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

Multiscale metabolomics techniques: Insights into neuroscience research

The field of metabolomics examines the overall composition and dynamic patterns of metabolites in living organisms. The primary methods used in metabolomics include liquid chromatography (LC), nuclear magnetic resonance (NMR), and mass spectrometry (MS) analysis. These methods enable the identification and examination of metabolite types and contents within organisms, as well as modifications to metabolic pathways and their connection to the emergence of diseases. Research in metabolomics has extensive value in basic and applied sciences. The field of metabolomics is growing quickly, with the majority of studies concentrating on biomedicine, particularly early disease diagnosis, therapeutic management of human diseases, and mechanistic knowledge of biochemical processes. Multiscale metabolomics is an approach that integrates metabolomics techniques at various scales, including the holistic, tissue, cellular, and organelle scales, to enable more thorough and in-depth studies of metabolic processes in organisms. Multiscale metabolomics can be combined with methods from systems biology and bioinformatics. In recent years, multiscale metabolomics approaches have become increasingly important in neuroscience research due to the nervous system's high metabolic demands. Multiscale metabolomics can offer novel concepts and approaches for the diagnosis, treatment, and development of medication for neurological illnesses in addition to a more thorough understanding of brain metabolism and nervous system function. In this review, we summarize the use of multiscale metabolomics techniques in neuroscience, address the promise and constraints of these techniques, and provide an overview of the metabolome and its applications in neuroscience.

Transcriptomic and epigenomic insights into pectoral muscle fiber formation at the late embryonic development in pure chicken lines

Long-term intensive genetic selection has led to significant differences between broiler and layer chickens, which are evident during the embryonic period. Despite this, there is a paucity of research on the genetic regulation of the initial formation of muscle fiber morphology in chick embryos. Embryonic d 17 (E17) is the key time point for myoblast fusion completion and muscle fiber morphology formation in chickens. This study aimed to explore the genetic regulatory mechanisms underlying the early muscle fiber morphology establishment in broiler chickens of Cornish (CC) and White Plymouth Rock (RR) and layer chickens of White Leghorn (WW) at E17 using the transcriptomic and chromatin accessibility sequencing of pectoral major muscles. The results showed that broiler chickens exhibited significant higher embryo weight and pectoral major muscle weight at E17 compared to layer chickens (P = 0.000). A total of 1,278, 1,248, and 892 differentially expressed genes (DEGs) of RNA-seq data were identified between CC vs. WW, RR vs. WW, and CC vs. RR, separately. All DEGs were combined for cluster analysis and they were divided into 6 clusters, including cluster 1 with higher expression in broilers and cluster 6 with higher expression in layers. DEGs in cluster 1 were enriched in terms related to macrophage activation (P = 0.002) and defense response to bacteria (P = 0.002), while DEGs in cluster 6 showed enrichment in protein-DNA complex (P = 0.003) and monooxygenase activity (P = 0.000). ATAC-seq data analysis identified a total of 38,603 peaks, with 13,051 peaks for CC, 18,780 peaks for RR, and 6,772 peaks for WW. Integrative analysis of transcriptomic and chromatin accessibility data revealed GOLM1, ISLR2, and TOPAZ1 were commonly upregulated genes in CC and RR. Furthermore, screening of all upregulated DEGs in cluster 1 from CC and RR identified GOLM1, ISLR2, and HNMT genes associated with neuroimmune functions and MYOM3 linked to muscle morphology development, showing significantly elevated expression in broiler chickens compared to layer chickens. These findings suggest active neural system connectivity during the initial formation of muscle fiber morphology in embryonic period, highlighting the early interaction between muscle fiber formation morphology and the nervous system. This study provides novel insights into late chick embryo development and lays a deeper foundation for further research.

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.

Mapping of dressed and processed poultry products in Bangladesh: Identifying the food safety risks for policy intervention

Bangladesh's commercial poultry production is growing rapidly, including the commercial processing of poultry. This expansion of poultry processing plants is fueled by the belief that this sub-sector provides safer food and has less food-borne disease risks compared to traditional live bird markets (LBMs). The purpose of this study is to describe Bangladesh's dressed and processed poultry production and distribution network (PDN), identify what and where quality control occurs, and suggest where improvements could be made. Engaging with PDN for dressed and processed poultry, we used in-depth interviews with key informants to identify the stakeholders involved and their connections with other poultry PDNs. In addition, we mapped out the supply and distribution of dressed and processed poultry and quality control processes occurring throughout the network. We argue that dressed and processed poultry PDNs are closely connected with traditional PDNs such as LBMs, with multiple crossover points between them. Also, there is a lack of consistency in quality control testing and a lack of meat traceability. Consequently, perceptions of dressed and processed poultry being safer than birds from LBMs needs to be treated with caution. Otherwise, unsubstantiated consumer confidence in dressed poultry may inadvertently increase the risk of food-borne diseases from these products.

Metabolomic profiling implicates mitochondrial and immune dysfunction in disease syndromes of the critically endangered black rhinoceros (Diceros bicornis)

The critically endangered black rhinoceros (Diceros bicornis; black rhino) experiences extinction threats from poaching in-situ. The ex-situ population, which serves as a genetic reservoir against impending extinction threats, experiences its own threats to survival related to several disease syndromes not typically observed among their wild counterparts. We performed an untargeted metabolomic analysis of serum from 30 ex-situ housed black rhinos (Eastern black rhino, EBR, n = 14 animals; Southern black rhino, SBR, n = 16 animals) and analyzed differences in metabolite profiles between subspecies, sex, and health status (healthy n = 13 vs. diseased n = 14). Of the 636 metabolites detected, several were differentially (fold change > 1.5; p < 0.05) expressed between EBR vs. SBR (40 metabolites), female vs. male (36 metabolites), and healthy vs. diseased (22 metabolites). Results suggest dysregulation of propanoate, amino acid metabolism, and bile acid biosynthesis in the subspecies and sex comparisons. Assessment of healthy versus diseased rhinos indicates involvement of arachidonic acid metabolism, bile acid biosynthesis, and the pentose phosphate pathway in animals exhibiting inflammatory disease syndromes. This study represents the first systematic characterization of the circulating serum metabolome in the black rhinoceros. Findings further implicate mitochondrial and immune dysfunction as key contributors for the diverse disease syndromes reported in ex-situ managed black rhinos.

The Implications in Meat Quality and Nutrition by Comparing the Metabolites of Pectoral Muscle between Adult Indigenous Chickens and Commercial Laying Hens

Aged chickens are often a secondary dietary choice, owing to the poor organoleptic qualities of their meat. With regard to the meat quality of chickens, the metabolic profiles of pectoral muscle in Guangyuan grey chickens (group G) and Hy-Line grey hens (group H) aged 55 weeks were compared via ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). A total of 74 metabolites were identified with differential changes in the ion model. Lipids and lipid-like molecules comprised the largest proportion among the different metabolites. The content of myristic acid and palmitic acid were found to be higher in the pectoral muscle of group G, while group H showed significantly higher levels of glycerophospholipid molecules, such as LPC(18:2/0:0), Pi(38:5), Pc(16:0/16:0), and Pe(16:1e/14-hdohe). KEGG pathway analysis indicated that the abundant metabolites in group G were mainly involved in energy metabolism and fatty acid biosynthesis and metabolism, whereas those of group H were mainly attributed to the metabolism of unsaturated fatty acids and amino acids. Overall, the differences in lipid and amino acid metabolism in pectoral muscle appear to be responsible for the difference in meat quality between indigenous chickens and commercial laying hens.

Authentication, chemical profiles analysis, and quality evaluation of corn silk via DNA barcoding and UPLC-LTQ/Orbitrap MS chemical profiling

Corn silk is commonly consumed in teas, food ingredients, and herbal medicines. Several varieties of corn silk are grown in different habitats in China. However, as information regarding their phytochemistry and genetic diversity is limited, their medicinal potential has not been utilized thoroughly. Thus, we aimed to use a combination of DNA barcoding based on specific primer ITSC sequences and ultra-performance liquid chromatography coupled with linear trap quadrupole-Orbitrap mass spectrometry (UPLC-LTQ/Orbitrap MS) approach for identifying and evaluating corn silk. ITSC barcoding helped us to identify that 52 samples could be classified into 7 groups of corn silk varieties, but the widely used nrITS and psbA-trnH barcodes failed to identify these varieties. UPLC-LTQ/Orbitrap MS was used to study the components in alcohol extracts derived from different corn silk varieties, and the detected chemical components were analyzed via bioinformatics techniques. We proposed 199 components using untargeted UPLC-LTQ/Orbitrap MS-based metabolomics analysis and identified 67 components. PCA and OPLS-DA analysis revealed two distinct chemotypes by selecting 27 components that could act as difference indicators. KEGG analysis showed that the 199 components were enriched in 12 metabolic pathways. The results showed that corn silk is rich in many types of chemicals and DNA barcoding is better than UPLC-LTQ/Orbitrap MS in distinguishing the differences between different varieties of corn silk. Our findings provide new insights into the chemical and molecular characteristics of different varieties of corn silk, which play a crucial role in the utilization of corn silk resources.

Plasma Metabolomic Profiling Reveals Preliminary Biomarkers of Pork Quality Based on pH Value

This study aimed to identify biomarkers for pork quality evaluation. Firstly, the correlation between indicators of pork quality evaluation was investigated. The pH of pork meat at 45 min post slaughter showed a significant negative correlation with meat color indicators (r: -0.4868--0.3040). Subsequently, porcine plasma samples were further divided into low pH (pH = 6.16 ± 0.22) or high pH (pH = 6.75 ± 0.08) groups. Plasma metabolites in both sample groups were investigated using untargeted metabolomics. In total, 90 metabolites were recognized as differential metabolites using partial least squares discriminant analysis. Pathway enrichment analysis indicated these differential metabolites were enriched in amino acid metabolism and energy metabolism. Correlation analysis revealed that creatinine, L-carnitine, D-sphingosine, citraconic acid, and other metabolites may constitute novel plasma biomarkers with the pH value of pork meat. The current study provides important insights into plasma biomarkers for predicting pork quality based on pH value.

Sustained injection of miR-499-5p alters the gastrocnemius muscle metabolome in broiler chickens

To investigate the effects of miR-499-5p on muscle metabolism in broiler chickens, eight broiler chicks were assigned to the control group and eight to the treatment group, and then we monitored the effects using metabolomics. Chicks were fed basal diets without or with miR-499-5p delivery. Gastrocnemius muscle samples were collected and analyzed by ultrahigh-performance liquid chromatography–tandem mass spectrometry. The results showed that miR-499-5p injection altered the concentrations of a variety of metabolites in the gastrocnemius muscle. Thereby, a total of 46 metabolites were identified at higher (P<0.05) concentrations and 30 metabolites were identified at lower (P<0.05) concentrations in the treatment group compared with the control group. These metabolites were primarily involved with the regulation of lipid and carbohydrate metabolism. Further metabolic pathway analysis revealed that fructose and mannose metabolism, galactose metabolism, inositol phosphate metabolism, and terpenoid backbone biosynthesis were the most critical pathway which may partially interpret the effects of miR-499-5p. To our knowledge, this research is the first report of metabolic signatures and related metabolic pathways in the skeletal muscle for miR-499-5p injection and provides new insight into the effect of miRNA on growth performance.

A Comparison of Different Tissues Identifies the Main Precursors of Volatile Substances in Chicken Meat

Amino acids and fatty acids are the main precursors of volatile organic compounds (VOCs) in meat. The purpose of this study was to determine the main VOC components in chicken breast muscle (BM) and abdominal fat (AF) tissue, as well as the source of VOCs, to provide a basis for quality improvement of broilers. BM and AF served as experimental and control groups, and gas chromatography-mass spectrometry (GC-MS) and untargeted metabolomics were employed to identify the source of VOCs. The results revealed nine VOCs in BM and AF tissues, including hexanal, octanal, and nonanal. VOCs including 1-octen-3-ol, (E,E)-2, 4-nonadienal, and benzaldehyde were significantly elevated in BM compared with AF (p < 0.05), while heptane and diethyl disulphide showed the opposite trend (p < 0.05). Levels of hexanal, heptanal, and octanal were similar in the two tissues. Metabolites of VOCs in chicken BM were investigated by weighted co-expression network analysis. However, only blue module in BM tissue was positively correlated with hexanal (r = 0.66, p = 0.01), heptanal (r = 0.67, p = 0.008), and (E,E)-2,4-nonadienal (r = 0.88, p = 3E-05). L-tyrosine, L-asparagine, adenosine, and valine were the main precursors of (E,E)-2,4-nonadienal and heptanal in BM tissue. Amino acids are the main precursors of 1-octen-3-ol, (E,E)-2, 4-nonadienal, and heptanal in chicken meat, while fatty acids are the main precursors of diethyl disulfide. However, hexanal can be synthesized from amino acids and small amounts of fatty acids as precursors. These findings expand our understanding of VOCs in chicken.

Combining DNA Mini-Barcoding and Species-Specific Primers PCR Technology for Identification of Heosemys grandis

Heosemys grandis, a species of Asian water turtle, that has a wide range of applications in the food and pharmaceutical industries. Since some processed products cannot be identified exclusively by morphological and microscopic identification, a reliable and quick approach to guarantee authenticity is critical. Thus, we fostered an effective and stable molecular identification system to identify Heosemys grandis based on DNA mini-barcoding and species-specific primers PCR technology. A total of 48 turtle samples from 16 different species were collected. To distinguish Heosemys grandis from its counterfeits, DNA mini-barcoding and a pair of species-specific primers were designed and verified by PCR after analyzing the COI sequences of samples. The results showed that only Heosemys grandis samples could generate a single clear band following amplification using species-specific primers. Employing DNA mini-barcoding to amplify samples can verify authenticity by sequence alignment. These findings indicated that species-specific primers PCR technology combined with DNA mini-barcoding could accurately detect the authenticity of Heosemys grandis. This technology broadens the application of molecular biology techniques in the food and pharmaceutical industries. It provides a reliable and convenient method for identifying raw materials to standardize the market and protect customers’ rights and interests.

The Effect of Breed and Age on the Growth Performance, Carcass Traits and Metabolic Profile in Breast Muscle of Chinese Indigenous Chickens

Indigenous chickens possess desirable characteristics and account for considerable proportions of the total chicken production in China. The current study examined the growth performance, carcass characteristics and muscle metabolites among a crossbred broiler and two indigenous, yellow-feathered chickens (Mahuang and Tuer) with different ages (60 and 75 days). Results indicated that the crossbred broiler had better feed efficiency, higher breast and thigh muscle yield, as well as a lower abdominal fat percentage than Mahuang and Tuer chickens (p < 0.05). Gas chromatography–mass spectrometry-based metabolomics and multivariate analysis revealed sugars, amino acids and organic acids were the predominant metabolites that differed among the three chicken breeds. Growth performance and carcass traits of yellow-feathered chickens exhibited significant differences with the extension of the feeding period (p < 0.05). Moreover, differential metabolites reflected altered aminoacyl-tRNA biosynthesis, ATP-binding cassette transporters, pantothenate and CoA biosynthesis, as well as glutathione metabolism in yellow-feathered chickens affected by age. Collectively, this study contributes to a deeper understanding of the production efficiency and chemical composition of precursor flavor in Chinese indigenous, yellow-feathered chicken.