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Insights into Increasing Meat Production Using Omics Technologies

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Animal Metabolism".

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 14927

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Special Issue Editors

Dr. Saulo L. Silva

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Guest Editor

Faculty of Animal Science and Food Engineering, Universidade de São Paulo, Pirassununga 13635-900, SP, Brazil
Interests: animal growth; food composition; meat quality; muscle biology

Dr. Nara Regina Brandão Cônsolo

E-Mail Website
Guest Editor

Faculty of Animal Science and Food Engineering, Universidade de São Paulo, Pirassununga, SP, Brazil
Interests: NMR-based metabolomics; meat quality; animal metabolism; animal production

Prof. Dr. David E. Gerrard

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Guest Editor

School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA
Interests: muscle; metabolism; fiber type; biochemistry; mitochondria; nutrition; energy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Meat animal production systems are constantly being challenged to improve the quantity and quality of products to satisfy consumers’ ever-growing appetite for more and better products—all while demanding a reduction in the use of valuable inputs and limiting impacts on the environment. To accomplish this lofty goal, the creation of new knowledge about muscle growth and meat quality development is absolutely essential if we are to realize gains necessary for feeding the burgeon global population by 2050. A systems-biology approach to studying animal production is a strategy for understanding the complexity of a myriad of biochemical and molecular mechanisms that change in the process of growing tissues that ultimately culminate into a highly nutritious and satiating food: meat. Factors include but are not restricted to feeding regime, genetics, stress, rearing environments, and harvesting and maturation conditions. Understanding the nature of these complex relationships and those variables that impinge on the process of producing high-quality lean meat need to be further understood if significant advances are to be realized in the future. In this regard, a muscle omics-based approach holds great potential to unravel the biochemical changes that occur in this valuable commodity during its production and maturation into meat. Therefore, this Special Issue aims to cover production animal livestock metabolomics and the integration with multi-omics to explore the complex interactions among various factors that impact animal performance and the quality of products produced from agronomically relevant species.

This Special Issue will also address sample preparation methods, advances in data processing, optimization for targeted and untargeted analysis, statistical data analysis using different platforms, and new frontiers and technological breakthroughs fostered by omics technologies. We strongly encourage the submission of research based on metabolic processes and networks, and on the integration with multi-omics and biomarkers discovery.

For this Special Issue of Metabolites, we invite original research papers and reviews that advance our knowledge and understanding of the complex processes that affect livestock biological systems, using varied omics approaches. We hope this Special Issue will contribute to the cutting-edge knowledge undergirding the production of high-quality food products from livestock.

We look forward to your contributions.

Prof. Dr. Saulo L. Silva
Dr. Nara Regina Brandão Cônsolo
Prof. Dr. David E. Gerrard
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

animal products
biomarkers
livestock
lipidomics
muscle metabolism
metabolites
metabolomics
proteomics
transcriptomics

Published Papers (6 papers)

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Research

19 pages, 2221 KiB

Open AccessArticle

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

by Shuji Ueda, Yasuharu Takashima, Yunosuke Gotou, Ryo Sasaki, Rio Nakabayashi, Takeshi Suzuki, Shinji Sasazaki, Ituko Fukuda, Biniam Kebede, Yuki Kadowaki, Maiko Tamura, Hiroki Nakanishi and Yasuhito Shirai

Metabolites 2022, 12(9), 777; https://doi.org/10.3390/metabo12090777 - 23 Aug 2022

Cited by 3 | Viewed by 3148

Abstract

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. Full article

(This article belongs to the Special Issue Insights into Increasing Meat Production Using Omics Technologies)

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14 pages, 1351 KiB

Open AccessArticle

Impact of Cattle Feeding Strategy on the Beef Metabolome

by Juan Fernando Morales Gómez, Nara Regina Brandão Cônsolo, Daniel Silva Antonelo, Mariane Beline, Mohammed Gagaoua, Angel Higuera-Padilla, Luiz Alberto Colnago, David Edwin Gerrard and Saulo Luz Silva

Metabolites 2022, 12(7), 640; https://doi.org/10.3390/metabo12070640 - 13 Jul 2022

Cited by 5 | Viewed by 1760

Abstract

The present study explored changes in the meat metabolome of animals subjected to different finishing systems and growth rates. Thirty-six Angus × Nellore crossbred steers were used in a completely randomized design with four treatments: (1) feedlot system with high average daily gain (ADG; FH); (2) feedlot system with low ADG (FL); (3) pasture system with high ADG (PH); and (4) pasture system with low ADG (PL). After harvest and chilling, Longissimus thoracis (LT) muscle samples were taken for metabolite profile analysis using nuclear magnetic resonance. Spectrum was analyzed using chenomx software, and multi- and mega-variate data analyses were performed. The PLS-DA showed clear separation between FH and PL groups and overlap among treatments with different finishing systems but similar for matching ADG (FL and PH) treatments. Using a VIP cut-off of around 1.0, ATP and fumarate were shown to be greater in meat from PL cattle, while succinate, leucine, AMP, glutamate, carnosine, inosine, methionine, G1P, and choline were greater in meat from FH. Comparing FL and PH treatments, glutamine, carnosine, urea, NAD+, malonate, lactate, isoleucine, and alanine were greater in the meat of PH cattle, while G6P and betaine were elevated in that of FL cattle. Relevant pathways were also identified by differences in growth rate (FH versus PL) and finishing system were also noted. Growth rate caused a clear difference in meat metabolism that was highlighted by energy metabolism and associated pathways, while the feeding system tended to alter protein and lipid metabolism. Full article

(This article belongs to the Special Issue Insights into Increasing Meat Production Using Omics Technologies)

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18 pages, 1157 KiB

Open AccessArticle

Characterizing the Flavor Precursors and Liberation Mechanisms of Various Dry-Aging Methods in Cull Beef Loins Using Metabolomics and Microbiome Approaches

by Derico Setyabrata, Kelly Vierck, Tessa R. Sheets, Jerrad F. Legako, Bruce R. Cooper, Timothy A. Johnson and Yuan H. Brad Kim

Metabolites 2022, 12(6), 472; https://doi.org/10.3390/metabo12060472 - 24 May 2022

Cited by 14 | Viewed by 2071

Abstract

The objective of this study was to characterize and compare the dry-aging flavor precursors and their liberation mechanisms in beef aged with different methods. Thirteen paired loins were collected at 5 days postmortem, divided into four sections, and randomly assigned into four aging methods (wet-aging (WA), conventional dry-aging (DA), dry-aging in a water-permeable bag (DWA), and UV-light dry-aging (UDA)). All sections were aged for 28 days at 2 °C, 65% RH, and a 0.8 m/s airflow before trimming and sample collection for chemical, metabolomics, and microbiome analyses. Higher concentrations of free amino acids and reducing sugars were observed in all dry-aging samples (p < 0.05). Similarly, metabolomics revealed greater short-chain peptides in the dry-aged beef (p < 0.05). The DWA samples had an increase in polyunsaturated free fatty acids (C18:2trans, C18:3n3, C20:2, and C20:5; p < 0.05) along with higher volatile compound concentrations compared to other aging methods (aldehyde, nonanal, octanal, octanol, and carbon disulfide; p < 0.05). Microbiome profiling identified a clear separation in beta diversity between dry and wet aging methods. The Pseudomonas spp. are the most prominent bacterial species in dry-aged meat, potentially contributing to the greater accumulation of flavor precursor concentrations in addition to the dehydration process during the dry-aging. Minor microbial species involvement, such as Bacillus spp., could potentially liberate unique and potent flavor precursors. Full article

(This article belongs to the Special Issue Insights into Increasing Meat Production Using Omics Technologies)

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18 pages, 673 KiB

Open AccessArticle

Transcriptome Profile Reveals Genetic and Metabolic Mechanisms Related to Essential Fatty Acid Content of Intramuscular Longissimus thoracis in Nellore Cattle

by Gustavo Pimenta Schettini, Elisa Peripolli, Pâmela Almeida Alexandre, Wellington Bizarria dos Santos, Angélica Simone Cravo Pereira, Lúcia Galvão de Albuquerque, Fernando Baldi and Rogério Abdallah Curi

Metabolites 2022, 12(5), 471; https://doi.org/10.3390/metabo12050471 - 23 May 2022

Cited by 2 | Viewed by 2556

Abstract

Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile in Longissimus thoracis of Nellore cattle finished in feedlot. Forty-four young bulls clustered in four groups of fifteen animals with extreme values for each FA were evaluated through differentially expressed genes (DEG) analysis and two co-expression methodologies (WGCNA and PCIT). We highlight the ECHS1, IVD, ASB5, and ERLIN1 genes and the TF NFIA, indicated in both FA. Moreover, we associate the NFYA, NFYB, PPARG, FASN, and FADS2 genes with LA, and the RORA and ELOVL5 genes with ALA. Furthermore, the functional enrichment analysis points out several terms related to FA metabolism. These findings contribute to our understanding of the genetic mechanisms underlying the beef EFA profile in Nellore cattle finished in feedlot. Full article

(This article belongs to the Special Issue Insights into Increasing Meat Production Using Omics Technologies)

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13 pages, 940 KiB

Open AccessArticle

Effects of Different Prenatal Nutrition Strategies on the Liver Metabolome of Bulls and Its Correlation with Body and Liver Weight

by Guilherme Henrique Gebim Polizel, Fernando Augusto Correia Queiroz Cançado, Evandro Fernando Ferreira Dias, Arícia Christofaro Fernandes, Roberta Cavalcante Cracco, Brenda Tonsic Carmona, Henrique Hespanhol Castellar, Mirele Daiana Poleti and Miguel Henrique de Almeida Santana

Metabolites 2022, 12(5), 441; https://doi.org/10.3390/metabo12050441 - 14 May 2022

Cited by 5 | Viewed by 2045

Abstract

This study investigated the effect of prenatal nutrition on liver metabolome and on body (BW) and liver weight (LW) of Nellore bulls at slaughter. Three treatments were applied in 126 cows during pregnancy: NP—control (mineral supplementation); PP—protein-energy supplementation in the third trimester; and FP—protein-energy supplementation during the entire pregnancy. Offspring BW and LW were evaluated, and a targeted metabolomics analysis was performed on their livers (n = 18, 22.5 ± 1 months of age). Data were submitted to principal component analysis (PCA), analysis of variance (ANOVA), enrichment analysis, and Pearson’s correlation analysis. The phenotypes did not show differences between treatments (p > 0.05). Metabolites PCA showed an overlap of treatment clusters in the analysis. We found significant metabolites in ANOVA (p ≤ 0.05; Glycine, Hydroxytetradecadienylcarnitine, Aminoadipic acid and Carnosine). Enrichment analysis revealed some biological processes (Histidine metabolism, beta-Alanine metabolism, and Lysine degradation). Pearson’s correlation analysis showed 29 significant correlated metabolites with BW and 1 metabolite correlated with LW. In summary, prenatal nutrition did not show effects on the phenotypes evaluated, but affected some metabolites and biological pathways, mainly related to oxidative metabolism. In addition, BW seems to influence the hepatic metabolome more than LW, due to the amount and magnitude of correlations found. Full article

(This article belongs to the Special Issue Insights into Increasing Meat Production Using Omics Technologies)

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15 pages, 1913 KiB

Open AccessArticle

Prenatal Supplementation in Beef Cattle and Its Effects on Plasma Metabolome of Dams and Calves

by Fernando José Schalch Junior, Guilherme Henrique Gebim Polizel, Fernando Augusto Correia Queiroz Cançado, Arícia Christofaro Fernandes, Isabela Mortari, Pedro Ratto Lisboa Pires, Heidge Fukumasu, Miguel Henrique de Almeida Santana and Arlindo Saran Netto

Metabolites 2022, 12(4), 347; https://doi.org/10.3390/metabo12040347 - 13 Apr 2022

Cited by 14 | Viewed by 2261

Abstract

This study investigated the effect of different prenatal nutrition on the plasma metabolome of Nellore dams and their offspring. For that purpose, three nutritional treatments were used in 126 cows during pregnancy: NP—(control) only mineral supplementation; PP—protein-energy supplementation in the final third; and FP—protein-energy supplementation during the entire pregnancy. Targeted metabolomics were analyzed in plasma at the beginning of pregnancy and in pre-delivery of cows (n = 27) as well as in calves (n = 27, 30 ± 9.6 days of age). Data were analyzed by the analysis of variance, partial least squares discriminant analysis, and the principal component analysis (PCA). The PCA showed a clear clustering in the periods investigated only in cows (early gestation and pre-delivery). We found significant metabolites in both supervised analyses (p < 0.05 and VIP score > 1) for cows (Taurine, Glutamic acid, Histidine, and PC aa C42:2) and for calves (Carnosine, Alanine, and PC aa C26:0). The enrichment analysis revealed biological processes (p < 0.1) common among cows and calves (histidine metabolism and beta-alanine metabolism), which may be indicative of transgenerational epigenetic changes. In general, fetal programming affected mainly the metabolism of amino acids. Full article

(This article belongs to the Special Issue Insights into Increasing Meat Production Using Omics Technologies)

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