An adapted isolation procedure reveals Photobacterium spp. as common spoilers on modified atmosphere packaged meats

In-depth metaproteomics analysis reveals the protein profile and metabolism characteristics in pork during refrigerated storage

Alterations in microbiotas and endogenous enzymes have been implicated in meat deterioration. However, the factors that mediate the interactions between meat quality and microbiome profile were inadequately investigated. In this study, we collected pork samples throughout the refrigeration period and employed metaproteomics to characterize both the pork and microbial proteins. Our findings demonstrated that pork proteins associated with the catabolic process are upregulated during storage compared to the initial stage. Pseudomonas, Clostridium, Goodfellowiella, and Gonapodya contribute to the spoilage process. Notably, we observed an elevated abundance of microbial proteins related to glycolytic enzymes in refrigerated pork, identifying numerous proteins linked to biogenic amine production, thus highlighting their essential role in microbial decay. Further, we reveal that many of these microbial proteins from Pseudomonas are ribosomal proteins, promoting enzyme synthesis by enhancing transcription and translation. This study provides intrinsic insights into the underlying mechanisms by which microorganisms contribute to meat spoilage.

Microbial consortia in commercial salmon products: A comparative study using cultivation-dependent and high-throughput sequencing approaches

Despite the widespread consumption of salmon products, an all-round microbiological survey on fresh salmon and smoked salmon products sold on the market directly to consumers remains to be undertaken. The present study conducted a comprehensive microbial investigation employing both conventional cultivation-based techniques and 16S rRNA amplicon sequencing. A total of 120 fresh salmon and 95 smoked salmon products were systematically collected across all four seasons (spring, summer, fall, and winter), accompanied by temperature assessments of each product's interior. The average aerobic plate counts for fresh salmon and smoked salmon were 3.63 log and 1.36 log CFU/g, respectively, and the highest seasonal concentrations occurred in summer. The average coliform count was higher in fresh salmon (1.50 log CFU/g) than in smoked salmon products (1.12 log CFU/g). Although smoked salmon exhibited CFU counts similar to those of fresh salmon according to culture-based methods, 16S sequencing unveiled a distinct microbial composition. Photobacterium and Pseudomonas, recognized as major spoilage-related microorganisms, were the predominant genera in all products, but especially in fresh salmon. Smoked salmon exhibited diverse variations in bacterial composition compared to fresh salmon. Three types of lactic acid bacteria-Leuconostoc, Lactobacillus, and Lactococcus-were found to be significantly more abundant in smoked salmon than in fresh salmon. The outcomes of this study contribute to an enhanced understanding of retail salmon products, shedding light on crucial areas for investigation and suggesting potential interventions regarding both sales and production of salmon products.

Transfer of beef bacterial communities onto food-contact surfaces

Introduction

Food spoilage and pathogenic bacteria on food-contact surfaces, especially biofilm-forming strains, can transfer to meats during processing. The objectives of this study were to survey the bacterial communities of beef cuts that transfer onto two commonly used food-contact surfaces, stainless steel (SS) and high-density polyethylene (HDPE) and identify potentially biofilm-forming strains.

Methods

Top round, flank, chuck, and ground beef were purchased from 3 retail stores. SS and HDPE coupons (approximately 2cm × 5cm) were placed on beef portions (3h, 10°C), after which, the coupons were submerged halfway in PBS (24h, 10°C). Bacteria from the beef cuts and coupon surfaces (n = 3) were collected, plated on tryptic soy agar plates and incubated (5 days, 25°C). Bacterial isolates were identified by 16S rRNA gene amplicon sequencing and assayed for biofilm formation using a crystal violet binding (CV) assay (72h, 10°C). Additionally, beef and coupon samples were collected for bacterial community analysis by 16S rRNA gene amplicon sequencing.

Results and discussion

Sixty-one of 972 beef isolates, 29 of 204 HDPE isolates, and 30 of 211 SS isolates were strong biofilm-formers (Absorbance>1.000 at 590 nm in the CV assay). Strong-binding isolates identified were of the genera Pseudomonas, Acinetobacter, Psychrobacter, Carnobacterium, and Brochothrix. Coupon bacterial communities among stores and cuts were distinct (p < 0.001, PERMANOVA), but there was no distinction between the communities found on HDPE or SS coupons (p > 0.050, PERMANOVA). The bacterial communities identified on the coupons may help determine the communities capable of transferring and colonizing onto surfaces, which can subsequently cross-contaminate foods.

Deciphering the growth responses and genotypic diversity of bioluminescent Photobacterium phosphoreum on chicken meat during aerobic refrigerated storage

The advent of high-throughput sequencing technologies in recent years has revealed the unexpected presence of genus Photobacterium within the chicken meat spoilage ecosystem. This study was undertaken to decipher the occurrence, the growth patterns and the genotypic biodiversity of Photobacterium phosphoreum on chicken breast fillets stored aerobically at 4 °C through conventional microbiological methods and molecular techniques. Samples were periodically cultured on marine broth agar (MA; supplemented with meat extract and vancomycin) for the enumeration of presumptive bioluminescent Photobacterium spp. In total, 90 bioluminescent bacteria were recovered from the initial (time of first appearance), middle and end stages of storage. Concomitantly, 95 total psychrotrophic/psychrophilic bacteria were isolated from the same medium to assess the presence and diversity of non-luminous photobacteria. Genetic diversity between bioluminescent isolates was assessed with two PCR-based DNA fingerprinting methods, i.e. RAPD and rep-PCR. Moreover, the characterization of selected bacterial isolates at the genus and/or species level was performed by sequencing of the 16S rRNA and/or gyrB gene. Bioluminescent bacteria were scarcely encountered in fresh samples at population levels of ca. 2.0 log CFU/g, whilst total psychrotrophic/psychrophilic bacteria were found at levels of ca. 4.4 log CFU/g. As time proceeded and close to shelf-life end, bioluminescent bacteria were encountered at higher populations, and were found at levels of 5.3 and 7.0 log CFU/g in samples from the second and third batch, respectively. In the first batch their presence was occasional and at levels up to 3.9 log CFU/g. Accordingly, total psychrotrophic/psychrophilic bacteria exceeded 8.4 log CFU/g at the end of storage, suggesting the possible underestimation of bioluminescent populations following the specific cultivation conditions. Sequence analysis assigned bioluminescent isolates to Photobacterium phosphoreum, while genetic fingerprinting revealed high intra-species variability. Respectively, total psychrotrophs/psychrophiles were assigned to genera Pseudomonas, Shewanella, Psychrobacter, Acinetobacter, Vibrio and Photobacterium. Non-luminous photobacteria were not identified within the psychrotrophs/psychrophiles. Results of the present study reveal the intra- and inter-batch variability on the occurrence and growth responses of P. phosphoreum and highlight its potential role in the chicken meat spoilage consortium.

Microbial investigation of aquacultured olive flounder (Paralichthys olivaceus) from farm to table based on high-throughput sequencing

The microbial ecologies of fish, such as the olive flounder (Paralichthys olivaceus), one of the most widely consumed fish in East Asia, remain to be elucidated. The microbiome of olive flounder and related environmental samples (i.e., feed, water, workers' aprons and gloves) were collected from six different sources (i.e., a fish farm, a transporting truck, a Wando market and restaurant, and a Seoul market and restaurant). These samples (n = 102) were investigated at various farm-to-distribution stages based on their 16S rRNA sequences. The microbial communities of fish from the farms and trucks were dominated by Photobacterium (>86 %) and showed distinct differences from fish from the Wando and Seoul markets and restaurants. There was also a significant difference in fish microbiomes according to geographical location. The relative abundances of Shewanella, Acinetobacter, Enterobacteriaceae, and Pseudomonas increased as the distribution and consumption stages of the supply chain advanced. The percentages of Shewanella (24.74 %), Acinetobacter (18.32 %), and Enterobacteriaceae (11.24 %) in Wando, and Pseudomonas (42.98 %) in Seoul markets and restaurants implied the importance of sanitation control in these areas. Alpha and beta diversity results corresponded to taxonomic analyses and showed the division of two groups (i.e., fish from the production and transporting stage (farm and truck fish) and fish from the distribution and consumption stages (market and restaurant fish)). The present study provides an in-depth understanding of olive flounder and its environmental microbiomes and suggests control measures to improve food safety.

Bacteriobiota and Chemical Changes during the Ripening of Traditional Fermented "Pirot 'Ironed' Sausage"

"Pirot 'ironed' sausage" (Pis) is a traditional, fermented sausage, made from different types of meat (beef and chevon), without additives or starter cultures. The physical-chemical properties (pH, water activity, fats, moisture, and protein contents) were examined in the initial meat batter stuffing and during ripening. Total bacterial diversity was examined at different time points using both culturable (traditional) and non-culturable (NGS sequencing) approaches. During the ripening, a decrease in pH value, a_w, and moisture content was observed, as well as an increase in protein and fat content. At least a two-fold significant decrease was noted for colorimetric values during the ripening period. The dominance of Proteobacteria and Firmicutes was observed in the non-culturable approach in all studied samples. During the ripening process, an increase in Firmicutes (from 33.5% to 63.5%) with a decrease in Proteobacteria (from 65.4% to 22.3%) was observed. The bacterial genera that were dominant throughout the ripening process were Lactobacillus, Photobacterium, Leuconostoc, Weissella, and Lactococcus, while Carnobacterium, Brochothrix, and Acinetobacter were found also, but in negligible abundance. Among the culturable bacteria, Latilactobacillus sakei (Lactobacillus sakei) and Leuconostoc mesenteoides were present in all stages of ripening.

Systematic review and critical reflection on the isolation and identification methods for spoilage associated bacteria in fresh marine fish

Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.

Impact of Modified Atmospheres on Growth and Metabolism of Meat-Spoilage Relevant Photobacterium spp. as Predicted by Comparative Proteomics

Modified atmosphere packaging (MAP) is a common strategy to selectively prevent the growth of certain species of meat spoiling bacteria. This study aimed to determine the impact of high oxygen MAP (70% O₂, 30% CO₂, red and white meats) and oxygen-free MAP (70% N₂, 30% CO₂, also white meat and seafood) on preventing the growth of spoiling photobacteria on meat. Growth of Photobacterium carnosum and P. phosphoreum was monitored in a meat simulation media under different gas mixtures of nitrogen, oxygen, and carbon dioxide, and samples were taken during exponential growth for a comparative proteomic analysis. Growth under air atmosphere appears optimal, particularly for P. carnosum. Enhanced protein accumulation affected energy metabolism, respiration, oxygen consuming reactions, and lipid usage. However, all the other atmospheres show some degree of growth reduction. An increase in oxygen concentration leads to an increase in enzymes counteracting oxidative stress for both species and enhancement of heme utilization and iron-sulfur cluster assembly proteins for P. phosphoreum. Absence of oxygen appears to switch the metabolism toward fermentative pathways where either ribose (P. phosphoreum) or glycogen (P. carnosum) appear to be the preferred substrates. Additionally, it promotes the use of alternative electron donors/acceptors, mainly formate and nitrate/nitrite. Stress response is manifested as an enhanced accumulation of enzymes that is able to produce ammonia (e.g., carbonic anhydrase, hydroxylamine reductase) and regulate osmotic stress. Our results suggest that photobacteria do not sense the environmental levels of carbon dioxide, but rather adapt to their own anaerobic metabolism. The regulation in presence of carbon dioxide is limited and strain-specific under anaerobic conditions. However, when oxygen at air-like concentration (21%) is present together with carbon dioxide (30%), the oxidative stress appears enhanced compared to air conditions (very low carbon dioxide), as explained if both gases have a synergistic effect. This is further supported by the increase in oxygen concentration in the presence of carbon dioxide. The atmosphere is able to fully inhibit P. carnosum, heavily reduce P. phosphoreum growth in vitro, and trigger diversification of energy production with higher energetic cost, highlighting the importance of concomitant bacteria for their growth on raw meat under said atmosphere.

Comparative genomics of Photobacterium species from terrestrial and marine habitats

Photobacterium (P.) is a genus widely studied in regards to its association with and ubiquitous presence in marine environments. However, certain species (P. phosphoreum, P. carnosum, P. iliopiscarium) have been recently described to colonize and spoil raw meats without a marine link. We have studied 27 strains from meat as well as 26 strains from marine environments in order to probe for intraspecies marine/terrestrial subpopulations and identify distinct genomic features acquired by environmental adaptation. We have conducted phylogenetic analysis (MLSA, ANI, fur, codon usage), search of plasmids (plasmidSPADES), phages (PHASTER), CRISPR-cas operons (CRISPR-finder) and secondary metabolites gene clusters (antiSMASH, BAGEL), in addition to a targeted gene search for specific pathways (e.g. TCA cycle, pentose phosphate, respiratory chain) and elements relevant for growth, adaptation and competition (substrate utilization, motility, bioluminescence, sodium and iron transport). P. carnosum appears as a conserved single clade, with one isolate from MAP fish clustering apart that doesn't, however, show distinct features that could indicate different adaptation. The species harbors genes for a wide carbon source utilization (glycogen/starch, maltose, pullulan, fucose) for colonization of diverse niches in its genome. P. phosphoreum is represented by two different clades on the phylogenetic analyses not correlating to their origin or distribution of other features analyzed that can be divided into two novel subspecies based on genome-wide values. A more diverse antimicrobial activity (sactipeptides, microcins), production of secondary metabolites (siderophores and arylpolyenes), stress response and adaptation (bioluminescence, sodium transporters, catalase, high affinity for oxygen cytochrome cbb3 oxidase, DMSO reductase and proton translocating NADH dehydrogenase) is predicted compared to the other species. P. iliopiscarium was divided into two clades based on source of isolation correlating with phylogeny and distribution of several traits. The species shows traits common to the other two species, similar carbon utilization/transport gene conservation as P. carnosum for the meat-isolated strains, and predicted utilization of marine-common DMSO and flagellar cluster for the sea-isolated strains. Results additionally suggest that photobacteria are highly prone to horizontal acquisition/loss of genetic material and genetic transduction, and that it might be a strategy for increasing the frequency of strain- or species-specific features that offers a growth/competition advantage.

The Potential Effect of Microbiota in Predicting The Freshness of Chilled Chicken

1. The goals of this study were to analyse the changes in microbiota composition of chilled chicken during storage and identify microbial biomarkers related to meat freshness.2. The study used 16S rDNA sequencing to track the microbiota shift in chilled chicken during storage. Associations between microbiota composition and storage time were analysed and microbial biomarkers were identified.3. The results showed that microbial diversity of chilled chicken decreased with the storage time. A total of 27 and 24 microbial biomarkers were identified by using orthogonal partial least squares (OPLS) and the random forest regression approach, respectively. The receiver operating characteristic (ROC) curve analysis indicated that the OPLS regression approach had better performance in identifying freshness-related biomarkers. The multiple stepwise regression analysis identified four key microbial biomarkers, including Streptococcus, Carnobacterium, Serratia and Photobacterium genera and constructed a predictive model.4. The study provided microbial biomarkers and a model related to the freshness of chilled chicken. These findings provide a basis for developing detection methods of the freshness of chilled chicken.

Influence of the packaging atmosphere and presence of co-contaminants on the growth of photobacteria on chicken meat

Fresh meat is commonly packaged in modified atmosphere to decelerate spoilage processes. The applied gas mixture affects the growth of spoilage organisms and selectively shapes the spoilage community. In this study, we investigated the impact of O₂ and CO₂ on the growth of Photobacterium (P.) phosphoreum and P. carnosum strains in situ on chicken meat by packaging under different modified atmospheres (air, 70% O₂/30% CO₂, 70% N₂/30% CO₂, 100% N₂). Combination of 70% O₂ and 30% CO₂ resulted in significant growth reduction of the analyzed strains, suggesting inhibitory effects of both gases in combination. In contrast, 30% CO₂ alone had only a minor effect and photobacteria are supposed to have a growth advantage over other meat spoilers in this atmosphere. Additionally, single growth of the strains in the different atmospheres was compared when challenged with the presence of Pseudomonas (Ps.) fragi or Brochothrix (B.) thermosphacta as prominent co-contaminants in different ratios (10:1, 1:1, 1:10). Presence of co-contaminants resulted in increased cell numbers of P. carnosum TMW2.2149 but reduced or unchanged cell numbers of P. phosphoreum TMW2.2103 in most packaging atmospheres. The initial ratio of photobacteria and co-contaminants defined the relative abundance during storage but did not change the type of the interaction. Our results suggest either a commensalistic (P. carnosum) or competitive interaction (P. phosphoreum) of photobacteria and co-contaminants on modified atmosphere packaged chicken, respectively. Furthermore, in a mix comprising seven prominent spoilers, strains of both Photobacterium species prevailed as a constant part of the spoilage microbiome during 7 days of refrigerated storage on chicken meat packaged under O₂/CO₂ atmosphere.

Aronia melanocarpa (Michx.) Elliot, Chaenomeles superba Lindl. and Cornus mas L. Leaf Extracts as Natural Preservatives for Pork Meat Products

The aim of this study was to investigate the possibility of using Aronia melanocarpa, Chaenomeles superba, and Cornus mas leaf extracts as natural preservatives for pork meat products. Pork sausages were stored in modified atmosphere packaging (MAP) (80% N₂ and 20% CO₂) at 4 °C for 29 days. The total psychrotrophic counts (TPC) were determined during the storage period, along with the numbers of Enterobacteriaceae and lactic acid bacteria (LAB). The extracts improved the microbial quality of the meat products but to a lesser extent than sodium nitrate (III). They reduced the amounts of Enterobacteriaceae and LAB. The A.melanocarpa leaf extract showed the strongest preservative effect. The bacterial biodiversity of the meat products was investigated based on high-throughput sequencing of the 16S rRNA gene. Two predominant bacteria phyla were identified, Proteobacteria and Firmucutes, mostly consisting of genera Photobacterium, Brochothrix, and Carnobacterium. The extracts also influenced microbial community in sausages decreasing or increasing bacterial relative abundance. The extracts significantly inhibited lipid oxidation and improved the water-holding capacity of the meat, with C. superba extract showing the strongest influence. In addition, A. melanocarpa and C. superba improved the redness (a*) of the sausages. The results of this study show that A. melanocarpa, C. superba, and C. mas leaf extracts can extend the shelf life of meat products stored in MAP at 4 °C.

Evaluation of the Spoilage-Related Bacterial Profiles of Vacuum-Packaged Chilled Ostrich Meat by Next-Generation DNA Sequencing Approach

Monitoring the development of the bacterial community in packaged raw meat refrigerated until two weeks is important for identifying the spoilage-related bacteria, preventing meat putrefaction, and prolong the shelf life. This study aimed to evaluate the influence of vacuum-packaging (VP) on the development of spoilage-related bacterial profiles in chilled ostrich meat among three manufacturing batches produced in different periods by using culture-dependent and 16S rDNA amplicon sequencing. Similar to the culture-dependent method, 16S rDNA sequencing showed that Photobacterium was the most prevalent genus detected in VP ostrich meat after 14 days of cold storage. The second-largest group was the population of lactic acid bacteria (LAB), mainly dominated by Carnobacteriaceae including Carnobacterium spp. and Lactobacillaceae with Lactobacillus spp. Our results suggest that these taxa could contribute to spoilage of VP ostrich meat and shorten its shelf life, especially Photobacterium spp., which is considered as a potential meat spoiler.

Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing

Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), Brochothrix thermosphacta, Pseudomonas spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of Acinetobacter, Brochothrix, Flavobacterium, Pseudomonas, Psychrobacter, and Vibrionaceae (family). These genera persisted until the end of storage in >80% of samples, except Psychrobacter and Flavobacterium, while Photobacterium was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in Pseudomonas, Acinetobacter, Photobacterium, and Vibrionaceae. Results of the present study highlight Photobacterium and Vibrionaceae, in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.

Characterization of chilled chicken spoilage using an integrated microbiome and metabolomics analysis

Spoilage of chilled chicken can occur as a result of microbial development and consumption of meat nutrients by spoilage bacteria, ultimately resulting in the release of undesired metabolites. Characterizing the profiles of the microbiota and metabolites and clarifying their relationships will contribute to an improved understanding of the mechanism underlying chilled chicken spoilage. In the present study, 16S rRNA gene sequencing and ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS)-based untargeted metabolomics analyses were applied to determine the microbial and metabolic profiles in chicken during chilled storage. The microbial and metabolic datasets were subjected to combined analysis using weighted gene co-expression network analysis (WGCNA) and Spearman's correlation analysis. Brochothrix, Carnobacterium, Photobacterium, Pseudomonas, Acinetobacter, Serratia, Kurthia, Shewanella, and Obesumbacterium genera were identified as the dominant spoilage bacteria in chilled chicken. Ten metabolic pathways, including histidine metabolism and purine metabolism, were identified as potential mechanisms underlying chilled chicken spoilage. Correlation analysis demonstrated that spoilage bacterial genera were highly correlated with spoilage-related metabolites. Taken together, the present study proposed an integrated microbiome and metabolomics approach to investigate the mechanism of chilled chicken spoilage caused by microbial activity. The results obtained by this approach provide a comprehensive insight into changes in the microbial and metabolic profiles of chilled chicken during spoilage.

Development of a rapid detection method for Photobacterium spp. using Loop-mediated isothermal amplification (LAMP)

While the abundance of photobacteria has previously been exclusively associated with marine environments and spoilage of seafood, several recent studies have demonstrated their status as pervasive constituents of the microbiota on packaged meats. Since their ubiquitous nature has been revealed, detection of their presence on meat, their entry route into meat processing environments and prevention of their growth is a novel emerging challenge for the food industry. In this study, we have developed a highly sensitive and specific loop-mediated isothermal amplification (LAMP) assay for the detection of relevant species of photobacteria on foods, and tested its efficacy on meats. The gene encoding trimethylamine-N-oxide reductase (torA) was chosen as the target for this assay. Designed primers based on the gene sequence proved their specificity by testing 67 isolates of 5 species of photobacteria (positive) as well as 63 strains of 16 species of other common meat spoilers (negative). The optimized assay takes 2 h including sample preparation and has a detection limit of only 10-11 copies (50 fg/reaction) of the average Photobacterium (P.) genome per reaction. Its applicability could be successfully demonstrated on naturally and artificially contaminated chicken, beef and pork samples and evaluated by comparison with a culture-dependent approach using selective media and MALDI-TOF MS for identification. The developed LAMP assay revealed presence of photobacteria on one naturally contaminated chicken sample stored at 4 °C long before (3 days) confirmation by the culture-dependent approach. This study demonstrates that the developed LAMP assay represents a reliable and sensitive method for rapid detection of photobacteria on meats. However, its specificity would allow the applicability of the methodology to be extended to other foods, e.g. fish and seafood where presence of photobacteria is directly linked to their shelf life. The method has no requirement for specialized equipment or specially trained personal allowing an easy implementation within the quality control of the food industry. Considering the lot-to-lot variations observed on meats regarding the presence of photobacteria and the impracticality of implementing quantitative methods within the routine control, the LAMP method can simplify and reduce the workload for detection of photobacteria on high sample numbers. Consequently, producers can identify batches/plants that need more stringent control, and are provided with a tool to determine the entry route of photobacteria into the processing and distribution chain of raw meats.

Hydrostatic pressure- and halotolerance of Photobacterium phosphoreum and P. carnosum isolated from spoiled meat and salmon

Photobacterium spp. occur frequently in marine environments but have been recently also found as common spoilers on chilled meats. The environmental conditions in these ecological niches differ especially regarding salinity and ambient pressure. Linking the occurrence of photobacteria in different niches may elucidate its ecology and bring insights for the food industry. We investigated tolerance of Photobacterium (P.) phosphoreum and P. carnosum strains to high hydrostatic pressure and salinity and aligned our observations with presence of relevant genes. The strains were isolated from packaged meats and salmon (or the sea) to identify adaptations to marine and terrestrial habitats. Growth of all P. carnosum strains was reduced by 40 MPa hydrostatic pressure and >3% sodium chloride, suggesting loss of traits associated with marine habitats. In contrast, P. phosphoreum strains were only slightly affected, suggesting general adaptation to marine habitats. In accordance, these strains had gene clusters associated with marine niches, e.g. flagellar and lux-operons, being incomplete in P. carnosum. Occurrence of P. carnosum strains on packaged salmon and P. phosphoreum strains on meats therefore likely results from cross-contamination in meat and fish processing. Still, these strains showed intermediate traits regarding pressure- and halotolerance, suggesting developing adaptation to their respective environment.

Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products

Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bacterial species, but these techniques are unable to describe the whole community of microbial species (microbiome) and the profile of AMR genes they carry (resistome), which is critical for getting a holistic perspective of AMR. The objective of this study was to characterize the microbiome and resistome of retail ground beef products labeled as coming from conventional or raised without antibiotics (RWA) production systems. Sixteen ground beef products were purchased from 6 retail grocery outlets in Fort Collins, CO, half of which were labeled as produced from cattle raised conventionally and half of products were from RWA production. Total DNA was extracted and isolated from each sample and subjected to 16S rRNA amplicon sequencing for microbiome characterization and target-enriched shotgun sequencing to characterize the resistome. Differences in the microbiome and resistome of RWA and conventional ground beef were analyzed using the R programming software. Our results suggest that the resistome and microbiome of retail ground beef products with RWA packaging labels do not differ from products that do not carry claims regarding antimicrobial drug exposures during cattle production. The resistome predominantly consisted of tetracycline resistance making up more than 90% of reads mapped to resistance gene accessions in our samples. Firmicutes and Proteobacteria predominated in the microbiome of all samples (69.6% and 29.0%, respectively), but Proteobacteria composed a higher proportion in ground beef from conventionally raised cattle. In addition, our results suggest that product management, such as packaging type, could exert a stronger influence on the microbiome than the resistome in consumer-ready products. Metagenomic analyses of ground beef is a promising tool to investigate community-wide shifts in retail ground beef. Importantly, however, results from metagenomic sequencing must be carefully considered in parallel with traditional methods to better characterize the risk of AMR in retail products.

Bacterial Community Assessed by Utilization of Single Carbon Sources in Broiler Ground Meat after Treatment with an Antioxidant, Carnosine, and Cold Plasma

ABSTRACT

Contaminated poultry meat is a major source of human foodborne illnesses. Many interventions have been developed to reduce and/or eliminate human foodborne pathogens in poultry products; however, treatments with cold plasma or carnosine or their combination have not been extensively investigated. In this study, the bacterial microflora of poultry meat samples after treatments with cold plasma and carnosine were characterized with EcoPlates in the OmniLog system. The plates were incubated at 25°C for 7 days in the OmniLog chamber, and bacterial growth was monitored by recording formazan production every 30 min at an optical density of 590 nm. The kinetics of lag, log, and stationary phases of bacterial growth followed the Gompertz sigmoidal model but with different inflection times and asymptotes at the log phase and the stationary phase, respectively. Results indicated that treatment of poultry meat samples with cold plasma technology and carnosine could inhibit growth of the bacteria in the treated meat samples. Of 31 chemicals tested, phenylethylamine, α-d-lactose, d,l-α-glycerol phosphate, 2-hydroxybenzoic acid, γ-hydroxybutyric acid, α-ketobutyric acid, and d-malic acid could not be metabolized by bacteria in the meat samples. Future research is required to determine whether these seven chemicals that inhibited growth of bacteria in these meat samples can be used as food preservatives for extending the shelf life of these products. Whether the bacterial flora can be an indicator of effectiveness for meat samples treated with cold plasma, carnosine, or both needs further study.

HIGHLIGHTS

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.

Biodiversity of Photobacterium spp. Isolated From Meats

Photobacteria are common psychrophilic bacteria found in marine environments. Recently, several studies revealed high numbers of Photobacterium (P.) spp. on packaged fresh meat. Their occurrence appears relevant for the spoilage of meat, since species of the genus are already known as potent fish spoilage organisms. Here we report on distribution, biodiversity, and specific traits of P. carnosum (n = 31), P. phosphoreum (n = 24), and P. iliopiscarium (n = 3) strains from different foods. Biodiversity was assessed by genomic fingerprinting, diversity index analysis, growth dynamics, comparison of metabolic activities, and antibiotic resistance. We observed a ubiquitous occurrence of the species on all common meats independent of packaging conditions and producer, suggesting contamination during an established processing or packaging step. Regarding biodiversity, the three species differed clearly in their growth properties and metabolic characteristics, with P. phosphoreum growing the fastest and showing the strongest alkalization of the media. On strain level we also recorded variations in enzymatic reactions, acid production, and antibiotic resistances not restricted to specific meat types. This depicts high biodiversity on species and strain level on each contaminated meat sample. Our analysis showed that meat-borne strains of P. phosphoreum and P. iliopiscarium clearly differ from their type strains from a marine habitat. Additionally, we report for the first time isolation of P. carnosum strains from packaged fish, which in contrast showed comparable phenotypic properties to meat-borne strains. This hints at different initial origins of P. phosphoreum/P. iliopiscarium (marine background) and P. carnosum (no demonstrated marine background) contaminations on fish and meat, respectively.

In vitro discrimination and classification of Microbial Flora of Poultry using two dispersive Raman spectrometers (microscope and Portable Fiber-Optic systems) in tandem with chemometric analysis

Discrimination and classification of eight strains related to meat spoilage and pathogenic microorganisms commonly found in poultry meat were successfully carried out using two dispersive Raman spectrometers (Microscope and Portable Fiber-Optic systems) in combination with chemometric methods. Principal components analysis (PCA) and multi-class support vector machines (MC-SVM) were applied to develop discrimination and classification models. These models were certified using validation data sets which were successfully assigned to the correct bacterial species and even to the right strain. The discrimination of bacteria down to the strain level was performed for the pre-processed spectral data using a 3-stage model based on PCA. The spectral features and differences among the species on which the discrimination was based were clarified through PCA loadings. In MC-SVM the pre-processed spectral data was subjected to PCA and utilized to build a classification model. When using the first two components, the accuracy of the MC-SVM model was 97.64% and 93.23% for the validation data collected by the Raman Microscope and the Portable Fiber-Optic Raman system, respectively. The accuracy reached 100% for the validation data by using the first eight and ten PC's from the data collected by Raman Microscope and by Portable Fiber-Optic Raman system, respectively. The results reflect the strong discriminative power and the high performance of the developed models, the suitability of the pre-processing method used in this study and that the low accuracy of the Portable Fiber-Optic Raman system does not adversely affect the discriminative power of the developed models.

Prediction of in situ metabolism of photobacteria in modified atmosphere packaged poultry meat using metatranscriptomic data

Modified atmosphere packaging (MAP) is widely used in food industry to extend the microbiological shelf life of meat. Common CO₂-containing gas atmospheres for poultry meat packaging are either nearly O₂-free or high O₂ MAPs. In this work, we compared spoilage microbiota of skinless chicken breast in CO₂/O₂ (30/70%) and CO₂/N₂ (30/70%) MAP, which are culturable with conventional methods and identified isolates by MALDI-TOF MS. These data were compared to metatranscriptome sequencing enabling a culture-independent overview on the composition of microbiota at species level. While typical MAP meat spoilers were confirmed in the transcriptomic approach, we also found high numbers of transcripts mapping to Photobacterium spp. sequences in these samples. As photobacteria were recently shown to occur in different MAP and vacuum packaged meats, we used the respective part of the metatranscriptomic data for prediction of Photobacterium spp. major metabolic routes in situ, upon growth in MAP poultry meat. It is predicted that they employ similar metabolism in both atmospheres: In the lack of carbohydrates upon meat spoilage, the pyruvate pool is filled via glycerol originating from lipolysis and amino acid conversions. From the pyruvate pool, gluconeogenesis is fed enabling cell wall biosynthesis and growth as well as catabolism to lactate and other metabolites, or anaplerosis towards the citric acid cycle. Production is predicted of several biogenic amines including tyramine and cadaverine, enabling generation of proton motive force. Taken together, photobacteria express metabolic pathways upon growth on meat, which should lead to compounds overlapping with those of known potent meat spoilers.