Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions

Improving the storage quality of Harbin red sausages by quaternized chitosan/sodium alginate coating curcumin nano-emulsion

In this study, the effect of sodium alginate and quaternized chitosan bis-polysaccharide-based shell transport curcumin nano-emulsions (Cur@QCS/SA) on the microbiological, physicochemical properties, quality characteristics of Harbin red sausage during storage is investigated. According to the microbiological results, the shelf life of Harbin red sausage is extended from 3 d to 6 d by adding 0.15% Cur@QCS/SA, and Bacillus is the most predominant bacterial before 6 d. Additionally, the physicochemical properties change significantly, the pH, weight loss (WL), water holding capacity (WHC), water activity (aw), L*, and a* of red sausage decrease gradually with the extension of storage time, as well as b*, lipid oxidation, proteolysis increase significantly (P < 0.05). Secondly, it is found that 0.15% treatment group can better maintain the quality characteristics of Harbin red sausage according to texture profile analysis (TPA), electronic nose (E-nose), and electronic tongue (E-tongue) (P < 0.05). This study provides a new way for nano-emulsions in food applications and a new option for the preservation of Harbin red sausage as well as other low-temperature meat products.

Characterization and long-read sequencing of biofilms formed by the microbiota present on inert surfaces in poultry slaughterhouses

Cross-contamination from inert slaughterhouse surfaces is among the main sources of contamination of poultry. The objective of the research reported here was to characterize the biofilms formed by the microbiota present on various surfaces in two poultry slaughterhouses in north-western Spain. Forty-four samples (22 from each slaughterhouse) were taken by swab rubbing at different points along the processing line (from stunning to cutting). The microbiota on all surfaces was able to form biofilms, which were studied by scanning confocal laser microscopy. The total biovolume in the observation field of 16,078.24 μm2 ranged from 22,106.8 ± 5544.3 μm3 to 414,229.6 ± 1621.0 μm3. Average values were higher in abattoir A than in abattoir B, with significant differences (P < 0.05) between surfaces. The percentage of biovolume of Gram-positive bacteria ranged between 0.02 % and 5.38 %. The highest percentages of Gram-positive bacteria were detected towards the beginning of the processing line. The microbiota of the biofilms was identified using long-read sequencing techniques (Oxford Nanopore). The predominant genera (found in >50.0 % of the biofilms) were Pseudomonas, Citrobacter, Klebsiella, Serratia, Escherichia, Enterobacter, Stenotrophomonas, Salmonella, Shewanella, Acinetobacter and Aeromonas. In addition, some pathogenic bacteria were detected, including Salmonella (31 surfaces), Yersinia enterocolitica (12), Escherichia coli O157:H7 (6), Campylobacter spp. (4) and Listeria monocytogenes (3). This research work has permitted identification of the most contaminated surfaces in poultry abattoirs and can serve as a starting point for the design of more effective cleaning and disinfection protocols.

Investigation of oxygen packaging to maintain beef color stability and microbiology safety after periods of long-term superchilled storage

This study aimed to develop an appropriate modified atmosphere packaging (MAP) system for displayed beef steaks following long-term superchilled (-1 °C) storage. After superchilled storage for 0, 2, 8, or 16 weeks, beef loins were fabricated into steaks and displayed with 20%, 50%, or 80% O2-MAP under chilled conditions. At each storage point, after display for 0, 3, 7, or 10 days, instrumental color, myoglobin redox forms percentage, lipid oxidation, total viable count (TVC), and total volatile basic nitrogen (TVB-N) were evaluated. Meat color stability decreased, with prolonged storage period and display time. When the storage period was within 8 weeks, under all the above MAP conditions, the display time for the beef steaks was up to 10 days. Considering 80% O2-MAP promoted lipid oxidation, 50% and 80% O2-MAP were not recommended for displaying steaks for more than 10 and 7 days respectively after 16 weeks of storage. However, 20%, 50%, or 80% O2-MAP could maintain 3 days of microbial shelf-life according to TVC and TVB-N results. Additionally, after long-term superchilled storage for 16 weeks, the various O2 concentrations had minimal impact on microbiota succession during the MAP display period. Furthermore, beef steaks packaged under various MAP systems exhibited similar microbial compositions, with the dominant bacteria alternating between Lactobacillus and Carnobacterium. This study provided practical guidance for improving beef color stability after long-term superchilled storage.

Microbial food spoilage: impact, causative agents and control strategies

Microbial food spoilage is a major contributor to food waste and, hence, to the negative environmental sustainability impacts of food production and processing. Globally, it is estimated that 15-20% of food is wasted, with waste, by definition, occurring after primary production and harvesting (for example, in households and food service establishments). Although the causative agents of food spoilage are diverse, many microorganisms are major contributors across different types of foods. For example, the genus Pseudomonas causes spoilage in various raw and ready-to-eat foods. Aerobic sporeformers (for example, members of the genera Bacillus, Paenibacillus and Alicyclobacillus) cause spoilage across various foods and beverages, whereas anaerobic sporeformers (for example, Clostridiales) cause spoilage in a range of products that present low-oxygen environments. Fungi are also important spoilage microorganisms, including in products that are not susceptible to bacterial spoilage due to their low water activity or low pH. Strategies that can reduce spoilage include improved control of spoilage microorganisms in raw material and environmental sources as well as application of microbicidal or microbiostatic strategies (for example, to products and packaging). Emerging tools (for example, systems models and improved genomic tools) represent an opportunity for rational design of systems, processes and products that minimize microbial food spoilage.

Monitoring of meat quality and change-point detection by a sensor array and profiling of bacterial communities

BACKGROUND

Real-time monitoring of food consumer quality remains challenging due to diverse bio-chemical processes taking place in the food matrices, and hence it requires accurate analytical methods. Thresholds to determine spoiled food are often difficult to set. The existing analytical methods are too complicated for rapid in situ screening of foodstuff.

RESULTS

We have studied the dynamics of meat spoilage by electronic nose (e-nose) for digitizing the smell associated with volatile spoilage markers of meat, comparing the results with changes in the microbiome composition of the spoiling meat samples. We apply the time series analysis to follow dynamic changes in the gas profile extracted from the e-nose responses and to identify the change-point window of the meat state. The obtained e-nose features correlate with changes in the microbiome composition such as increase in the proportion of Brochothrix and Pseudomonas spp. and disappearance of Mycoplasma spp., and with representative gas sensors towards hydrogen, ammonia, and alcohol vapors with R2 values of 0.98, 0.93, and 0.91, respectively. Integration of e-nose and computer vision into a single analytical panel improved the meat state identification accuracy up to 0.85, allowing for more reliable meat state assessment.

SIGNIFICANCE

Accurate identification of the change-point in the meat state achieved by digitalizing volatile spoilage markers from the e-nose unit holds promises for application of smart miniaturized devices in food industry.

Towards Reducing Food Wastage: Analysis of Degradation Products Formed during Meat Spoilage under Different Conditions

Foodstuffs, particularly perishable ones such as meat, are frequently discarded once the best-before date has been reached, despite the possibility of their continued suitability for human consumption. The implementation of intelligent packaging has the potential to contribute to a reduction in food wastage by enabling the monitoring of meat freshness during storage time independently of the best-before date. The process of meat spoilage is associated with the formation of specific degradation products, some of which can be potentially utilized as spoilage indicators in intelligent packaging. The aim of the review is to identify degradation products whose concentration correlates with meat shelf life and to evaluate their potential use as spoilage indicators in intelligent packaging. To this end, a comprehensive literature research was conducted to identify the factors influencing meat spoilage and the eight key degradation products (carboxylic acids, biogenic amines, total volatile basic nitrogen, aldehydes, alcohols, ketones, sulfur compounds, and esters) associated with this process. These degradation products were analyzed for their correlation with meat shelf life at different temperatures, atmospheres, and meat types and for their applicability in intelligent packaging. The review provides an overview of these degradation products, comparing their potential to indicate spoilage across different meat types and storage conditions. The findings suggest that while no single degradation product universally indicates spoilage across all meat types and conditions, compounds like carboxylic acids, biogenic amines, and volatile basic nitrogen warrant further investigation. The review elucidates the intricacies inherent in identifying a singular spoilage indicator but underscores the potential of combining specific degradation products to expand the scope of applications in intelligent packaging. Further research (e.g., storage tests in which the concentrations of these substances are specifically examined or research on which indicator substance responds to these degradation products) is recommended to explore these combinations with a view to broadening their applicability.

Early Detection of Food Safety and Spoilage Incidents Based on Live Microbiome Profiling and PMA-qPCR Monitoring of Indicators

The early detection of spoilage microorganisms and food pathogens is of paramount importance in food production systems. We propose a novel strategy for the early detection of food production defects, harnessing the product microbiome. We hypothesize that by establishing microbiome datasets of proper and defective batches, indicator bacteria signaling production errors can be identified and targeted for rapid quantification as part of routine practice. Using the production process of pastrami as a model, we characterized its live microbiome profiles throughout the production stages and in the final product, using propidium monoazide treatment followed by 16S rDNA sequencing. Pastrami demonstrated product-specific and consistent microbiome profiles predominated by Serratia and Vibrionimonas, with distinct microbial signatures across the production stages. Based on the established microbiome dataset, we were able to detect shifts in the microbiome profile of a defective batch produced under lactate deficiency. The most substantial changes were observed as increased relative abundances of Vibrio and Lactobacillus, which were subsequently defined as potential lactate-deficiency indicators. PMA-qPCR efficiently detected increased levels of these species, thus proving useful in rapidly pinpointing the production defect. This approach offers the possibility of the in-house detection of defective production events with same-day results, promoting safer food production systems.

Changes in meat quality, metabolites and microorganisms of mutton during cold chain storage

During the cold chain storage process, changes in metabolites and microorganisms are highly likely to lead to changes in meat quality. To elucidate the changes in the composition of metabolites and microbiota during cold chain storage of mutton, this study utilized untargeted metabolome and 5R 16S rRNA sequencing analyses to investigate the changes in the longissimus dorsi under different cold chain temperatures (4 °C and -20 °C). With the extension of cold chain storage time, the meat color darkened and the content of C18:2n-6, C20:3n-6, and C23:0 were significantly increased in mutton. In this study, nine metabolites, including 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine, alanylphenylala-nine, indole-3-acrylic acid and the others, were significantly altered during cold chain storage. The abundance of the dominant microorganisms, including Brachymonas, Aeromonas, Corynebacterium and Steroidobacter, was significantly altered. Furthermore, a high correlation was observed between the different metabolites and microorganisms. These findings provide an in-depth understanding of the effects of different cold chain storage temperatures and times on the quality of mutton.

Microbial dynamics of South Korean beef and surroundings along the supply chain based on high-throughput sequencing

Microbiological safety and quality of beef is crucial as beef can serve as a reservoir for a variety of bacteria, including spoilage-related and foodborne pathogens. Controlling microbial contamination is a critical aspect of food quality and safety, but it is difficult to prevent as there are several potential sources of contamination from production to distribution. In this study, the microbiological ecology of cattle/beef and associated environmental samples (n = 69) were trace-investigated to reveal microbiome shifts in cattle/beef and possible cross-contaminants throughout the entire supply chain using 16S rRNA gene sequencing. Pseudomonas, Psychrobacter, and Acinetobacter, known as spoilage bacteria, opportunistic pathogens, or antibiotic-resistant bacteria, were the main microorganisms present in cattle/beef, and Staphylococcus became abundant in the final products. The dominance of Acinetobacter and Pseudomonas was noticeable in the slaughtered carcasses and slaughterhouse environment, indicating that the slaughterhouse is a critical site where hygienic practices are required to prevent further contamination. Taxonomic similarities between cattle/beef and several environmental samples, as well as diversity analysis, presented a high potential for microbial transmission. Source tracking identified environmental samples that primarily contributed to the microbiota of cattle/beef. Farm floor (48%), workers' gloves (73%), and carcass splitters (20%) in the slaughterhouse were found to be major sources influencing the microbiome of cattle/beef at the farm, slaughterhouse, and processing plant, respectively. These findings demonstrated the dynamics of bacterial communities in cattle/beef according to stage and detected potential contamination sources, which may aid in a better understanding and control of microbial transmission in beef production.

Preparation of chitosan photodynamic antibacterial film loaded with VK3 complex in the preservation of chilled mutton

To effectively utilize the photodynamic antibacterial ability of vitamin K3 (VK3), by solving the photothermal instability of VK3, it was combined with natural polymers to apply the preservation of chilled mutton. We encapsulated VK3 in the (2-Hydroxypropyl)-β-cyclodextrin (HP-β-CD) to construct VK3-HP-β-CD complex and then introduced the complex to chitosan (CS) and polyvinyl alcohol (PVA) to fabricate an antibacterial film (CS/PVA-VK3-HP-β-CD film). Through the packaging performance test of the film, the content of VK3-HP-β-CD was an important factor determining the properties of film including tensile strength, elongation at break, water vapor permeability, water content and water contact angle. Meanwhile, CS/PVA-VK3-HP-β-CD films could continuously release ROS under light and suspended in dark, thus realizing >99 % antibacterial rate for Escherichia coli and Staphylococcus aureus. In the application experiment of chilled mutton, CS/PVA-VK3-1-HP-β-CD film could significantly inhibit the increase of total viable count (TVC), pH value (pH) and total volatile base nitrogen (TVB-N) of chilled mutton, and extended its shelf life for at least 12 days. These results indicated that the CS/PVA film with the VK3-HP-β-CD complex might have promising potential as an antibacterial material for packaging and preserving food.

Bacterial and Genetic Features of Raw Retail Pork Meat: Integrative Analysis of Antibiotic Susceptibility, Whole-Genome Sequencing, and Metagenomics

The global antibiotic resistance crisis, driven by overuse and misuse of antibiotics, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat through various methods, including the isolation, antibiotic susceptibility testing (AST), whole-genome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 pre-selected retail stores in Gauteng, South Africa. The samples were aseptically separated, with portions sent to an external laboratory for isolating indicator bacteria and testing for antibiotic residues. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system (Beckman Coulter, Brea, CA, USA). WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument (San Diego, CA, USA). The isolated E. coli and E. faecalis exhibited minimal phenotypic resistance, with WGS revealing the presence of tetracycline resistance genes. Both the isolated bacteria and meat samples harboured tetracycline resistance genes and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin. The resistome analysis primarily indicated beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance.

Bio-enriched composite materials derived from waste cooking oil for selective reduction of odour intensity

Currently, pathogenic microorganisms are becoming more active in public utility areas like parking lots and waste shelters due to the accumulation of organic waste. This uncontrolled waste leads to decay, altering its composition and presenting a microbiological risk to public health. Additionally, it emits unpleasant odors containing chemicals that irritate the mucous membranes, causing discomfort in the nose, throat, and eyes by stimulating the trigeminal nerve. These odors can have various negative effects on both quality of life and public health. The study investigated the physicochemical properties of oil composites enriched with natural additives and determined their effectiveness in reducing the intensity of nuisance odours. The research showed over 82% reduction in decaying meat odour and almost 65% reduction in ammonia odour. A higher impact of the given composites on reducing the odour from decaying meat than from ammonia was observed. This may be due to the biocidal properties of the additives used (turmeric, thymol, salicylic acid, hops and curly sorrel) and the higher intensity of ammonia odor compared to meat-derived odour. Despite the non-porous nature of the solids tested (with similar specific surface areas ranging from 0.66 to 0.88 m2/g), they were capable of sorbing NH3.

Investigation of different cold adaptation abilities in Salmonella enterica serotype Typhimurium strains using extracellular metabolomic approach

This study explored the extracellular metabolomic responses of three different Salmonella enterica serotype Typhimurium (S. Typhimurium) strains-ATCC 13311 (STy1), NCCP 16964 (STy4), and NCCP 16958 (STy8)-cultured at refrigeration temperatures. The objective was to identify the survival mechanisms of S. Typhimurium under cold stress by analyzing variations in their metabolomic profiles. Qualitative and quantitative assessments identified significant metabolite alterations on day 6, marking a critical inflection point. Key metabolites such as trehalose, proline, glycerol, and tryptophan were notably upregulated in response to cold stress. Through multivariate analyses, the strains were distinguished using three metabolites-4-aminobutyrate, ethanol, and uridine-as potential biomarkers, underscoring distinct metabolic responses to refrigeration. Specifically, STy1 exhibited unique adaptive capabilities through enhanced metabolism of betaine and 4-aminobutyrate. These findings highlight the variability in adaptive strategies among S. Typhimurium strains, suggesting that certain strains may possess more robust metabolic pathways for enhancing survival in refrigerated conditions.

Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features

The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.

Oregano essential oil encapsulated in zein-pectin-chitosan nanoparticles to improve the storage quality of Harbin red sausage

In this study, the effect of oregano essential oil loaded in zein-pectin-chitosan (Zein-PC-CS-OEO) nanoparticles on the quality of Harbin red sausage during storage was examined. Zein-PC-CS-OEO nanoparticles exhibit the better encapsulation efficiency, antioxidant and antibacterial properties than these of other prepared nanoparticles, which were subsequently incorporated into Harbin red sausage with different concentrations. The physicochemical properties, bacterial community structure, and flavor characteristics of the Harbin red sausage were determined. Both thiobarbituric acid values and the growth of dominant spoilage bacteria in Harbin red sausage are inhibited by Zein-PC-CS-OEO nanoparticles, while the total aerobic bacteria count is reduced. These results indicate that the storage quality of Harbin red sausage is improved by Zein-PC-CS-OEO nanoparticles. It is worth noting that the shelf life of Harbin red sausage supplemented with 0.1 % Zein-PC-CS-OEO nanoparticles is extended to 9 d, and the flavor characteristics of which are better maintained. This study provides a new approach to extend the application of essential oil and improve the storage quality of Harbin red sausage.

Listeria spp., Listeria monocytogenes

Listeriosis is a disease caused by L. monocytogenes, a relevant microorganism as a causative agent of foodborne diseases - FBD. This study aimed to evaluate the distribution of Listeria spp., and L. monocytogenes in different production areas in two small plants (A and B) and two micro-food processing plants (C and D) producing meat derivatives, located in different cities of Colombia. The methodology implemented was i. The analysis of sampling points is based on a harmonised tool. ii. Four samplings in each production plant between 2019 and 2020. iii. Isolation and identification of microorganisms through conventional microbiology, a semi-automated system, molecular serotyping and clonal characterisation by ERIC-PCR. L. monocytogenes frequency in the production plants belonging to the study ranged between 5.9 and 28.6 %; for Listeria spp., plants A and D had isolated, plant A had the highest proportion, while for L. monocytogenes geno-serotypes found were: 1/2a, 1/2c, 4a-4c, 4b, 4d - 4e, with geno-serotype 4b as the most frequent. Furthermore, possible persistent isolates were detected in plant C as the feasible sources of contamination, based on failures in flow management, raw material contaminated with L. monocytogenes, lack of standardised cooking processes and transfer of the microorganism through equipment and surfaces. Finally, in three of the four production plants assayed, L. monocytogenes or Listeria spp. were present in the packaging area in some of the samples taken during the study, which calls for increased and frequent monitoring, as well as constant technical support for the control of L. monocytogenes in micro and small-scale production plants.

Combined effects of cold and acid on dual-species biofilms of Pseudomonas fluorescens and Listeria monocytogenes under simulated chilled beef processing conditions

Interactions across bacterial species boundaries are usually influenced by environmental stresses, yet little has been evaluated regarding multifactorial stresses on the fate of dual-species biofilm formation in food industry. In this study, the processing conditions of chilled beef were established as a combination of cold and acid stresses (4 °C and pH 5.4), with pH 7.0 or 25 °C serving as the controls, to investigate the interaction of dual-species biofilm between Pseudomonas fluorescens and Listeria monocytogenes. Dual-species biofilms significantly increased biofilm formation at 72 h under the condition of 25°C-pH7.0 and 25°C-pH5.4 (P < 0.05). Compared with mono-species biofilms, the cell numbers of L. monocytogenes in dual-species biofilms were lower at 25 °C (P < 0.05), however, the adherent cells of L. monocytogenes was higher in dual-species biofilms at 4 °C (P < 0.05). Furthermore, the amount of extracellular polysaccharides and proteins secreted by single P. fluorescens biofilms at 4 °C was more than three times than those at 25 °C. The surface-enhanced Raman spectroscopy further profiled the variability of extracellular polymeric substances (EPS) composition. Additionally, RT-qPCR results revealed an upregulation of biofilm-related and genes in co-culture species. It provides valuable insights into the strategies for removing mixed biofilms under diverse stressful conditions in practical food processing.

Effect of Yeast Inoculation on the Bacterial Community Structure in Reduced-Salt Harbin Dry Sausages: A Perspective of Fungi-Bacteria Interactions

Yeast strains are promising starters to compensate for the flavor deficiencies of reduced-salt dry sausages, but their influence on the bacterial community's structure has not yet been clarified. In this study, the effect of separately inoculating Pichia kudriavzevii MDJ1 (Pk) and Debaryomyces hansenii HRB3 (Dh) on the bacterial community structure in reduced-salt dry sausage was investigated. The results demonstrated that the inoculation of two yeast strains significantly reduced the pH, and enhanced the total acid content, lactic acid bacteria (LAB) counts, and total bacterial counts of reduced-salt sausages after a 12-day fermentation (p < 0.05). Furthermore, high-throughput sequencing results elucidated that the inoculation of yeast strains significantly affected the bacterial composition of the dry sausages. Especially, the relative abundance of bacteria at the firmicute level in the Pk and Dh treatments exhibited a significant increase of 83.22% and 82.19%, respectively, compared to the noninoculated reduced-salt dry sausage treatment (Cr). The relative abundance of Latilactobacillus, especially L. sakei (0.46%, 2.80%, 65.88%, and 33.41% for the traditional dry sausage (Ct), Cr, Pk, and Dh treatments, respectively), increased significantly in the reduced-salt sausages inoculated with two yeast strains. Our work demonstrates the dynamic changes in the bacterial composition of reduced-salt sausages inoculated with different yeast strains, which could provide the foundation for the in-depth study of fungi-bacteria interactions in fermented foods.

Beef carcass microbiota after slaughtering and primary cooling: A metataxonomic assessment to infer contamination drivers

The impact of primary cooling on beef microbiota was investigated on six beef carcasses consecutively processed with the parallel use of metataxonomic and culture-dependent analysis. Samples were collected immediately after slaughtering (AS) and after the 24th-hour post-cooling (PC) from three different surfaces, namely neck, flank and thigh. The main objective was to examine whether the microbiota composition of beef carcasses changes as function of the surface sampled, primary cooling (from AS to PC) and animal's origin (breeder). The outcomes underline that primary cooling did not affect qualitatively the composition of the potentially active microbiota or the carcass superficial counts. Although slight changes in chemical-physical parameters like volatile organic compounds (VOCs) were observed after cooling, the carcasses microbiota and its inferred metabolic pathways varied among animals as a function of their origin. Co-occurrence and co-exclusion analyses underlined competition for the colonisation of the carcass surface between Brochothrix-Psychrobacter and Carnobacterium-Serratia-Pseudomonas. Once integrated in a comprehensive monitoring of the supply chain, the metataxonomic characterisation of the beef carcasses microbiota might represent a valid integrative approach to define the cuts' perishability and their appropriateness to specific packaging and storage methods. These new bits of knowledge could be the base to define good strategies for the prevention of meat spoilage.

Tracking the contamination sources of microbial population and characterizing Listeria monocytogenes in a chicken slaughterhouse by using culture-dependent and -independent methods

Listeria monocytogenes is the etiologic agent of listeriosis, a foodborne disease that poses a threat to public health globally. Chicken meat exhibits heightened susceptibility to L. monocytogenes contamination during butchery. The persistence of this pathogen in the slaughterhouse environment enables recurring contamination of meat products. This study aimed at identifying the sources and transmission routes of L. monocytogenes contamination within an abattoir where it was consistently detected for three consecutive years (2019-2021). Furthermore, the environmental factors aiding contamination along chicken processing lines were determined by surveying the microbiome within the facility. Samples collected in 2019 to 2021 were subjected to culture-dependent analysis to assess the prevalence, serotypes, and multi-locus sequence typing (MLST) of L. monocytogenes. Additionally, the specimens collected in 2021 underwent culture-independent analysis via real-time quantitative polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing to identify the contamination sources and characterize the entire microbial community within the slaughterhouse. L. monocytogenes was isolated only from the clean zone, where the final slaughtering stage occurs. Most strains isolated from the final carcasses showed the same genetic cluster as the isolate in the chilling water and were assigned to MLST profile ST3. Culture-independent qPCR confirmed L. monocytogenes contamination in all samples, excluding post-scalding carcasses, prewashed post-evisceration carcasses, and the bleeding areas. Consequently, qPCR enabled more comprehensive identification of L. monocytogenes contamination points than culture-dependent approaches. Moreover, 16S rRNA gene amplicon sequencing demonstrated that psychro-tolerant and spoilage-related bacteria with L. monocytogenes-like attributes exhibited enhanced viability in the clean zone and immersion-chilling water. Metagenomics-based source tracking analysis further revealed that the shackles and chilling waters represent predominant sources of cross-contamination between different slaughterhouse zones, whereas the grading and packaging workstations and chilling water in the clean zone were deemed crucial sources affecting final carcass contamination. Collectively, these findings demonstrate through culture-dependent and -independent methods that L. monocytogenes spreads along the slaughter line, contaminating the slaughterhouse. Moreover, by investigating changes in microbial community and bacterial flow along the slaughter line within the facility, the sources influencing carcass contamination can be effectively traced.

Combining the oxygen sensor based respirometry and 16S rRNA amplicon sequencing for the analysis of microbiota in commercial mince products

In this study, rapid respirometric microbial testing was combined with 16S rRNA amplicon sequencing, to assess the composition of microbiota in a total of 64 samples of commercial beef, turkey, lamb and pork mince. The O2 sensor-based respirometry system, while producing the anticipated total aerobic viable counts (TVC) data and patterns for most samples, also revealed unusual (linear) respiration profiles for some samples, mostly lamb and pork mince. The TVC values for beef mince, produced by respirometry and calculated using the available calibration equation, correlated well with the conventional plate counting method, ISO 4833-1:2013, 2013, while for the other species the correlation was less good. These effects, not observed in previous studies employing various food matrices, require further investigation. Using the same samples (crude homogenates) as in respirometry, the whole microbiome was also analysed by 16S rRNA amplicon sequencing for each mince-type. The sequencing showed an overall decrease in alpha diversity over shelf-life, with lamb and pork mince maintaining a proportion of rare taxa. Some taxa exhibited significant changes in abundance over shelf-life and after the respirometric analysis, with beef mince exhibiting a decrease in aerobic bacteria and an increase in facultative anaerobes. Beta diversity was also seen to depend on mince-type. Thus, the combined use of respirometry and sequencing techniques shows promise as a useful and unique analytical approach for food quality and safety evaluation, However, more data points and in-depth analysis are required to back up the findings of this initial study.

Differences in Bacterial Communities of Retail Raw Pork in Different Market Types in Hangzhou, China

Pork is widely consumed globally, and pigs' microbiota can potentially harbor foodborne pathogens. Contaminated pork in retail markets poses significant implications for food quality and safety. However, limited studies have compared pork microbiomes in various marketing environments. In this study, we utilized traditional microbial culture methods and high-throughput 16S rRNA sequencing to assess pathogen contamination and bacterial diversity in raw pork samples purchased from farmers' markets and two types of supermarkets (upscale and ordinary) in Hangzhou, China. Traditional microbial plate cultures identified E. coli and Salmonella spp. in 32.1% (27/84) and 15.5% (13/84) of the collected pork samples, respectively. Moreover, 12 out of 13 Salmonella strains were found in farmers' markets. The MIC results indicated a high prevalence of MDR strains, accounting for 51.9% in E. coli and 53.8% in Salmonella. The prevalence of NaClO tolerant strains was 33.3% and 92.3% for E. coli and Salmonella, respectively. Sequencing results indicated significantly higher microbial diversity in farmers' market samples compared to supermarket samples. Farmers' market pork samples exhibited a greater abundance of Acinetobacter, while Pseudomonas and Brochothrix were predominant in supermarket samples. The total abundance of pathogenic and spoilage bacteria was also higher for the farmers' market samples. Cross-contamination during market trading was evident through a high correlation between bacterial abundance in pork from different stalls within the same farmers' market. PICRUSt2 analysis identified significant differences in the average proportions of genes for carbohydrate, energy, and lipid metabolism from the farmers' markets, suggesting an exacerbation of microbial metabolic activity and increased perishability of pork in this environment. In conclusion, this study revealed variations in the characteristics of raw pork bacterial contamination across different types of retail stores, as well as differences in the composition and diversity of their respective bacterial communities.

A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities

Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.

The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination

BACKGROUND

Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3).

METHODS

A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples.

RESULTS

The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples.

CONCLUSIONS

This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.

Growth performance of Listeria monocytogenes and background microbiota from mushroom processing environments

Interaction between Listeria monocytogenes and resident background microbiota may occur in food processing environments and may influence the survival of this pathogen in a factory environment. Therefore the aim of this study was to characterize the growth performance of microbiota isolated from the processing environments of frozen sliced mushrooms, and to investigate the competitive performance of L. monocytogenes when co-cultured with accompanying environmental microbiota. Acinetobacter, Enterobacteriaceae, Lactococcus and Pseudomonas were the most prominent background microbiota isolated from the processing environment of frozen sliced mushrooms. All individual microbiota strains were able to grow and form biofilm in filter-sterilized mushroom medium, with the mannitol-consumers Raoultella and Ewingella as top performers, reaching up to 9.6 and 9.8 log CFU/mL after 48 h incubation at room temperature. When L. monocytogenes mushroom isolates were co-cultured with the microbiota strains, L. monocytogenes counts ranged from 7.6 to 8.9 log CFU/mL after 24 h of incubation, while counts of the microbiota strains ranged from 5.5 to 9.0 log CFU/mL. Prolonged incubation up to 48 h resulted in further increase of L. monocytogenes counts when co-cultured with non-acidifying species Pseudomonas and Acinetobacter reaching 9.1 to 9.2 log CFU/mL, while a decrease of L. monocytogenes counts reaching 5.8 to 7.7 log CFU/mL was observed in co-culture with Enterobacteriaceae and acidifying Lactococcus representatives. In addition, L. monocytogenes grew also in spent mushroom media of the microbiota strains, except in acidified spent media of Lactococcus strains. These results highlight the competitive ability of L. monocytogenes during co-incubation with microbiota in fresh and in spent mushroom medium, indicative of its invasion and persistence capacity in food processing factory environments.

Oxygen Sensor-Based Respirometry and the Landscape of Microbial Testing Methods as Applicable to Food and Beverage Matrices

The current status of microbiological testing methods for the determination of viable bacteria in complex sample matrices, such as food samples, is the focus of this review. Established methods for the enumeration of microorganisms, particularly, the 'gold standard' agar plating method for the determination of total aerobic viable counts (TVC), bioluminescent detection of total ATP, selective molecular methods (immunoassays, DNA/RNA amplification, sequencing) and instrumental methods (flow cytometry, Raman spectroscopy, mass spectrometry, calorimetry), are analyzed and compared with emerging oxygen sensor-based respirometry techniques. The basic principles of optical O₂ sensing and respirometry and the primary materials, detection modes and assay formats employed are described. The existing platforms for bacterial cell respirometry are then described, and examples of particular assays are provided, including the use of rapid TVC tests of food samples and swabs, the toxicological screening and profiling of cells and antimicrobial sterility testing. Overall, O₂ sensor-based respirometry and TVC assays have high application potential in the food industry and related areas. They detect viable bacteria via their growth and respiration; the assay is fast (time to result is 2-8 h and dependent on TVC load), operates with complex samples (crude homogenates of food samples) in a simple mix-and-measure format, has low set-up and instrumentation costs and is inexpensive and portable.

Slight Temperature Deviation during a 56-Day Storage Period Does Not Affect the Microbiota of Fresh Vacuum-Packed Pork Loins

It is profitable to export fresh meat overseas, where it is often regarded as a premium commodity. Meeting this demand for fresh meat, however, necessitates long export times, during which uncontrolled temperature increases can affect the microbiological quality of the meat and thereby, reduce shelf life or compromise food safety. To study the impact of temperature deviations on microbial community composition and diversity, we used 16S rRNA gene sequencing for Listeria monocytogenes and Salmonella spp. detection to describe the surface microbiota of eight batches of vacuum-packed loins stored at -1.5 °C (control) for 56 days and subjected to a 2 °C or 10 °C temperature deviation for a few hours (mimicking problems regularly encountered in the industry) at day 15 or 29. The presence of pathogens was negligible. The applied temperature deviations were not associated with different microbiota. Sequencing analysis showed the presence of Yersinia, an unexpected pathogen, and relative abundance increased in the groups subjected to temperature deviations. Over time, Lactobacillales_unclassified genus became the main constituent of the microbiota of vacuum-packed pork loins. Although the microbiota of the eight batches appeared similar at the beginning of storage, differences were revealed after 56 days, suggesting unequal aging of the microbiota.

Microbial spoilage mechanisms of vacuum-packed lamb meat: A review

Lamb meat is an important export commodity, however chilled vacuum-packed (VP) lamb has approximately half the shelf-life of beef under the same storage conditions. This makes the industry more vulnerable to financial losses due to long shipping times and unexpected spoilage. Understanding the spoilage mechanisms of chilled VP lamb in relation to VP beef is important for developing effective strategies to extend the shelf-life of lamb. This review has discussed various key factors (i.e., pH, fat, and presence of bone) that have effects on microbial spoilage of VP lamb contributing to its shorter shelf-life relative to VP beef. A range of bacterial organisms and their metabolisms in relevance to lamb spoilage are also discussed. The data gap in the literature regarding the potential mechanisms of spoilage in VP red meat is highlighted. This review has provided the current understanding of key factors affecting the shelf-life of VP lamb relative to VP beef. It has also identified key areas of research to further understand the spoilage mechanisms of VP lamb. These include investigating the potential influence of fat and bone (including bone marrow) on the shelf-life, as well as assessing changes in the meat metabolome as the spoilage microbial community is developing using an integrated approach. Such new knowledge would aid the development of effective approaches to extend the shelf-life of VP lamb.

Thériault W, Longpré J, Thibodeau A, Hocine MN, Fravalo P. Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse

The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.

Exploration of the roles of microbiota on biogenic amines formation during traditional fermentation of Scomber japonicus

The influence of microbiota composition and metabolisms on the safety and quality of fermented fish products is attracting increasing attention. In this study, the total viable count (TVC), pH, total volatile base nitrogen (TVB-N) as well as biogenic amines (BAs) of traditional fermented Scomber japonicus (zaoyu) were quantitatively determined. To comprehend microbial community variation and predict their functions during fermentation, 16S rRNA-based high-throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. The fresh samples stored without fermentation were used as controls. TVC and TVB-N values increased rapidly, and the content of BAs exceeded the permissible limit on day 2 in the controls, indicating serious spoilage of the fish. In contrast, a slower increase in TVC and TVB-N was observed and the content of BAs was within the acceptable limit throughout the fermentation of zaoyu. Significant differences in microbiota composition were observed between zaoyu and the controls. The bacterial community composition of zaoyu was relatively simple and Lactobacillus was identified as the dominant microbial group. The accumulation of histamine was inhibited in zaoyu, which was positively correlated with the relative abundance of Vibrio, Enterobacter, Macrococcus, Weissella, et al. based on Redundancy analysis (RDA), while Lactobacillus showed a positive correlation with tyramine, cadaverine, and putrescine. Functional predictions, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, revealed that the relative abundance of metabolic function exhibited a decreasing trend with prolonged fermentation time and the abundance of metabolism-related genes was relatively stable in the later stage of fermentation. Those metabolisms related to the formation of BAs like histidine metabolism and arginine metabolism were inhibited in zaoyu. This study has accompanied microbiota analysis and functional metabolism with the accumulation of BAs to trace their correspondences, clarifying the roles of microorganisms in the inhibition of BAs during fermentation of Scomber japonicus.

Microbiological Safety and Shelf-Life of Low-Salt Meat Products-A Review

Salt is widely employed in different foods, especially in meat products, due to its very diverse and extended functionality. However, the high intake of sodium chloride in human diet has been under consideration for the last years, because it is related to serious health problems. The meat-processing industry and research institutions are evaluating different strategies to overcome the elevated salt concentrations in products without a quality reduction. Several properties could be directly or indirectly affected by a sodium chloride decrease. Among them, microbial stability could be shifted towards pathogen growth, posing a serious public health threat. Nonetheless, the majority of the literature available focuses attention on the sensorial and technological challenges that salt reduction implies. Thereafter, the need to discuss the consequences for shelf-life and microbial safety should be considered. Hence, this review aims to merge all the available knowledge regarding salt reduction in meat products, providing an assessment on how to obtain low salt products that are sensorily accepted by the consumer, technologically feasible from the perspective of the industry, and, in particular, safe with respect to microbial stability.

Effect of the combination of superchilling and super-chilled storage on shelf-life and bacterial community dynamics of beef during long-term storage

This study investigated the effect of superchilling (-30 °C until the core temperature achieved -3 °C, and - 1 °C until 24 h, SC) on shelf-life and bacterial community dynamics of beef loins, with a typical very fast chilling (-30 °C until the core temperature achieved 0 °C, and - 1 °C until 24 h, VFC) and conventional chilling (0- 4 °C for 24 h, CC) as controls. The super-chilled storage (-1 °C) was adopted after each chilling procedure, and physicochemical traits and microbiological quality were evaluated during a long-term storage. No remarkable adverse impact on meat color and lipid oxidation were observed in SC treatment. The bacterial composition results showed that Carnobacterium spp. were the main bacteria in SC treatment in the late storage period (63- 84 days). The loss of Lactobacillus spp., due to the "ultra-low temperature" during the superchilling, might be the reason that the SC did not result in a longer shelf-life compared with CC samples.

Similar Carcass Surface Microbiota Observed Following Primary Processing of Different Pig Batches

Bacterial contamination during meat processing is a concern for both food safety and for the shelf life of pork meat products. The gut microbiota of meat-producing animals is one of the most important sources of surface contamination of processed carcasses. This microbiota is recognized to vary between pigs from different farms and could thus be reflected on the bacterial contamination of carcasses at time of processing. In this study, the microbiota of 26 carcasses of pigs originating from different farms (i.e., batches) were compared to determine if an association could be observed between carcass surface microbiota (top and bottom) and the origin of slaughtered animals. The microbiota of the top and bottom carcass surface areas was analyzed by culturing classical indicator microorganisms (mesophilic aerobic bacteria, Enterobacteria, Escherichia coli, Pseudomonas, and lactic bacteria), by the detection of Salmonella, and by 16S rRNA gene sequencing. Culture results showed higher Enterobacteria, E. coli, and lactic bacteria counts for the bottom areas of the carcasses (neck/chest/shoulder) when compared to the top areas. Salmonella was not detected in any samples. Globally, 16S rRNA gene sequencing showed a similar composition and diversity between the top and bottom carcass areas. Despite the presence of some genera associated with fecal contamination such as Terrisporobacter, Escherichia-Shigella, Turicibacter, Clostridium sensustricto1, and Streptococcus on the carcass surface, sequencing analysis suggested that there was no difference between the different batches of samples from the top and bottom areas of the carcasses. The primary processing therefore appears to cause a uniformization of the carcass global surface microbiota, with some specific bacteria being different depending on the carcass area sampled.

Efficacy of Selected Powdered Floor Treatments Against Salmonella, E. coli, and L. monocytogenes on Polyurethane-Concrete Flooring Material Carriers

Food processing environment flooring can become contaminated with pathogens in many ways including foot and equipment traffic, incoming materials, and floor drain backups.  Natural antimicrobial turmeric and commercially available powdered floor treatments may reduce the levels of pathogens on flooring thereby reducing the risk of cross contamination from the floor to food contact surfaces. These chemicals were evaluated to determine their effectiveness against cocktails of Salmonella , Escherichia coli , and Listeria monocytogenes dried onto the surfaces of carriers made from polyurethane-concrete commercial flooring material.  Aqueous test solutions were prepared from the minimum treatment required per m 2 from the manufacturer's instructions diluted in sterile water.  Potential synergy between turmeric and a percarbonate based commercial floor treatment was explored with a mixture of turmeric and sodium percarbonate, each at approximately 37g/m 2 application rate.  Each inoculated carrier was exposed to the treatment solutions or a sterile water control for 10 minutes at room temperature, neutralized with Hi-Cap neutralizing broth, the bacteria suspended, enumerated, and log 10 reductions calculated for each treatment and inoculum combination.  Mean log 10 CFU/carrier reductions with standard deviations ranged between 4.29±0.34 for the sodium percarbonate (SPC) based treatment and 0.004±0.23 for turmeric for Salmonella , 4.81±0.16 for SPC based treatment and -0.16±0.62 for turmeric for E. coli , and 4.88±0.6 for SPC based treatment and -0.16±0.15 for turmeric for L. monocytogenes .

Metagenomics Approaches for Improving Food Safety: A Review

ABSTRACT

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology.

HIGHLIGHTS

Analysis of microbiota structure in cooked ham as influenced by chemical composition and processing treatments: Identification of spoilage bacteria and elucidation on contamination route

Spoilage in cooked ham is one of the main challenges where microbial contamination can play a fundamental role. This study aimed to characterize pork-cooked ham's microbial community changes among different food production conditions (formulation and processing) using 16S rRNA sequencing and also to investigate the spoilage bacteria in order to elucidate their contamination route. Samples of three pork-cooked ham references with and without post-pasteurization treatment and in contact with the slicing-packaging conveyor belt and slicer and packager surfaces were performed by 16S rRNA gene sequencing. In order to clarify the contamination route, surfaces were sampled by conventional microbiological methods. Results showed that Leuconostoc spp. was the principal genera in spoiled cooked ham and had no relation neither to formulation nor contact with the slicing-packaging conveyor belt. The contamination route found for Leuconostoc spp. was associated with the storage and packaging zone. In addition, the calculated shelf-life decreased to 57.5% independently of the environment interaction minimization when ham casing permeability was changed and linked to contamination of spoilage bacteria during the slicing and packaging process. This research illustrates how the combined approach provides complementary results to implement suggestions in the facility to reduce the cross-contamination with spoilage bacteria. It also generates tools to comprehend and propose transference models understanding the environmental and intrinsic factors related to microbial transfer rate.

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The structure of the bacterial community in cooked ham had no relation to the formulation.

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Genus Leuconostoc dominated the spoilage in cooked ham.

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The methodology allows validating the contamination route for spoilage bacteria.

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Post-pasteurization treatment reduce microbiota diversity.

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The ham shelf lifetime decrease get related to cross-contamination during slicing.

Impact of Electrolyzed Water on the Microbial Spoilage Profile of Piedmontese Steak Tartare

A low initial contamination level of the meat surface is the sine qua non to extend the subsequent shelf life of ground beef for as long as possible. Therefore, the short- and long-term effects of a pregrinding treatment with electrolyzed water (EW) on the microbiological and physicochemical features of Piedmontese steak tartare were here assessed on site, by following two production runs through storage under vacuum packaging conditions at 4°C. The immersion of muscle meat in EW solution at 100 ppm of free active chlorine for 90 s produced an initial surface decontamination with no side effects or compositional modifications, except for an external color change that was subsequently masked by the grinding step. However, the initially measured decontamination was no longer detectable in ground beef, perhaps due to a quick recovery by bacteria during the grinding step from the transient oxidative stress induced by the EW. We observed different RNA-based metataxonomic profiles and metabolomic biomarkers (volatile organic compounds [VOCs], free amino acids [FAA], and biogenic amines [BA]) between production runs. Interestingly, the potentially active microbiota of the meat from each production run, investigated through operational taxonomic unit (OTU)-, oligotyping-, and amplicon sequence variant (ASV)-based bioinformatic pipelines, differed as soon as the early stages of storage, whereas microbial counts and biomarker dynamics were significantly distinguishable only after the expiration date. Higher diversity, richness, and abundance of Streptococcus organisms were identified as the main indicators of the faster spoilage observed in one of the two production runs, while Lactococcus piscium development was the main marker of shelf life end in both production runs. IMPORTANCE Treatment with EW prior to grinding did not result in an effective intervention to prolong the shelf life of Piedmontese steak tartare. Our RNA-based approach clearly highlighted a microbiota that changed markedly between production runs but little during the first shelf life stages. Under these conditions, an early metataxonomic profiling might provide the best prediction of the microbiological fate of each batch of the product.

Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Microbiota and volatilome of dry-cured pork loins manufactured with paprika and reduced concentration of nitrite and nitrate

Dry-cured pork loin is a very popular meat product in Mediterranean countries. Pork-loin is manufactured rubbing curing salts, nitrite and nitrate, and spices on the surface of the loin which is then dry-cured or smoked for several months. Although nitrite-derived compounds are crucial for the microbiological safety and development of a distinct flavour, there have been recent concerns about the adverse health effects of nitrite-derived compounds driving to the reduction of curing agents in meat products. In this study, we have evaluated the differences in microbiota and aroma of dry-cured pork loins manufactured with or without paprika and reduced ingoing amounts of nitrate and nitrite. Staphylococcus dominated the microbiota of pork loins without paprika, regardless of the nitrite and nitrate reduction. On the contrary, the reduction of nitrite and nitrate in loins with paprika had an important effect on the microbiota. In these loins a codominance of Staphylococcus and Bacillus together by Enterobacteriaceae occurred. Moreover, paprika addition and reduction of nitrite and nitrate seemed to promote proliferation of lactic acid bacteria. Occurrence of these genera was correlated with the generation of free amino acids and their derived volatile compounds setting clear differences in the aroma profile of dry-cured loins.

Microbial Diversity and Non-volatile Metabolites Profile of Low-Temperature Sausage Stored at Room Temperature

Sausage is a highly perishable food with unique spoilage characteristics primarily because of its specific means of production. The quality of sausage during storage is determined by its microbial and metabolite changes. This study developed a preservative-free low-temperature sausage model and coated it with natural casing. We characterized the microbiota and non-volatile metabolites in the sausage after storage at 20°C for up to 12 days. Bacillus velezensis was the most prevalent species observed after 4 days. Lipids and lipid-like molecules, organoheterocyclic compounds, and organic acids and their derivatives were the primary non-volatile metabolites. The key non-volatile compounds were mainly involved in protein catabolism and β-lipid oxidation. These findings provide useful information for the optimization of sausage storage conditions.

An investigation into the anaerobic spoilage microbiota of beef carcass and rump steak cuts using high- throughput sequencing

The presence of anaerobic microflora on fresh beef carcass and rump steaks, which may contribute to meat spoilage, was explored in this study. A total of 120 carcass and 120 rump steak swabs were collected immediately after slaughtering and boning, respectively from five meat plants, anaerobically incubated and enriched at 4°C for 3 weeks. This was followed by DNA extraction and 16S rRNA amplicon sequencing using the Illumina MiSeq, with subsequent bioinformatics analysis. The enriched microbiota of the samples was classified and grouped into 149 operational taxonomic units (OTUs). The microbiota recovered from both sample types consisted mainly of Carnobacterium, with an average relative abundance of 28.4% and 32.8% in beef carcasses and beef rump steaks, respectively. This was followed by Streptococcus, Serratia, Lactococcus, Enterococcus, Escherichia-Shigella, Raoultella and Aeromonas ranging from 1.5 to 20% and 0.1 to 29.8% in enriched carcasses and rump steak swabs, respectively. Trichococcus, Bacteroides, Dysgomonas, Providencia, Paraclostridium and Proteus were also present ranging from 0 to 0.8% on carcass and 0 to 1.8% on rump steak swabs, respectively. Alpha and beta diversity measurements showed limited diversity between the two sample types, but some differences between samples from the beef plants investigated were evident. This study highlights the presence of potential spoilage bacteria, mainly anaerobic genera on and between carcass and rump steaks, as an indication of contamination on and between these samples.