor subunit 14A, and regulator of calcineurin 2. These genes were highly and specifically expressed in intramuscular fat tissue. Immunohistochemical analysis revealed a collagen network, including COL4A5, in the basement membrane around the intramuscular fat tissue. Moreover, pathway analysis revealed that, in intramuscular fat tissue, differentially expressed genes are related to cell adhesion, proliferation, and cancer pathways. Furthermore, pathway analysis showed that the transforming growth factor-β (TGF-β) and small GTPases regulators RASGRP3, ARHGEF26, ARHGAP10, ARHGAP24, and DLC were upregulated in intramuscular fat. Our study suggests that these genes are involved in intramuscular fat formation in Japanese Black cattle.

Sexual Dimorphism of Metabolite Profiles in Pigs Depends on the Genetic Background

The study aimed to investigate possible systematic effects in the basic underlying variability of individual metabolomic data. In this context, the extent of gender- and genotype-dependent differences reflected in the metabolic composition of three tissues in fattening pigs was determined. The 40 pigs belonged to the genotypes PIx(LWxGL) and PIxGL with gilts and boars, respectively. Blood and tissue samples from M. longissimus dorsi and liver were directly taken at the slaughtering plant and directed to GC × GC qMS metabolite analysis. Differences were observed for various metabolite classes like amino acids, fatty acids, sugars, or organic acids. Gender-specific differences were much more pronounced than genotype-related differences, which could be due to the close genetic relation of the fattening pigs. However, the metabolic dimorphism between gilts and boars was found to be genotype-dependent, and vice versa metabolic differences between genotypes were found to be gender-dependent. Most interestingly, integration into metabolic pathways revealed different patterns for carbon (C) and nitrogen (N) usage in boars and gilts. We suppose a stronger N-recycling and increased energy metabolism in boars, whereas, in gilts, more N is presumably excreted and remaining carbon skeletons channeled into lipogenesis. Associations of metabolites to meat quality factors confirmed the applicability of metabolomics approaches for a better understanding about the impact of drivers (e.g., gender, age, breed) on physiological processes influencing meat quality. Due to the huge complexity of the drivers-traits-network, the derivation of independent biomarkers for meat quality prediction will hardly be possible.

Exploring the Lipids Involved in the Formation of Characteristic Lactones in Japanese Black Cattle

The meat from Japanese Black cattle (Japanese Wagyu) is finely marbled and exhibits a rich and sweet aroma known as Wagyu beef aroma. To clarify the key metabolites involved in the aroma, we analyzed the correlation between lactone and lipid composition in Japanese Black cattle. Using gas chromatography-olfactometry, we identified 39 characteristic odorants of the intermuscular fat. Seven characteristic lactones considered to be involved in Wagyu beef aroma were quantified and compared in the marbled area and intermuscular fat using a stable isotope dilution assay. Among them, γ-hexalactone was the only lactone whose level was significantly higher in the marbled area. To explore the lipid species involved in lactone formation, we analyzed samples with different aroma characteristics. Liquid chromatography-mass spectrometry revealed eight lipid classes and showed significant differences in triacylglycerides (TAGs). To determine the molecular species of TAGs, we performed high-performance liquid chromatography analysis and identified 14 TAG species. However, these analyses showed that seven lactones had a low correlation with the TAGs. However, γ-hexalactone showed a positive correlation with linoleic acid. This study suggests that lipid composition affects the characteristic lactone profile involved in the Wagyu beef aroma.

Exploring the Characteristic Aroma of Beef from Japanese Black Cattle (Japanese Wagyu) via Sensory Evaluation and Gas Chromatography-Olfactometry

Beef from Japanese Black cattle (Japanese Wagyu) is renowned for its flavor characteristics. To clarify the key metabolites contributing to this rich and sweet aroma of beef, an omics analysis combined with GC-olfactometry (GC-O) and metabolomics analysis with gas chromatography-mass spectrometry (GC-MS) were applied. GC-O analysis identified 39 odor-active odorants from the volatile fraction of boiled beef distilled by solvent-assisted flavor evaporation. Eight odorants predicted to contribute to Wagyu beef aroma were compared between Japanese Black cattle and Holstein cattle using a stable isotope dilution assay with GC-tandem quadrupole mass spectrometry. By correlating the sensory evaluation values of retronasal aroma, γ-hexalactone, γ-d2ecalactone, and γ-undecalactone showed a high correlation with the Wagyu beef aroma. Metabolomics data revealed a high correlation between the amounts of odorants and multiple metabolites, such as glutamine, decanoic acid, lactic acid, and phosphoric acid. These results provide useful information for assessing the aroma and quality of beef.

Food Phenotyping: Recording and Processing of Non-Targeted Liquid Chromatography Mass Spectrometry Data for Verifying Food Authenticity

Experiments based on metabolomics represent powerful approaches to the experimental verification of the integrity of food. In particular, high-resolution non-targeted analyses, which are carried out by means of liquid chromatography-mass spectrometry systems (LC-MS), offer a variety of options. However, an enormous amount of data is recorded, which must be processed in a correspondingly complex manner. The evaluation of LC-MS based non-targeted data is not entirely trivial and a wide variety of strategies have been developed that can be used in this regard. In this paper, an overview of the mandatory steps regarding data acquisition is given first, followed by a presentation of the required preprocessing steps for data evaluation. Then some multivariate analysis methods are discussed, which have proven to be particularly suitable in this context in recent years. The publication closes with information on the identification of marker compounds.

1H NMR-based metabolomics study of breast meat from Pekin and Linwu duck of different ages and relation to meat quality

This study investigated the effects of breed and age on meat quality, and metabolite profiles of duck breast meat, and the relationship between changes in metabolite profiles and the meat quality. The meat quality and 1H nuclear magnetic resonance (NMR)-based metabolomics of breast meat from Pekin and Linwu ducks at 2 different ages (42 and 72d) was analyzed. The results showed that age exerted a greater effect on the observed meat quality traits of breast meat than breed, and its interaction (breed × age) effect on pH values and yellowness (b*) of duck breast meat was significant. Total of 32 metabolites were detected in breast meat of Pekin and Linwu duck. The difference of metabolite profiles in breast meat between Pekin and Linwu duck at 72 d was greater than that at 42 d, while the effects of age on metabolites of duck meat from both breeds were similar. Anserine, aspartate, and carnosine were the most relevant metabolites of duck breast meat quality, and nicotinamide in duck breast meat was negatively correlated with cooking loss. These results provide an overall perspective for bridging the gap between the breed and age on duck meat quality and metabolome, and improve the understanding of the relationship between metabolites and duck meat quality.

MEATabolomics: Muscle and Meat Metabolomics in Domestic Animals

In the past decades, metabolomics has been used to comprehensively understand a variety of food materials for improvement and assessment of food quality. Farm animal skeletal muscles and meat are one of the major targets of metabolomics for the characterization of meat and the exploration of biomarkers in the production system. For identification of potential biomarkers to control meat quality, studies of animal muscles and meat with metabolomics (MEATabolomics) has been conducted in combination with analyses of meat quality traits, focusing on specific factors associated with animal genetic background and sensory scores, or conditions in feeding system and treatments of meat in the processes such as postmortem storage, processing, and hygiene control. Currently, most of MEATabolomics approaches combine separation techniques (gas or liquid chromatography, and capillary electrophoresis)-mass spectrometry (MS) or nuclear magnetic resonance (NMR) approaches with the downstream multivariate analyses, depending on the polarity and/or hydrophobicity of the targeted metabolites. Studies employing these approaches provide useful information to monitor meat quality traits efficiently and to understand the genetic background and production system of animals behind the meat quality. MEATabolomics is expected to improve the knowledge and methodologies in animal breeding and feeding, meat storage and processing, and prediction of meat quality.

Food authentication in real life: How to link nontargeted approaches with routine analytics?

In times of increasing globalization and the resulting complexity of trade flows, securing food quality is an increasing challenge. The development of analytical methods for checking the integrity and, thus, the safety of food is one of the central questions for actors from science, politics, and industry. Targeted methods, for the detection of a few selected analytes, still play the most important role in routine analysis. In the past 5 years, nontargeted methods that do not aim at individual analytes but on analyte profiles that are as comprehensive as possible have increasingly come into focus. Instead of investigating individual chemical structures, data patterns are collected, evaluated and, depending on the problem, fed into databases that can be used for further nontargeted approaches. Alternatively, individual markers can be extracted and transferred to targeted methods. Such an approach requires (i) the availability of authentic reference material, (ii) the corresponding high-resolution laboratory infrastructure, and (iii) extensive expertise in processing and storing very large amounts of data. Probably due to the requirements mentioned above, only a few methods have really established themselves in routine analysis. This review article focuses on the establishment of nontargeted methods in routine laboratories. Challenges are summarized and possible solutions are presented.

Gas Chromatography-Mass Spectrometry-Based Metabolomic Analysis of Wagyu and Holstein Beef

Japanese Black cattle (Wagyu) beef is characterized by high intramuscular fat content and has a characteristic sweet taste. However, the chemical components for characterizing the sweet taste of Wagyu beef have been unclear. In this experiment, we conducted a metabolomic analysis of the longissimus muscle (sirloin) in Wagyu and Holstein cattle to determine the key components associated with beef taste using gas chromatography–mass spectrometry (GC-MS). Holstein sirloin beef was characterized by the abundance of components such as glutamine, ribose-5-phosphate, uric acid, inosine monophosphate, 5-oxoproline, and glycine. In contrast, Wagyu sirloin beef was characterized by the abundance of sugar components (maltose and xylitol). Dietary fat is known to increase the intensity of sweet taste. These results suggest that the sweet taste of Wagyu beef is due to the synergetic effects of higher sugar components and intramuscular fat.

Predicting the Quality of Meat: Myth or Reality?

This review is aimed at providing an overview of recent advances made in the field of meat quality prediction, particularly in Europe. The different methods used in research labs or by the production sectors for the development of equations and tools based on different types of biological (genomic or phenotypic) or physical (spectroscopy) markers are discussed. Through the various examples, it appears that although biological markers have been identified, quality parameters go through a complex determinism process. This makes the development of generic molecular tests even more difficult. However, in recent years, progress in the development of predictive tools has benefited from technological breakthroughs in genomics, proteomics, and metabolomics. Concerning spectroscopy, the most significant progress was achieved using near-infrared spectroscopy (NIRS) to predict the composition and nutritional value of meats. However, predicting the functional properties of meats using this method-mainly, the sensorial quality-is more difficult. Finally, the example of the MSA (Meat Standards Australia) phenotypic model, which predicts the eating quality of beef based on a combination of upstream and downstream data, is described. Its benefit for the beef industry has been extensively demonstrated in Australia, and its generic performance has already been proven in several countries.