Bacterial populations and the volatilome associated to meat spoilage

Chemical composition, extraction sources and action mechanisms of essential oils: Natural preservative and limitations of use in meat products

The antimicrobial activity of essential oils (EO) is associated with the presence of secondary metabolites synthesized by plants. Its mechanism of action involves the interaction of its hydrophobic components with the lipids present in the cell membrane of microorganism, resulting in metabolic damages and cell death. Spoilage and pathogenic microorganisms are contaminants in meat and meat products with considerable impacts on food quality and safety. Research shows the potential of applying essential oils in the preservation of meat food systems as compounds of low toxicity, extracted from a natural source, and as an alternative to consumer demand for healthy foods with a more natural appeal. In addition, there is a great diversity of plants from which essential oils can be extracted, whose antimicrobial activity in vitro and in meat and meat products has been proven.

Microbial biopreservatives for controlling the spoilage of beef and lamb meat: their application and effects on meat quality

Biopreservation is a recognized natural method for controlling the growth of undesirable bacteria on fresh meat. It offers the potential to inhibit spoilage bacteria and extend meat shelf-life, but this aspect has been much less studied compared to using the approach to target pathogenic bacteria. This review provides comprehensive information on the application of biopreservatives of microbial origin, mainly bacteriocins and protective cultures, in relation to bacterial spoilage of beef and lamb meat. The sensory effect of these biopreservatives, an aspect that often receives less attention in microbiological studies, is also reviewed. Microbial biopreservatives were found to be able to retard the growth of the major meat spoilage bacteria, Brochothrix thermosphacta, Pseudomonas spp., and Enterobacteriaceae. Their addition did not have any discernible negative impact on the sensory properties of meat, whether assessed by human sensory panels or instrumental and chemical analyses. Although results are promising, the concept of biopreservation for controlling spoilage bacteria on fresh meat is still in its infancy. Studies in this area are still lacking, especially for lamb. Biopreservatives need more testing under conditions representative of commercial meat production, along with studies of any possible sensory effects, in order to validate their potential for large-scale industrial applications.

Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis

To identify the microbial community and origin of the spoilage flora of bacon, the changes in microbial population numbers and community structure were followed along the processing line, using culture-independent and culture-dependent methods. 16S rRNA gene amplicon sequencing (16S-seq) analysis showed that community complexity and structure significantly differed at different processing stages. Some 428 bacterial groups were ascertained at genus level, and Acinetobacter, Pseudomonas, Psychrobacter, and Brochothrix were the predominant bacteria on raw meats. After curing specimens dominated by Psychrobacter, Weissella, Vibrio, Leuconostoc, Myroides, Acinetobacter, and Lactobacillus, a total of 33 species were identified by traditional microbiological analyses and direct sequence determination methods. Our results indicated that curing should be considered one of the primary factors during various processing steps, presumably contaminating the products directly or indirectly.

Enhanced preservation of vacuum-packaged Atlantic salmon by hyperbaric storage at room temperature versus refrigeration

Hyperbaric storage at room temperature (HS/RT: 75 MPa/25 °C) of vacuum-packaged fresh Atlantic salmon (Salmo salar) loins was studied for 30 days and compared to atmospheric pressure at refrigerated temperatures (AP/5 °C, 30 days) and RT (AP/25 °C, 5 days). Most of the fatty acids were not affected by storage conditions, with only a slight decrease of docosahexaenoic acid (DHA) content (n-3 polyunsaturated fatty acid) for AP samples, reflected in the lower polyene index values obtained and higher oxidation extent. For HS, a lower lipid oxidation extension and a slower increase of myofibrillar fragmentation index values were observed, when compared to AP samples. The volatile profile was similar for the HS and fresh samples, with the HS samples retaining fresh-like alcohols and aldehydes components, which disappeared in AP samples, mainly in AP/25 °C samples. The volatile profile for AP samples (5 and 25 °C) revealed mostly spoilage-like compounds due to microbial activity. Drip loss increased progressively during the 30 days of storage under HS, while a slight decrease of water holding capacity after 5 days was observed, increasing further after 30 days. Regarding textural properties, only resilience was affected by HS, decreasing after 30 days. So, HS/RT could represent an interesting extended preservation methodology of fresh salmon loins, since allows retaining important physicochemical properties for at least 15 days, while refrigeration after 5 days showed already volatile spoilage-like compounds due to microbial activity. Furthermore, this methodology allows additional considerable energy savings when compared to refrigeration.

High incidence of cold-tolerant Clostridium frigoriphilum and C. algidicarnis in vacuum-packed beef on retail sale in Germany

Sixty vacuum-packed beef samples retailed in Germany were investigated for the occurrence of cold-tolerant Clostridium spp. After a storage period at 4 °C for eight weeks, meat juice from all samples was processed for culturing, DNA extraction and SYBR green qPCR for Clostridium species. After that, a previously developed multiplex qPCR, sequence analysis of the 16S rRNA gene, and MALDI-TOF MS were applied in order to identify Clostridium spp. found in samples. Subsequently, 23 samples were found positive for C. frigoriphilum (n = 19), C. estertheticum (n = 2), C. tagluense (n = 1) and C. lacusfryxellense/C. frigoris (n = 1). By using a new multiplex qPCR and a new RFLP method developed in this study, a further 15 meat juice samples were revealed to be contaminated with C. algidicarnis. With some samples being co-contaminated with two different species, 53% (n = 32) of all investigated vacuum-packed beef samples were found to be positive for cold-tolerant clostridia. This is the first report of detection and identification of C. algidicarnis in meat samples in Germany and Central Europe.

Effect of Different Aging Methods on the Formation of Aroma Volatiles in Beef Strip Loins

This study investigated the effects of different aging methods on the changes in the concentrations of aroma volatiles of beef. One half (n = 15) of the beef strip loins were dry-aged, and the other half were wet-aged, and both aging processes continued for 28 days. The aroma volatiles from dry- and wet-aged samples were analyzed at seven-day intervals (n = 3 for each aging period). As the aging period increased, dry-aged beef showed higher concentrations of volatile compounds than those in wet-aged beef (p < 0.05). Most changes in the concentrations of aroma volatiles of dry-aged beef were associated with propanal, 2-methylbutanal, 2-methylpropanal, 1-butanamine, trimethylamine, 2-methyl-2-propanethiol, and ethyl propanoate, which were mainly produced by lipid oxidation and/or microbial activity (e.g., proteolysis and lipolysis) during the dry aging period. Therefore, we suggest that the differences in aroma between dry- and wet-aged beef could result from increased lipid oxidation and microbial activity in dry-aged beef possibly owing to its ambient exposure to oxygen.

Dry-aged beef manufactured in Japan: Microbiota identification and their effects on product characteristics

We aimed to determine the mold, yeast, and bacterial distributions in dry-aged beef (DAB) manufactured in Hokkaido, Japan, and to study their effects on meat quality compared to wet-aged beef (WAB). Two rump blocks from Holstein steer were dry- and wet-aged for 35 days at 2.9 °C and 90% RH. The psychrophilic molds Mucor flavus and Helicostylum pulchrum and other fungi (Penicillium sp. and Debaryomyces sp.) appeared on the crust of DAB, while lactic acid bacteria and coliforms were suppressed in the inner part of the meat. The composition of C16:0, C18:0, and C18:1 fatty acids did not differ between DAB and WAB, while more C17:0 fatty acids were detected in DAB. Dry aging suppressed acids and increased the production of various aroma compounds with mushroom-like, nutty, and other pleasant flavors. The meat quality and free amino acid (FAA) contents of DAB and WAB did not differ significantly. In this study, we identified major molds on DAB, which might contribute to an increase in aroma. Keywords: dry-aged beef; Mucor flavus; Helicostylum pulchrum; psychrophilic mold; meat quality; volatile aroma compounds.

Fatty Acid Composition and Volatile Profile of M. longissimus thoracis from Commercial Lambs Reared in Different Forage Systems

Animal production factors can affect the fatty acid and volatile profile of lamb meat. The fatty acid and volatile composition of the M. longissimus thoracis was evaluated from 150 lambs from 10 groups of commercial lambs that differed in age, sex, diet and breed, from three farms, which represent typical forage lamb production systems in New Zealand. The meat from 4-month-old composite lambs slaughtered at weaning had a similar polyunsaturated to saturated fatty acid ratio compared to 6- to 8-month-old composite lambs, but a greater ratio than that of 12-month-old Merino lambs (p < 0.05), with all ratios being lower than the recommended ≥0.45. All lamb production systems produced meat with an omega-6 to omega-3 ratio below 1.5, well below the recommended ratio ≤ 4.0. Meat from 4-month-old lambs had higher C12:0, C14:0 and C16:0 and lower C18:0, reflecting the composition of the milk diet, resulting in higher atherogenic index than meat from other animal groups, while meat from 12-month-old Merino lambs, with lower content of polyunsaturated fatty acids, showed higher thrombogenic index. Meat from lambs processed at weaning contained the greatest concentration of eicosapentaenoic and docosahexaenoic acids, which would qualify as a 'source' or 'good source' of these target fatty acids based on the Commission of Regulation of the European Union or the Food Standards Australia New Zealand guidelines, respectively. Volatiles were extracted from the headspace of raw lean meat and 36 volatile compounds were identified. The abundance of carbon disulphide, isododecane, heptanal, 2,5-hexanediol and 3-octanone and pentanoic, octanoic, nonanoic and heptanoic acids was similar between all groups of lambs. Meat from 12-month-old Merino lambs had low abundance of acetic, propanoic, butanoic and hexanoic acids, and hexanal, octanal and dimethyl sulphide. For 6- to 8-month-old composite lambs, hexanal, octanal and nonanal were present at higher relative abundance in meat from lambs that grazed on chicory than perennial ryegrass. The significant differences in the fatty acid and volatile profiles in meat from 12-month-old Merino lambs compared with lambs slaughtered at weaning or further grazed on red clover, chicory or mixed pasture may result in distinctive nutritional value and lamb flavour.

Suitability of Biodegradable Materials in Comparison with Conventional Packaging Materials for the Storage of Fresh Pork Products over Extended Shelf-Life Periods

The packaging of fresh meat has been studied for decades, leading to improved packaging types and conditions such as modified atmosphere packaging (MAP). While commonly used meat packaging uses fossil fuel-based materials, the use of biodegradable packaging materials for this application has not been studied widely. This study aimed at evaluating the sustainability of biodegradable packaging materials compared to established conventional packaging materials through analyses of the quality of freshly packaged pork. The quality was assessed by evaluating sensory aspects, meat color and microbiological attributes of the pork products. The results show no significant differences (p > 0.05) in ground pork and pork loin stored in biodegradable MAP (BioMAP) and conventional MAP for the evaluated sensory attributes, meat color or total bacterial count (TBC) over extended storage times. The data suggest that BioMAP could be a viable alternative to MAP using conventional, fossil fuel-based materials for the storage of fresh meats, while simultaneously fulfilling the customers’ wishes for a more environmentally friendly packaging alternative.

Antilisterial Activity of Bacteriocins Produced by Lactic Bacteria Isolated from Dairy Products

Sixty-nine Lactic Acid Bacteria (LAB) and bifidobacteria were isolated and identified from Italian dairy products (raw milk, cream, butter, soft cheese and yoghurt) to find new antimicrobial compounds to use as food bio-preservatives. All the isolates were preliminarily screened by the deferred antagonism method for bacteriocin production. Afterwards, to evaluate the release of bacteriocin in liquid medium, the Cell-Free Supernatant Fluid (CFSF) of the best producers was tested by agar well diffusion assay. The study allowed the selection of three bacteriocin producing strains (Enterococcus faecium E23, Bifidobacterium thermophilum B23 and Lactobacillus bulgaricus L21), endowed with the strongest and broadest inhibitory capability against the pathogen Listeria monocytogenes. The molecular characteristics and the chemical–physical properties of both producers and the respective bacteriocins were studied and compared. The results showed that E. faecium E23 was the best producer strain and its class IIa bacteriocins, called enterocin E23, exhibited a good spectrum of activity towards L. monocytogenes. Enterocin E23 was stable over a wide range of pH and at low temperatures for at least four months and, for this reason, it can be employed in refrigerated foods for the control of L. monocytogenes, the major concern in dairy products.

Diversity and succession of the microbial community and its correlation with lipid oxidation in dry-cured black carp (Mylopharyngodon piceus) during storage

This study aimed to achieve deeper insights into the microbiota composition and dynamic succession of the dry-cured black carp during storage using a high-throughput sequencing technique (HTS). The effect of lipid oxidation on microorganisms was also evaluated. Over 651 bacterial genera belonging to 37 phyla were identified. Firmicutes, Proteobacteria and Actinobacteria were the main bacterial phylum, some are highly associated with meat spoilage. Staphylococcus, Macrococcus and Acinetobacter were the most three microbial genera throughout the entire storage period (30 days). Between two different storage temperature, refrigeration at 4 °C could facilitate maintaining the microbial diversity, while 25 °C storage led to the formation of dominant microflora and the reduction of community diversity. Canonical correspondence analysis (CCA) showed that acid value (AV), malondialdehyde (MDA) and 4-hydroxy-2-hexenal (HHE) contents were three key environmental factors (oxidation products) affecting the profile of the microbiota. Staphylococcus presented a positive correlation with HHE content, while Macrococcus and Acinetobacter were negatively correlated with HHE content. These results could expand our knowledge on the effect of lipid oxidation on change of microbial distribution, it could also present an guideline to develop advanced storage methods for the vacuum packed dry-cured fish products.

How Volatile Compounds, Oxidative Profile and Sensory Evaluation Can Change with Vacuum Aging in Donkey Meat

Simple Summary

Aging in donkey meat was never investigated. It represents an important process, because it leads the muscle to become meat. There are many ways to age meat, and vacuum aging is one of these. The present paper characterised donkey meat Volatile Organic Compounds (VOCs) production during 14 vacuum aging days, its oxidative status and the consequent sensory evaluation. Lipid oxidative processes are delayed, but some protein oxidative processes happen, influencing VOCs production and sensory evaluation.

Abstract

This study aims to improve knowledge on donkey meat and the vacuum aging effect on the Volatile Organic Compounds (VOCs), oxidative profile and status and the sensory characteristics. Ten 18-month old Martina Franca donkeys’ male foals were involved in the trial. Longissimus thoracis (LT) muscle was extracted from each left half carcass, between the fourth and the ninth rib. Each muscle was divided into five sections, vacuum packaged, stored at 2 °C, and randomly assigned to one of the different aging time (1, 3, 6, 9, and 14 days of aging). Volatile compounds, oxidation parameters, and antioxidant enzymes were analysed, and a sensory test was performed. A nested one-way analysis of variance (ANOVA) was performed for aging time as an independent variable. Significance was set at p < 0.05. Aldehydes are the most produced VOCs, but no changes were observed during vacuum aging (p > 0.05). Nitrogen compounds increased during aging (p < 0.01). TBARs and hydroperoxides did not change during the storage, whereas the protein carbonyls increased (p < 0.05). Vacuum aging slowed down lipid oxidation and put in evidence the presence of protein oxidation and degradation, influencing the VOCs productions and sensory evaluation.

Development of a Dye-Based Device to Assess Poultry Meat Spoilage. Part I: Building and Testing the Sensitive Array

The rationale behind the material and dye selection and the investigation of the properties of a solid-phase sensor array designed for following chicken meat spoilage is presented, having in mind that the final target must be the naked eye identification of the degradation steps. The device is obtained by fixing five acid-base indicators, m-cresol purple (1), o-cresol red (2), bromothymol blue (3), thymol blue (4), and chlorophenol red (5), and a sensing molecule specific for thiols, 5,5'-dithiobis(2-nitrodibenzoic acid), called Ellman's reagent, (6) on a commercial cellulose-based support. The dimensions of the sensor and the amount of dye sorbed on the solid are carefully studied. The preparation protocol to get reproducible sensing materials is established, based on the kinetic study and the color change investigation. The material stability and the capacity of changing color, according to the acid-base properties of the dyes, are tested. The sources of uncertainty, coming from the technique employed for signal data acquisition and treatment and from the intrinsic variability of the spots based on the commercial support, are established. The highest variability does not come from photo acquisition by a mobile phone, the effect of the illumination equipment, the partial least-squares (PLS) model employed to assess the amount of dye sorbed into the solid but from the variability of different spots and was found equal to 10%. The uncertainty is adequate for final employment since it is referred to as replicates under different conditions that are definitively judged almost always identical by naked eye evaluation, which is our last target for assessing a change of the colors associated with spoilage.

Development of a Dye-Based Device to Assess the Poultry Meat Spoilage. Part II: Array on Act

This work presents a colorimetric dye-based array for naked-eye detection of chicken meat spoilage. The array is obtained by fixing five acid-base indicators, m-cresol purple (1), o-cresol red (2), bromothymol blue (3), thymol blue (4), and chlorophenol red (5), and a sensing molecule specific for thiols, 5,5'-dithiobis(2-nitrodibenzoic acid), called Ellman's reagent (6), on a cellulose-based support. The dyes, being permanently charged, are fixed on the support via ion-exchange. The entire degradation process of beast poultry meat, at ambient temperature and in a domestic fridge, is followed by the change of the color of the array, placed in the headspace over the meat samples. The device is set after selection of the most suitable starting form, which could be the acidic or the basic color of indicators, being the proper dye concentration and the dimension of the spots already established. Basing on sensors colors, we identified three levels of the degradation process of chicken meat, named SAFE, WARNING, and HAZARD. By instrumental analysis, we demonstrated that sensors response was correlated to volatile organic compounds (VOCs) composition in the headspace and, thus, to meat spoilage progress. We demonstrated that biogenic amines (BAs), commonly considered a critical spoilage marker, are indeed produced into the samples but never present in the headspace, even in traces, during the investigated time-lapse. The VOC evolution nevertheless allows one to assign the sample as WARNING and further HAZARD. Some indicators turned out to be more informative than others, and the best candidates for a future industrial application resulted in a bromothymol blue (3)-, chlorophenol red (5)-, and Ellman's reagent (6)-based array.

Development of two specific multiplex qPCRs to determine amounts of Pseudomonas, Enterobacteriaceae, Brochothrix thermosphacta and Staphylococcus in meat and heat-treated meat products

Culturing methods are conventionally applied to investigate the contamination of food with several microorganisms after heat processing. However, with these methods, it is not possible to evaluate whether heat-treated meat products, such as cooked sausages, contained parts of spoiled meat. Therefore, two specific multiplex qPCRs were developed in this study in order to determine the microbiological quality of the raw materials used for these products. The PCR targets focused on four bacterial groups often found on meat (family Enterobacteriaceae, genus Pseudomonas, genus Staphylococcus and species Brochothrix thermosphacta). Specificity as well as sensitivity of the developed multiplex qPCRs, validated by using 68 microbial species, were 100%. The applicability of both multiplex qPCRs compared to culturing methods was performed using 96 meat samples (fresh and naturally spoiled) and 12 inhouse-made "Lyoner" sausages containing variable ratios of spoiled meat (0%, 5%, 12% and 25%; n = 3 for each group). Both methods showed similar results by evaluating the ∆log₁₀ cfu/g, the relative accuracy and the t-test analysis (p > 0.05). Comparing qPCR results of the different sausage groups, a significant difference between sausages containing fresh meat and sausages containing spoiled meat (12% and 25%) was found only for Pseudomonas and B. thermosphacta in both raw and cooked sausages. The statistical difference between 5% vs. 12% and 25% spoiled meat in cooked sausages, was also found only for these two bacterial groups. The developed multiplex qPCRs were further applied to 30 commercially available "Bologna-type" sausages. The results showed a total of 14 sausages considered to be suspicious for Food Fraud. While the role of Staphylococcus spp. in meat spoilage remains unclear, Pseudomonas, Enterobacteriaceae and B. thermosphacta could together be used as an indicator for "spoiled meat" used in sausages. The developed qPCR systems in this study allow the detection of four relevant bacterial groups in the heated Bologna-type sausages and provide information about the hygienic quality of raw materials used. This method could thus be helpful for screening food suspected of Food Fraud.

The effects of storage and hop extract on aroma and flavour compounds in Balkan-style sausages packed under a CO2-containing anaerobic atmosphere

Changes in the levels of pH, lactic acid, acetic acid, headspace volatile compounds, and spoilage odour intensity during a 35 day refrigerated storage period in two sets of a Balkan-style fresh sausage, a control sausage (CON) and a sausage containing an aqueous hop extract (HOP), packaged under a 20% CO2 and 80% N2 atmosphere were evaluated. Storage resulted in progressive sausage acidification and increased the levels of acetic acid, 1-methylbutanol, ethyl acetate, ethyl hexanoate, and 2-ethylhexanol; all of which are associated with anaerobic microbial metabolism under sugar restricted conditions. Storage decreased the levels of hexanal, heptanal, pentanol, and garlic-derived organosulfur compounds. Hop extract showed oxygen scavenging abilities, and decreased the levels of the volatile compounds derived from lipid auto-oxidation while contributing to the presence of specific terpene compounds. The use of hop extract did not improve the shelf life of sausages packed under anaerobic atmosphere. The spoilage odour appeared in both types of sausages on the 14th day, and it was considered strong from day 21 onwards.

Effect of abattoir, livestock species and storage temperature on bacterial community dynamics and sensory properties of vacuum packaged red meat

Shelf life of red meat is influenced by a number of intrinsic and extrinsic factors making its prediction challenging. Here we investigated the influence of geographically distant abattoir facilities and storage temperature relevant to commercial supply chain on the shelf lives of vacuum packaged (VP) beef and lamb meat. Samples of VP beef and lamb were analysed for surface pH, total viable counts, lactic acid bacterial counts, sensory properties, and associated bacterial community using Illumina MiSeq based 16S rRNA gene amplicon sequencing over a period of >200 days. The consistent 0.41 pH unit difference between beef and lamb was found to have a profound effect on bacterial community diversity and composition, bacterial growth rates and the rate of loss of sensory quality. Though different community structures were derived from different abattoir source, bacterial growth rate and rate of sensory quality deterioration were found to be comparable for individual meat type. The greatest variation in rates was found resulting from storage temperature and livestock species themselves. Our findings indicate that bacterial growth and sensory quality loss are essentially predictable when considering their temperature dependency, however for successful meat export validation of shelf life predictive models is required due to stochastic variation in abattoir seeded bacterial populations.

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

To identify metabolic biomarkers related to the freshness of chilled chicken, ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) was used to obtain profiles of the metabolites present in chilled chicken stored for different lengths of time. Random forest regression analysis and stepwise multiple linear regression were used to identify key metabolic biomarkers related to the freshness of chilled chicken. A total of 265 differential metabolites were identified during storage of chilled chicken. Of these various metabolites, 37 were selected as potential biomarkers by random forest regression analysis. Receiver operating characteristic (ROC) curve analysis indicated that the biomarkers identified using random forest regression analysis showed a strong correlation with the freshness of chilled chicken. Subsequently, stepwise multiple linear regression analysis based on the biomarkers identified by using random forest regression analysis identified indole-3-carboxaldehyde, uridine monophosphate, s-phenylmercapturic acid, gluconic acid, tyramine, and Serylphenylalanine as key metabolic biomarkers. In conclusion, our study characterized the metabolic profiles of chilled chicken stored for different lengths of time and identified six key metabolic biomarkers related to the freshness of chilled chicken. These findings can contribute to a better understanding of the changes in the metabolic profiles of chilled chicken during storage and provide a basis for the further development of novel detection methods for the freshness of chilled chicken.

Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.

Microorganisms and their communities on foods are important determinants and indicators of food safety and quality. Despite growing interests in studying food and food-related microbiomes, how effective and practical it is to glean various food safety and quality information from food commodity microbiomes remains underinvestigated. Microbiomes of retail chicken breast from 4 processing establishments in 3 major U.S. broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with individual processing environments. Packaging type and processing environment but not antibiotic usage and seasonality affected composition and diversity of the microbiomes. Low abundances of antimicrobial resistance genes were found on chicken breasts, and no significant resistome difference was observed between antibiotic-free and conventional products. Benchmarked by culture enrichment, shotgun metagenomics sequencing delivered sensitive and specific detection of Salmonella enterica from chicken breasts.

IMPORTANCE Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.

Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

Microbial detection and identification methods: Bench top assays to omics approaches

Rapid detection of foodborne pathogens, spoilage microbes, and other biological contaminants in complex food matrices is essential to maintain food quality and ensure consumer safety. Traditional methods involve culturing microbes using a range of nonselective and selective enrichment methods, followed by biochemical confirmation among others. The time-to-detection is a key limitation when testing foods, particularly those with short shelf lives, such as fresh meat, fish, dairy products, and vegetables. Some recent detection methods developed include the use of spectroscopic techniques, such as matrix-assisted laser desorption ionization-time of flight along with hyperspectral imaging protocols.This review presents a comprehensive overview comparing insights into the principles, characteristics, and applications of newer and emerging techniques methods applied to the detection and identification of microbes in food matrices, to more traditional benchtop approaches. The content has been developed to provide specialist scientists a broad view of bacterial identification methods available in terms of their benefits and limitations, which may be useful in the development of future experimental design. The case is also made for incorporating some of these emerging methods into the mainstream, for example, underutilized potential of spectroscopic techniques and hyperspectral imaging.

Volatile Organic Compounds, Oxidative and Sensory Patterns of Vacuum Aged Foal Meat

The study aimed to evaluate the effect of 14-day vacuum aging on the volatile compounds (VOC) profile, oxidative profile, antioxidant enzymes activity, and sensory evaluation in the Longissimusthoracis muscle of foal meat under vacuum aging. Longissimusthoracis (LT) was sampled in 20 mm thick slices, vacuum packed, and stored at 4 °C. Samples were randomly assigned to different aging times (1, 6, 9, 14 days after slaughtering). VOCs, thiobarbituric acid reactive substances (TBARs), hydroperoxides, carbonyl proteins, superoxide dismutase, catalase, and glutathione peroxidase were analyzed, and a sensory test was performed. A nested one-way analysis of variance (ANOVA) was performed for aging time as an independent variable. Significance was set at p < 0.05. The main VOCs originating from cooked steaks were aldehydes, (from 47.18% to 58.81% of the total volatile compounds), followed by hydrocarbons (from 9.32% and 31.99%). TBARs and hydroperoxides did not show variations due to aging (p > 0.05), instead, protein carbonyls showed higher values at the 14th day (p < 0.01). Catalase, superoxide dismutase, and glutathione peroxidase showed increasing values during aging time (p < 0.01). Vacuum aging slowed down lipid oxidation, and protein oxidation was shown to be present. However, the best vacuum aging duration is in the range of 6-9 days from slaughtering, with an improvement of sensory evaluation.

Spoilage of Chilled Fresh Meat Products during Storage: A Quantitative Analysis of Literature Data

A literature search was performed on spoilage of fresh meat products by combining keyword query, text mining and expert elicitation. From the 258 collected studies, a quantitative analysis was first performed to identify the methods which are the most used to evaluate spoilage beside the preservation strategies suggested. In a second step focusing on a subset of 24 publications providing quantitative data on spoilage occurrence time, associations between spoilage occurrence time of meat products and specific spoilage indicators were investigated. The analysis especially focused on factors well represented in the 24 publications, i.e., gas packaging (O2 and CO2) and storage temperature. Relationships between spoilage occurrence and several microbiological indicators were also sought. The results point out possible advantages of removing dioxygen in packaging to delay spoilage occurrence, whereas, in the presence of dioxygen, the carbon dioxide proportion in the gas mixtures was shown to influence spoilage occurrence. The collected data clearly reveal a potentially protective role of lactic acid bacteria. Besides, while a spoilage role could be attributed to Pseudomonas spp., the growth of mesophilic aerobic microbes, Brochothrix spp. and Enterobacteriaceae seemed independent of spoilage occurrence time.

Use of Essential Oils to Increase the Safety and the Quality of Marinated Pork Loin

This study aimed at evaluating the effects of the addition of an oil/beer/lemon marinade solution with or without the inclusion of oregano, rosemary and juniper essential oils on the quality, the technological properties as well as the shelf-life and safety of vacuum-packed pork loin meat. The results obtained suggested that, aside from the addition of essential oils, the marination process allowed to reduce meat pH, thus improving its water holding capacity. Instrumental and sensorial tests showed that the marination also enhanced the tenderness of meat samples, with those marinated with essential oils being the most positively perceived by the panelists. In addition, microbiological data indicated that the marinated samples showed a lower microbial load of the main spoiling microorganisms compared to the control samples, from the 6th to the 13th day of storage, regardless of the addition of essential oils. Marination also allowed to inhibit the pathogens Salmonella enteritidis, Listeria monocytogenes and Staphylococcus aureus, thus increasing the microbiological safety of the product. Overall outcomes suggest that the oil/beer/lemon marinade solution added with essential oils might represent a promising strategy to improve both qualitative and sensory characteristics as well as the safety of meat products.

Effect of three kinds of natural preservative cocktails on vacuum-packed chilled pork

The aim of this study was to investigate the effects of three different natural preservatives on the microbial profile, the total volatile base nitrogen (TVB-N), and biogenic amine contents of vacuum-packed chilled pork during storage at 4°C. Solution A comprised of tea polyphenols, chitosan, spice extract, propolis, and nisin. Solution B comprised of clove extract, cassia bark extract, ginger juice, garlic juice, and lactobacillus fermentation solution. Solution C consisted of only lactobacillus fermentation solution. The results indicated that solution A was a good natural preservative with higher bacteria inhibitory effect and higher sensory score than B and C. Besides the effect on appealing color, solution B could inhibit microbial activity although its inhibition effect was not as good as solution A. Thus, solution A could be used as a good preservative in industry. Solution C could inhibit the initial growth of Pseudomonas and partially inhibited the growth of Enterobacteriaceae; however, the content of putrescine in the pork treated with solution C was as high as 30.14 ± 2.89 mg/kg after 21 days of storage at 4°C. Hence, solution C is not an ideal preservative for vacuum-packed chilled pork.

Effect of glucose, pH and lactic acid on Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens within a commercial heat-shrunk vacuum-package film

Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens are common spoilage organisms found within the microbiome of refrigerated vacuum-packaged (VP) beef. Extending and predicting VP beef shelf-life requires knowledge about how spoilage bacteria growth is influenced by environmental extrinsic and intrinsic factors. Multifactorial effects of pH, lactic acid (LA) and glucose on growth kinetics were quantified for C. maltaromaticum, B. thermosphacta and S. liquefaciens within a heat shrink-wrapped VP commercial film containing a simulated beef medium. LA, pH, and undissociated lactic acid (UDLA) significantly affected bacterial growth rate (p < 0.001), whereas 5.55 mM glucose produced a marginal effect. At 1.12 mM UDLA, growth rate and maximum population density decreased 20.9 and 3.5%, 56 and 7%, and 11 and 2% for C. maltaromaticum, B. thermosphacta, and S. liquefaciens, respectively.

qPCR quantification of Carnobacterium maltaromaticum, Brochothrix thermosphacta, and Serratia liquefaciens growth kinetics in mixed culture

Quantifying growth kinetics of specific spoilage microorganisms in mixed culture is required to describe the evolution of food microbiomes. A qPCR method was developed to selectively amplify individual meat spoilage bacteria, Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens, within a broth medium designed to simulate the composition of beef. An optimized method of DNA extraction was produced for standard curve construction. Method specificity was determined by individual single peaks in melt curves. Reaction efficiency for standard curves of C. maltaromaticum, B. thermosphacta and S. liquefaciens was high (R² = 0.98-0.99), and linear quantification was achieved over a 5 log CFU/ml range. Coefficient of variation was calculated considering both threshold cycle (C_t) and bacterial concentration; the value did not exceed 14% for inter- or intra-runs for either method. Comparison of growth kinetic parameters derived from plate count and qPCR showed no significant variation (P > .05) for growth rate (GR) and maximum population density (MPD); lag phase duration (LPD) was not included in this comparison due to high innate variability. Log quantification of each isolate was validated in a mixed-culture experiment for all three species with qPCR and plate count differing less than 0.3 log CFU/ml (average 0.10 log CFU/ml, R² = 0.98).

Metatranscriptomic analysis of modified atmosphere packaged poultry meat enables prediction of Brochothrix thermosphacta and Carnobacterium divergens in situ metabolism

In this study, in situ-expressed metabolic routes of Brochothrix (B.) thermosphacta and Carnobacterium (C.) divergens were evaluated based on a metatranscriptomic dataset from bacteria growing on MAP chicken meat (O₂/CO₂; N₂/CO₂). Both species exhibited no (C. divergens) or minor transcription regulation (B. thermosphacta) within their main metabolic routes in response to different atmospheres. Both employ pathways related to glucose and ribose. Gluconeogenesis from lipid-borne glycerol is active in the progressing lack of carbohydrates. Pyruvate fates in both species comprise lactate, ethanol, acetate, CO₂, formate, C4-compounds and H₂O₂ (only B. thermosphacta). Both species express genes for a minimal aerobic respiratory chain, but do not possess the genetic setting for a functional citric acid cycle. While products of carbohydrate and glycerol metabolism display mild to medium sensorial off-characteristics, predicted end products of their amino acid metabolism comprise, e.g., isobutyrate and isovalerate (B. thermosphacta) or cadaverine and tyramine (C. divergens) as potent spoilage compounds.

Colorimetric Sensor Array for Monitoring, Modelling and Comparing Spoilage Processes of Different Meat and Fish Foods

Meat spoilage is a very complex combination of processes related to bacterial activities. Numerous efforts are underway to develop automated techniques for monitoring this process. We selected a panel of pH indicators and a colourimetric dye, selective for thiols. Embedding these dyes into an anion exchange cellulose sheets, i.e., the commercial paper sheet known as “Colour Catcher^®” commonly used in the washing machine to prevent colour run problems, we obtained an array made of six coloured spots (here named Dye name-CC@). The array, placed over the tray containing a sample of meat or fish (not enriched at any extend with spoilage products), progressively shows a colour change in the six spots. Photos of the array were acquired as a function of time, RGB indices were used to follow the spoilage, Principal Component Analysis to model the data set. We demonstrate that the array allows for the monitoring the overall spoilage process of chicken, beef, pork and fish, obtaining different models that mimic the degradation pathway. The spoilage processes for each kind of food, followed by the array colour evolution, were eventually compared using three-way PCA, which clearly shows same degradation pattern of protein foods, altered only according to the different substrates.

Malodorous gases production from food wastes decomposition by indigenous microorganisms

Volatile organic compounds (VOCs) produced during the degradation of food wastes may harm to the health of people and create annoyance in adjacent communities. In this work, the VOCs emitted from the decomposition food wastes including fruit, meat and vegetable, and their microbial communities were measured in three individual 57-L reactors for 61 days. Total of 232.8, 373.5, and 191.1 μg·kg^-1·h^-1 VOCs with oxygenated VOCs (57.6%), volatile organic sulfur compounds (VOSCs, 58.6%) and VOSCs (54.9%) as the main group were detected during fruit, meat and vegetable fermentation, respectively. 2-Butanone (55.1%) and ethyl acetate (13.8%) were the two most abundant VOCs from fruit wastes, while dimethyl sulfide (68.0 and 26.6%) and dimethyl disulfide (89.2 and 10.1%) were in vegetable and meat wastes. The predominant Firmicutes represented 93.0-99.9% of the bacterial communities of meat decomposition, while Firmicutes and Proteobacteria were the dominant phyla throughout the fruit digestion process. Proteobacteria (16.9%-83.6%) was the dominant phylum in vegetable wastes, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Malodorous VOCs emissions were highly affected by microbial activity, the abundant Weissella, Leuconostoc and Enterobacteriaceae in vegetable wastes showed correlation with carbon disulfide and dimethyl sulfide, while dominant Peptococcus, Bacteroides, Lactobacillales and Peptoniphilus in meat wastes was related to dimethyl disulfide. Overall, significant differences and correlation between VOCs emission profiles and bacterial communities among different food wastes decomposition were observed. These data contribute to a more comprehensive understanding the relationship between microbial community dynamics and malodorous VOCs emission.

Spoilage Potential of Pseudomonas (P. fragi, P. putida) and LAB (Leuconostoc mesenteroides, Lactobacillus sakei) Strains and Their Volatilome Profile During Storage of Sterile Pork Meat Using GC/MS and Data Analytics

The aim of the present study was to investigate the evolution of the volatile compounds of aerobically stored sterile pork meat as a consequence of the metabolic activities of inoculated specific spoilage microorganisms. Thus, Pseudomonas fragi, Pseudomonas putida, Lactobacillus sakei and Leuconostoc mesenteroides were inoculated in monocultures, dual cultures and a cocktail culture of all strains on sterile pork meat stored aerobically at 4 and 10 °C. Microbiological and sensory analyses, as well as pH measurements, were performed, along with headspace solid-phase microextraction gas chromatography/mass spectroscopy (headspace SPME-GC/MS) analysis. Data analytics were used to correlate the volatile compounds with the spoilage potential of each stain using multivariate data analysis. The results for the sensory discrimination showed that the volatiles that dominated in spoiled samples consisted mostly of alcohols, ketones and two esters (butyl acetate and ethyl acetate), while at fresh samples, dimethyl sulfide, furans, acetoin and ethyl lactate were detected. On the other hand, 2-butanone, diacetyl and acetaldehyde were among the volatile compounds that were mainly correlated with the inoculated meat during storage. In addition, P. fragi was positively correlated with a higher number of volatiles compared to the other strains, strengthening the hypothesis that volatile compound production is strain-dependent.

Volatilome of Chill-Stored European Seabass (Dicentrarchus labrax) Fillets and Atlantic Salmon (Salmo salar) Slices under Modified Atmosphere Packaging

Fish spoilage occurs due to production of metabolites during storage, from bacterial action and chemical reactions, which leads to sensory rejection. Investigating the volatilome profile can reveal the potential spoilage markers. The evolution of volatile organic molecules during storage of European seabass (Dicentrarchus labrax) fillets and Atlantic salmon (Salmo salar) slices under modified atmosphere packaging at 2 °C was recorded by solid-phase microextraction combined with gas chromatography-mass spectrometry. Total volatile basic nitrogen (TVB-N), microbiological, and sensory changes were also monitored. The shelf life of seabass fillets and salmon slices was 10.5 days. Pseudomonas and H₂S-producing bacteria were the dominant microorganisms in both fish. TVB-N increased from the middle of storage, but never reached concentrations higher than the regulatory limit of 30–35 mg N/100 g. The volatilome consisted of a number of aldehydes, ketones, alcohols and esters, common to both fish species. However, different evolution patterns were observed, indicating the effect of fish substrate on microbial growth and eventually the generation of volatiles. The compounds 3-hydroxy-2-butanone, 2,3-butanediol, 2,3-butanedione and acetic acid could be proposed as potential spoilage markers. The identification and quantification of the volatilities of specific fish species via the development of a database with the fingerprint of fish species stored under certain storage conditions can help towards rapid spoilage assessment.

Modeling the Growth and Interaction Between Brochothrix thermosphacta, Pseudomonas spp., and Leuconostoc gelidum in Minced Pork Samples

The aim of this study was to obtain the growth parameters of specific spoilage micro-organisms previously isolated in minced pork (MP) samples and to develop a three-spoilage species interaction model under different storage conditions. Naturally contaminated samples were used to validate this approach by considering the effect of the food microbiota. Three groups of bacteria were inoculated on irradiated samples, in mono- and in co-culture experiments (n = 1152): Brochothrix thermosphacta, Leuconostoc gelidum, and Pseudomonas spp. (Pseudomonas fluorescens and Pseudomonas fragi). Samples were stored in two food packaging [food wrap and modified atmosphere packaging (CO2 30%/O2 70%)] at three isothermal conditions (4, 8, and 12°C). Analysis was carried out by using both 16S rRNA gene amplicon sequencing and classical microbiology in order to estimate bacterial counts during the storage period. Growth parameters were obtained by fitting primary (Baranyi) and secondary (square root) models. The food packaging shows the highest impact on bacterial growth rates, which in turn have the strongest influence on the shelf life of food products. Based on these results, a three-spoilage species interaction model was developed by using the modified Jameson-effect model and the Lotka Volterra (prey-predator) model. The modified Jameson-effect model showed slightly better performances, with 40-86% out of the observed counts falling into the Acceptable Simulation Zone (ASZ). It only concerns 14-48% for the prey-predator approach. These results can be explained by the fact that the dynamics of experimental and validation datasets seems to follow a Jameson behavior. On the other hand, the Lotka Volterra model is based on complex interaction factors, which are included in highly variable intervals. More datasets are probably needed to obtained reliable factors, and so better model fittings, especially for three- or more-spoilage species interaction models. Further studies are also needed to better understand the interaction of spoilage bacteria between them and in the presence of natural microbiota.