Transcriptomic-proteomic integration: A powerful synergy to elucidate the mechanisms of meat spoilage in the cold chain

Recent advances in spoilage mechanisms and preservation technologies in beef quality: A review

Beef is a popular meat product that can spoil and lose quality during postharvest handling and storage. This review examines different preservation methods for beef, from conventional techniques like low-temperature preservation, irradiation, vacuum packing, and chemical preservatives, to novel approaches like bacteriocin, essential oil, and non-thermal technologies. It also discusses how these methods work and affect beef quality. The review shows that beef spoilage is mainly due to enzymatic and microbial activities that impact beef freshness, texture, and quality. Although traditional preservation methods can extend beef shelf life, they have some drawbacks and limitations. Therefore, innovative preservation methods have been created and tested to improve beef quality and safety. These methods have promising results and potential applications in the beef industry. However, more research is needed to overcome the challenges and barriers for their commercialization. This review gives a comprehensive and critical overview of the current and emerging preservation methods for beef and their implications for the beef supply chain.

Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance

Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.

Antibacterial efficacy of phenyllactic acid against Pseudomonas lundensis and Brochothrix thermosphacta and its synergistic application on modified atmosphere/air-packaged fresh pork loins

Microbial contamination is a crucial problem that is difficult to solve for the meat industry. Therefore, this study explored the antibacterial efficacy of phenyllactic acid (PLA) against Pseudomonas lundensis (PL) and Brochothrix thermosphacta (BT) solely and in combination (PL + BT). It also provided insights into its synergistic preservation effect during inoculation in chilled (4 °C) fresh pork loins under air (AP) and modified atmosphere packaging (MAP). The minimum inhibitory concentration (MIC) of PLA was 10 mg/mL. Growth kinetics, scanning electron microscopy (SEM), zeta potential, and cell viability investigations showed that PLA treatment exhibited reduced bacterial growth, aided morphological alterations, and leakage in cell membrane integrity in vitro. Nonetheless, PLA and MAP (70 %N2/30 %CO2) showed an excellent synergistic antibacterial ability against spoilage indicators(total glucose, pH, TVB-N, and TBARS), bacterial counts than AP, without impairing organoleptic acceptability. These results demonstrate the broad antibacterial efficacy of PLA as a biopreservative for the meat industry.

Integrative deep learning framework predicts lipidomics-based investigation of preservatives on meat nutritional biomarkers and metabolic pathways

Preservatives are added as antimicrobial agents to extend the shelf life of meat. Adding preservatives to meat products can affect their flavor and nutrition. This review clarifies the effects of preservatives on metabolic pathways and network molecular transformations in meat products based on lipidomics, metabolomics and proteomics analyses. Preservatives change the nutrient content of meat products via altering ionic strength and pH to influence enzyme activity. Ionic strength in salt triggers muscle triglyceride hydrolysis by causing phosphorylation and lipid droplet splitting in adipose tissue hormone-sensitive lipase and triglyceride lipase. DisoLipPred exploiting deep recurrent networks and transfer learning can predict the lipid binding trend of each amino acid in the disordered region of input protein sequences, which could provide omics analyses of biomarkers metabolic pathways in meat products. While conventional meat quality assessment tools are unable to elucidate the intrinsic mechanisms and pathways of variables in the influences of preservatives on the quality of meat products, the promising application of omics techniques in food analysis and discovery through multimodal learning prediction algorithms of neural networks (e.g., deep neural network, convolutional neural network, artificial neural network) will drive the meat industry to develop new strategies for food spoilage prevention and control.

Bacterial microbiota in different types of processed meat products: diversity, adaptation, and co-occurrence

As a double-edged sword, some bacterial microbes can improve the quality and shelf life of meat products, but others mainly responsible for deterioration of the safety and quality of meat products. This review aims to present a landscape of the bacterial microbiota in different types of processed meat products. After demonstrating a panoramic view of the bacterial genera in meat products, the diversity of bacterial microbiota was evaluated in two dimensions, namely different types of processed meat products and different meats. Then, the influence of environmental factors on bacterial communities was evaluated according to the storage temperature, packaging conditions, and sterilization methods. Furthermore, microbes are not independent. To explore interactions among those genera, co-occurrence patterns were examined. In these respects, this review highlighted the recent advances in fundamental principles that underlie the environmental adaption tricks and why some species tend to occur together frequently, such as metabolic cross-feeding, co-aggregate at microscale, and the intercellular signaling system. Further investigations are required to unveil the underlying molecular mechanisms that govern microbial community systems, ultimately contributing to developing new strategies to harness beneficial microorganisms and control harmful microorganisms.

Overview of omics applications in elucidating the underlying mechanisms of biochemical and biological factors associated with meat safety and nutrition

Over the years, significant technological discoveries have facilitated the improvement of meat-related research. Recent studies of complex and interactive factors contributing to variations in meat safety are increasingly focused on data-driven omics approaches such as proteomics. This review highlighted omics advances in elucidating the biochemical and biological actions on meat safety. Also, the impacts of the nutritional characteristics of meat and meat products on human health are emphasized. Future perspectives should explore multi-omics and in situ investigations to elucidate the implications in microbiological studies, including nutritional and health-related assessments. Also, creating meat safety assessment and prediction models based on biomarkers of meat safety traits will help to mitigate application constraints, thereby evaluating meat quality more accurately. This could provide a scientific basis for increasing the meat industry's profitability and producing high-quality meat and meat products for consumers. SIGNIFICANCE OF THE REVIEW: This review highlighted omics advances in elucidating underlying mechanisms of biochemical and biological factors associated with meat safety. Also, the impacts of meat proteins on human health are emphasized. Future perspectives should explore multi-omics and in situ investigations to elucidate the implications in microbiological studies, including nutritional and health-related assessments. Also, creating meat safety assessment and prediction models based on biomarkers of meat safety traits will help to mitigate application constraints, thereby evaluating meat quality more accurately. This could provide a scientific basis for increasing the meat industry's profitability and producing high-quality meat and meat products for consumers.

Antibacterial Activity and Mechanism of Oxidized Bacterial Nanocellulose with Different Carboxyl Content

Oxidized bacterial nanocellulose (OBC) is reported to prevent microbial growth, but its antibacterial characteristics and mechanism are still unclear. Here, the antibacterial mechanism of OBC is explored by detecting and assessing the interaction of OBC with different carboxyl content on Staphylococcus aureus and Escherichia coli. The results show that OBC has strong antibacterial activity and antibiofilm activity against S. aureus and E. coli, which is positively correlated with the carboxyl content of OBC. After OBC treatment, the bacteria adhesion is inhibited and the cell membrane is destroyed leading to increased permeability. Further investigation reveals that the concentration of cyclic diguanosine monophosphate (c-di-GMP) that induced biofilm formation is significantly decreased to 1.81 pmol mg^-1 after OBC treatment. In addition, OBC inactivates mature biofilms, with inactivation rates up to 79.3%. This study suggests that OBC has excellent antibacterial and antiadhesion properties, which can increase the cell membrane permeability and inhibit c-di-GMP formation. In addition, OBC also has a strong inactivation effect on mature biofilm, which can be used as an effective antibiofilm agent.

The background microbiota and sanitization agent drive the fate of Listeria monocytogenes in multispecies biofilms formed on a plasma-polymerized coating applied on stainless steel

The present study evaluates the anti-biofilm activity of a coating applied with an atmospheric-pressure plasma jet system on AISI 316 stainless steel (SS) against multispecies biofilms containing Listeria monocytogenes (using background microbiota from three different meat industries) using culture-dependent and culture-independent approaches. Also, the disinfection effectiveness and biofilm evolution after sanitization with two food industry biocides were assessed. The anti-biofilm activity of the coating against L. monocytogenes, observed on mono-species biofilms (p < 0.05), was lost on the multispecies biofilms developed for 7 days at 12 °C (p > 0.05), with L. monocytogenes counts ranging from 5.5 ± 0.7 to 6.1 ± 0.5 CFU/cm² on the uncoated SS and from 4.4 ± 0.2 to 6.4 ± 0.5 CFU/cm² on the coated SS. The taxonomic composition of the formed biofilms was highly dependent on the industry but not affected by the artificial inoculation with L. monocytogenes and the nature of the surface (coated vs uncoated SS). When L. monocytogenes was artificially inoculated, its growth was partially controlled in the biofilms developed, with the magnitude of this effect being lower (p < 0.05 on coated SS) for the industry with the lowest taxonomy richness and diversity (3.8 ± 0.2 CFU/cm²), as compared the other two sampled industries (2.4 ± 0.4 and 1.6 ± 0.2 CFU/cm²). The 15-min disinfection treatments with either sodium hypochlorite or peracetic acid at 0.5 % resulted in total viable and L. monocytogenes counts below the limit of detection in most cases, immediately after treatment. The subsequent incubation of the sanitized plates for another 7 days at 12 °C in fresh BHI media led to the development of biofilms with lower bacterial richness and alpha diversity, and higher beta diversity. Even though sodium hypochlorite was in general slightly less effective than peracetic acid immediately after application, it caused a stronger growth control (p < 0.05) of the naturally present L. monocytogenes on the multispecies biofilms developed. This finding highlights the importance of understanding the interspecific competitive relationships between the members of the background microbiota and L. monocytogenes for the long-term control of this pathogen in food processing facilities.

Enhancing the Inhibition Potential of AHL Acylase PF2571 against Food Spoilage by Remodeling Its Substrate Scope via a Computationally Driven Protein Design

The N-acyl homoserine lactone (AHL) acylases are widely used as quorum sensing (QS) blockers to inhibit bacterial food spoilage. However, their substrate specificity for long-chain substrates weakens their efficiency. In this study, a computer-assisted design of AHL acylase PF2571 was performed to modify its substrate scope. The results showed that the variant PF2571^{H194Y, L221R} could effectively quench N-hexanoyl-l-homoserine lactone and N-octanoyl-l-homoserine lactone without impairing its activity against long-chain AHLs. Kinetic analysis of the enzymatic activities further corroborated the observed substrate expansion. The inhibitory activities of this variant were significantly enhanced against the QS phenotype of Aeromonas veronii BY-8, with inhibition rates of 45.67, 78.25, 54.21, and 54.65% against proteases, motility, biofilms, and extracellular polysaccharides, respectively. Results for molecular dynamics simulation showed that the steric hindrance, induced by residue substitution, could have been responsible for the change in substrate scope. This study dramatically improves the practicability of AHL acylase in controlling food spoilage.

Prospects for the next generation of artificial enzymes for ensuring the quality of chilled meat: Opportunities and challenges

As living standards rise, the demand for high-quality chilled meat among consumers also grows. Researchers and enterprises have been interested in ensuring the quality of chilled meat in all links of the downstream industry. Nanozyme has shown the potential to address the aforementioned requirements. Reasons and approaches for the application of nanozymes in the freshness assessment or shelf life extension of chilled meat were discussed. The challenges for applying these nanozymes to ensure the quality of chilled meat were also summarized. Finally, this review examined the safety, regulatory status, and consumer attitudes toward nanozymes. This review revealed that the freshness assessment of chilled meat is closely related to mimicking the enzyme activities of nanozymes, whereas the shelf life changes of chilled meat are mostly dependent on the photothermal activities and pseudophotodynamic activities of nanozymes. In contrast, studies regarding the shelf life of chilled meat are more challenging to develop, as excessive heat or reactive oxygen species impair its quality. Notably, meat contains a complex matrix composition that may interact with the nanozyme, reducing its effectiveness. Nanopollution and mass manufacturing are additional obstacles that must be overcome. Therefore, it is vital to choose suitable approaches to ensure meat quality. Furthermore, the safety of nanozymes in meat applications still needs careful consideration owing to their widespread usage.

Studies on the molecular level changes and potential resistance mechanism of Coreius guichenoti under temperature stimulation

In this study, we used transcriptome and proteome technology to analyze molecular level changes in tissues of Coreius guichenoti cultured at high temperature (HT) and low temperature (LT). We also screened for specific anti-stress genes and proteins and evaluated the relationships between them. We identified 201,803 unigenes and 10,623 proteins. Compared with the normal temperature (NT), 408 genes and 1,204 proteins were up- or down-regulated in brain tissues, respectively, at HT, and the numbers were 8 and 149 at LT. In gill tissues, the numbers were 101 and 1,745 at HT and 27 and 511 at LT. In gill tissues at both temperatures, the degree of down-regulation (average, HT 204.67-fold, LT 443.13-fold) was much greater than that of up-regulation (average, HT 28.69-fold, LT 17.68-fold). The protein expression in brain (average, up 52.67-fold, down 13.54-fold) and gill (average, up 73.02-fold, down 12.92-fold) tissues increased more at HT than at LT. The protein expression in brain (up 3.77-fold, down 4.79-fold) tissues decreased more at LT than at HT, whereas the protein expression in gill (up 8.64-fold, down 4.35-fold) tissues was up-regulated more at LT than at HT. At HT, brain tissues were mainly enriched in pathways related to metabolism and DNA repair; at LT, they were mainly enriched in cancer-related pathways. At both temperatures, gill tissues were mainly enriched in pathways related to cell proliferation, apoptosis, immunity, and inflammation. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed more differentially expressed proteins in gill tissues than in brain tissues at HT and LT, and temperature stimulation led to the strengthening of metabolic pathways in both tissues. Of the 96 genes we identified as potentially being highly related to temperature stress (59 from transcriptome and 38 from proteome data), we detected heat shock protein 70 in both the transcriptome and proteome. Our results improved our understanding of the differential relationship between gene expression and protein expression in C. guichenoti. Identifying important temperature stress genes will help lay a foundation for cultivating C. guichenoti, and even other fish species, that are resistant to HT or LT.

Preparation and characterization of chitosan films incorporating epigallocatechin gallate: Microstructure, physicochemical, and bioactive properties

Novel chitosan films incorporating epigallocatechin gallate (EGCG) were prepared and demonstrated the ideal physical and mechanical properties required of candidate food packaging materials alongside desirable antioxidant and antibacterial activity. Compared with traditional chitosan films, chitosan films incorporated with EGCG were thicker, had higher tensile strength and water solubility, and had lower elongation at break, moisture content, degree of swelling, and water contact angles. Although EGCG-containing films were slightly darker in color than pure chitosan films, they exhibited a greater inhibitory effect on light-induced oxidation with obviously improved UV-vis barrier capability and opacity. Scanning electron microscopy results suggested that EGCG-incorporated samples had a rougher surface structure. This was further confirmed by atomic force microscopy and indicated that the addition of EGCG facilitated the formation of protective barriers through the interaction between the film and food surface. FTIR spectroscopy confirmed that EGCG interacted with chitosan by intermolecular hydrogen bonding and effectively improved the thermal stability of chitosan films. Notably, the incorporation of EGCG significantly enhanced the antioxidant and antibacterial activity of chitosan films. Hence, chitosan films incorporating EGCG have potential applications in the food industry as a novel active packaging material, especially in preventing food oxidation and spoilage in perishable foods.