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

Behavior of Spoilage Bacterial Communities in Different Cuts of Enshi Black Pork under Refrigerated Storage (4 °C)

The Enshi black pig is a Chinese native breed known for its rich nutrition content and high quality, which has notable traction in the consumer market. In this study, the potential impact of the main commercial cuts from Enshi black pork carcasses (ham, loin, and belly) on the bacteria community of spoiled meat under refrigerated storage (4 °C) was assessed by using a high-throughput sequencing method. Moreover, the spoilage potential of isolated strains from spoiled pork was investigated. The results demonstrated significant differences (p < 0.05) in bacterial community diversity and composition among spoiled ham, loin, and belly samples. Linear discriminant analysis effect size (LEfSe) analysis revealed a total of 20 significantly different potential bacterial biomarkers, with the dominant genera of Pseudomonas, Psychrobacter, Shewanella and Carnobacterium. Additionally, C. divergens THT1-5, isolated from spoiled ham samples, displayed cold adaptation and higher spoilage potential in Enshi black pork. These findings are helpful for identifying key factors contributing to spoilage in Enshi black pork and developing strategies to inhibit bacterial growth during preservation.

Characterization and interactions of spoilage of Pseudomonas fragi C6 and Brochothrix thermosphacta S5 in chilled pork based on LC-MS/MS and screening of potential spoilage biomarkers

Pseudomonas and Brochothrix are the main spoilage organisms in pork, and each of these plays an essential role in the spoilage process. However, the effect of co-contamination of these two organisms in pork has not been elucidated. The changing bacterial communities during spontaneous spoilage of pork at 4 °C were evaluated using high-throughput sequencing. The dominant spoilage bacteria were isolated and these were identified as Pseudomonas fragi C6 and Brochothrix thermosphacta S5. Chilled pork was then experimentally contaminated with these strains, individually and in combination, and the progression of spoilage was assessed by analyzing various physicochemical indicators. These included total viable counts (TVC), pH, color, total volatile basic nitrogen (TVB-N), and detection of microbial metabolites. After 7 days of chilled storage, co-contaminated pork produced higher TVC and TVB-N values than mono-contaminated samples. Metabolomic analysis identified a total of 8,084 metabolites in all three groups combined. Differential metabolites were identified, which were involved in 38 metabolic pathways. Among these pathways, the biosynthesis of alkaloids derived from purine and histidine was identified as an important pathway related to spoilage. Specifically, histidine, histamine, AMP, IMP, GMP, succinic acid, and oxoglutaric acid were identified as potential spoilage biomarkers. The study showed that the combined presence of P. fragi C6 and B. thermosphacta S5 bacteria makes chilled pork more prone to spoilage, compared to their individual presence. This study provides insights that can assist in applying appropriate techniques to maintain quality and safety changes in meat during storage and further the assessment of freshness.

Rapid and non-destructive microbial quality prediction of fresh pork stored under modified atmospheres by using selected-ion flow-tube mass spectrometry and machine learning

Volatile organic compounds (VOCs) indicative of pork microbial spoilage can be quantified rapidly at trace levels using selected-ion flow-tube mass spectrometry (SIFT-MS). Packaging atmosphere is one of the factors influencing VOC production patterns during storage. On this basis, machine learning would help to process complex volatolomic data and predict pork microbial quality efficiently. This study focused on (1) investigating model generalizability based on different nested cross-validation settings, and (2) comparing the predictive power and feature importance of nine algorithms, including Artificial Neural Network (ANN), k-Nearest Neighbors, Support Vector Regression, Decision Tree, Partial Least Squares Regression, and four ensemble learning models. The datasets used contain 37 VOCs' concentrations (input) and total plate counts (TPC, output) of 350 pork samples with different storage times, including 225 pork loin samples stored under three high-O2 and three low-O2 conditions, and 125 commercially packaged products. An appropriate choice of cross-validation strategies resulted in trustworthy and relevant predictions. When trained on all possible selections of two high-O2 and two low-O2 conditions, ANNs produced satisfactory TPC predictions of unseen test scenarios (one high-O2 condition, one low-O2 condition, and the commercial products). ANN-based bagging outperformed other employed models, when TPC exceeded ca. 6 log CFU/g. VOCs including benzaldehyde, 3-methyl-1-butanol, ethanol and methyl mercaptan were identified with high feature importance. This elaborated case study illustrates great prospects of real-time detection techniques and machine learning in meat quality prediction. Further investigations on handling low VOC levels would enhance the model performance and decision making in commercial meat quality control.

Dellaglioa spp. an underestimated genus isolated from high-oxygen modified-atmosphere packaged meat

The genus Dellaglioa (D.) actually comprises two species, i.e., D. algida and the recently described species D. carnosa. Both species are adapted to cold and have been typically recovered from meat products. However, their importance has thus far been underestimated, since routine culture-based analysis failed to support their growth. Furthermore, their occurrence on meat packed under high-oxygen MA conditions (HiOx-MAP) is controversial because they have been described as being oxygen-sensitive. In this study, we focused on the targeted isolation of Dellaglioa spp. from HiOx-MAP meat samples and the characterization of our isolates regarding their adaption to HiOx-MAP conditions, their spoilage potential, as well as food safety aspects. We used a medium recently developed specifically for strains of this genus and investigated ten meat batches from seven different suppliers. Our study confirms that the occurrence of Dellaglioa spp. on HiOx-MAP meat is non-sporadic, reaching cell counts ranging from log10 5.8-7.1 CFU/cm2 at a late stage of chilled storage. Autochthonous Dellaglioa spp. and Leuconostoc (L.) gasicomitatum dominated the microbiota of the beef steaks with similar growth behavior. Our results suggest that Dellaglioa spp. benefits from the heme-dependent respiration of oxygen by L. gasicomitatum. Furthermore, whole genome analysis revealed the presence of genes predictively involved in oxidative stress defense, survival, and adaptation in meat environments. Moreover, we predict a weak aminogenic potential of D. algida strains. Tyramine production from tyrosine seems to be a species-specific characteristic of D. carnosa. The extent to which D. algida and D. carnosa occurrence is influenced by or even dependent on the composition of the entire microbiota remains to be investigated.

Potential inhibitory effect of carbon dioxide on the spoilage behaviors of Pseudomonas fragi in high-oxygen packaged beef during refrigerated storage

Pseudomonas fragi is a dominant meat spoilage organism under high-oxygen modified atmosphere packaging (HiOx-MAP). This work investigated the effects of CO₂ on P. fragi growth and the related spoilage phenomena of HiOx-MAP beef. Minced beef incubated with P. fragi T1, a strain owning the strongest spoilage potential among isolates, was stored under CO₂-enriched HiOx-MAP (TMAP; 50% O₂/40% CO₂/10% N₂) or non-CO₂ HiOx-MAP (CMAP; 50% O₂/50% N₂) at 4 °C for 14 days. Compared to CMAP, TMAP maintained sufficient O₂ levels to endow beef with higher a* values and meat color stability due to lower P. fragi counts from day 1 (P < 0.05). TMAP samples also showed lower (P < 0.05) lipase activity and protease activity within 14-days and 6-days than CMAP samples respectively. TMAP delayed the significantly increased pH and total volatile basic nitrogen contents occurred in CMAP beef during storage. Despite TMAP markedly promoted the lipid oxidation associated with higher concentrations of hexanal and 2,3-octanedione than CMAP (P < 0.05), TMAP beef retained an acceptable organoleptic odor due to a CO₂-inhibition on the microbial-induced 2,3-butanedione and ethyl 2-butenoate formation. This study provided a comprehensive insight into the antibacterial mechanism of CO₂ on P. fragi in HiOx-MAP beef.

Selected-ion flow-tube mass spectrometry for the identification of volatile spoilage markers for fresh pork packaged under modified atmospheres

Microbial behavior during meat storage leads to the generation of volatile organic compounds (VOCs) and unpleasant off-odors. This study focused on a novel real-time analytical method, selected-ion flow-tube mass spectrometry (SIFT-MS), to monitor VOC quality and identify spoilage indicators for fresh pork stored under different packaging atmospheres (air, 70/0/30, 70/30/0, 5/30/65, 0/30/70 - v/v% O₂/CO₂/N₂) at 4 °C. A comprehensive selection methodology was used to identify compounds with good instrumental data quality as well as a strong relationship with microbial growth and olfactory rejection. Based on the volatolome quantified by SIFT-MS, storage periods and conditions can be discriminated using multivariate statistics. Acetoin (or ethyl acetate) represented a significant pork quality marker for high-O₂ conditions, whereas ethanol, 3-methylbutanal and sulfur compounds can indicate the anaerobic storage progress. Considering the applicability in monitoring different VOC profiles, SIFT-MS is expected to be promising in many storage scenarios to improve analytical efficiency and ensure reliability.

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.

Transcriptomic analysis of the response of Photobacterium phosphoreum and Photobacterium carnosum to co-contaminants on chicken meat

This study investigated the impact of Brochothrix (B.) thermosphacta and Pseudomonas (Ps.) fragi on the transcriptomes of Photobacterium (P.) phosphoreum and P. carnosum on chicken meat under modified atmosphere (MA) and air atmosphere (AA). P. phosphoreum TMW2.2103 responded to MA with a reduced transcript number related to cell division and an enhanced number related to oxidative stress. Concomitantly, the analysis revealed upregulation of fermentation and downregulation of respiration. It predicts enhanced substrate competition in presence of co-contaminants/MA. In contrast, the strain upregulated the respiration in AA, supposably due to improved substrate accessibility in this situation. For P. carnosum TMW2.2149 the respiration was downregulated, and the pyruvate metabolism upregulated under MA. MA/co-contaminant resulted in multiple upregulated metabolic routes. Conversely, AA/co-contaminant resulted only in minor regulations, showing inability to cope with fast growing competitors. Observations reveal different strategies of photobacteria to react to co-contaminants on meat.

Non-Destructive Measuring Systems for the Evaluation of High Oxygen Stored Poultry: Development of Headspace Gas Composition, Sensory and Microbiological Spoilage

As poultry is known to be a perishable food, the use-by date is set in such a way that food safety is guaranteed even with a higher initial bacterial count. This means, however, that some products are wasted, even if they are still safe to eat. Therefore, non-destructive measurement devices might be a good opportunity for individual shelf-life prediction, e.g., in retail. The aim of this study was therefore to use non-destructive measurement devices based on fluorescence quenching (oxygen detection) and mid-infrared laser spectroscopy (carbon dioxide detection) for the monitoring of high-oxygen-packed poultry in different storage conditions. During 15 days of storage, the gas composition of the headspace was assessed (non-destructively and destructively), while total plate count was monitored and a comprehensive sensory evaluation was performed by a trained panel. We were able to demonstrate that in most cases, non-destructive devices have comparable precision to destructive devices. For both storage conditions, the sensory attribute slime was correlated with reaching the critical microbiological value of 10⁷ CFU/g; the attribute buttery was also useful for the prediction of regularly stored poultry. The change in the gas atmosphere as a sign of premature spoilage, however, was only possible for samples stored in irregular conditions.

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.

Metabolomics workflow for quality control of differently-processed pre-cooked chicken fillets

The contents and profiles of small molecules in a food can provide information about quality-related properties. Processing methods and deterioration during storage, e.g. from bacterial proliferation and degradation, might also lead to changes in the metabolome, which can be determined by mass spectrometry-based metabolomics. By measuring as many metabolites as possible in differently treated pre-cooked chicken fillets in an untargeted approach, we studied individual and combined effects of vacuum packaging (VP), soluble gas stabilisation (SGS), high pressure processing (HPP), and microwave volumetric heating (MW) on the quality and shelf-life of the finished product. The extensive dataset was processed using an optimised workflow of consecutive software tools with stringent statistical analysis to prevent over-interpretation, which is an inherent risk of metabolomics data. Our results showed the predominant influence of VP on storage quality since SGS, HPP, and MW did not have the potential to extent shelf-life.

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.