Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels stored at 4oC

Multi-omics signature profiles of cold-smoked salmon from different processing plants: Insights into spoilage dynamics

Cold-smoked salmon (CSS) is highly susceptible to spoilage due to its processing and storage requirements. This study leverages a multi-omics approach to unravel the complex interactions between microbiota, biochemical changes, and sensory characteristics during the storage of CSS produced in three distinct processing plants. By integrating high-throughput metabarcoding, volatile organic compound (VOC) profiling, biochemical assays, and sensory evaluations, plant-specific spoilage trajectories and molecular signatures that influence product quality were identified. Initial storage phases revealed a shared unspoiled profile across all samples marked by high levels of phenolic VOCs. However, as storage progressed, spoilage pathways diverged depending on the processing plant, driven by variations in microbiota composition and metabolic activity. Distinct bacterial communities, including genera such as Photobacterium, Aliivibrio, Carnobacterium, and Brochothrix, shaped the production of spoilage-related VOCs. Statistical analyses using the DIABLO framework uncovered strong correlations between bacterial taxa, volatile organic compounds (VOCs), and sensory attributes, emphasizing the distinct spoilage signatures associated with each processing plant. This study provides new insights into the spoilage mechanisms of cold-smoked salmon by integrating multi-omics data to identify plant-specific microbiota and their metabolic contributions. Beyond identifying distinct spoilage signatures, this study highlights the potential of multi-omics approaches to develop targeted interventions for maintaining product quality.

Compositional Shifts in the Mycobiota of 'Shine Muscat' Grape (Vitis labruscana Baily × V. vinifera L.) Bunches During Cold Storage at Different Temperatures

The cultivation of 'Shine Muscat' grapes is rapidly expanding in East Asia due to their desirable qualities and muscat flavor. Studies have revealed that storing these grapes at an controlled freezing-point temperature diminishes their muscat flavor, whereas storage at 10 °C preserves it. However, the impact of a higher storage temperature on the evolution of microbial communities remains unclear. This study aimed to analyze the mycobiota dynamics of 'Shine Muscat' grape bunches under different cold storage temperatures. A total of 1,892,842 and 1,643,200 sequences were obtained from berries and pedicels, identifying over 208 fungal genera from 6 phyla. Xylariaceae was the most abundant family, with a prevalence between 7.21% and 69.27% across all sample groups. The primary genera included Zygosporium, Cladosporium, Aspergillus, Acremonium, Podosordaria, Zasmidium, Penicillium, and Alternaria. Spoilage-related fungi varied with storage temperature, with Aspergillus, Penicillium, and Alternaria being dominant at 0 °C and Cladosporium, Aspergillus, Penicillium, and Alternaria being prevalent at 10 °C. The fungal profiles of berries and pedicels differed significantly, and storage temperature further influenced these variations. Our findings highlight distinct fungal diversity and spoilage patterns in 'Shine Muscat' grape bunches from the Nanning region compared to those grown in temperate areas, revealing the unique microbial evolution of grape bunches stored at different temperatures in Nanning.

Effects of temperature fluctuations on the quality and microbial diversity of beef meatballs during simulated cold chain distribution

BACKGROUND

Cold chain distribution with multiple links maintains low temperatures to ensure the quality of meat products, whereas temperature fluctuations during this are often disregarded by the industry. The present study simulated two distinct temperatures cold chain distribution processes. Quality indicators and high-throughput sequencing were employed to investigate the effects of temperature fluctuations on the quality and microbial diversity of beef meatballs during cold chain distribution.

RESULTS

Quality indicators revealed that temperature fluctuations during simulated cold chain distribution significantly (P < 0.05) exacerbated the quality deterioration of beef meatballs. High-throughput sequencing demonstrated that temperature fluctuations affected the diversity and structure of microbial community. Lower microbial species abundance and higher microbial species diversity were observed in the temperature fluctuations group. Proteobacteria and Pseudomonas were identified as the dominant phylum and genus in beef meatballs, respectively, exhibiting faster growth rates and greater relative abundance under temperature fluctuations.

CONCLUSION

The present study demonstrates that temperature fluctuations during simulated cold chain distribution can worsen spoilage and shorten the shelf life of beef meatballs. It also offers certain insights into the spoilage mechanism and preservation of meat products during cold chain distribution. © 2024 Society of Chemical Industry.

The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing

Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56-100%) and total psychrotrophic bacteria counted >7 log CFU g-1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.

Effects of curing concentration and drying time on flavor and microorganisms in dry salted Spanish mackerel

This study investigated the quality changes of dry salted mackerel during curing and drying process and the relationship between flavor substances and microorganisms. The results showed that the thiobarbituric acid reactive substances (TBARS) values increased gradually with the increase of salt concentration and treatment time. The total volatile base nitrogen (TVB-N) values and total viable counts (TVC) values showed the same trend. Under 3% condition, the TVB-N values exceeded the standard and was not suitable for consumption. A total of 61 volatile flavor substances were identified by Gas chromatography-ion mobility spectrometry (GC-IMS), among which aldehydes contributed the most. Staphylococcus and Cobetia were the most abundant by High-throughput sequencing (HTS). There was significant correlation between TOP15 microorganisms and TOP20 flavor substances. Staphylococcus and Cobetia were positively correlated with 13 volatile flavor substances, which contributed to the formation of flavor in naturally fermented Spanish mackerel.

A multi-study analysis of gut microbiome data from the blue mussel (Mytilus edulis) emphasises the impact of depuration on biological interpretation

The blue mussel (Mytilus edulis) is a suspension feeder which has been used in gut-microbiome surveys. Although raw 16S sequence data are often publicly available, unifying secondary analyses are lacking. The present work analysed raw data from seven projects conducted by one group over 7 years. Although each project had different motivations, experimental designs and conclusions, all selected samples were from the guts of M. edulis collected from a single location in Long Island Sound. The goal of this analysis was to determine which independent factors (e.g., collection date, depuration status) were responsible for governing composition and diversity in the gut microbiomes. Results indicated that whether mussels had undergone depuration, defined here as voidance of faeces in a controlled, no-food period, was the primary factor that governed gut microbiome composition. Gut microbiomes from non-depurated mussels were mixtures of resident and transient communities and were influenced by temporal factors. Resident communities from depurated mussels were influenced by the final food source and length of time host mussels were held under laboratory conditions. These findings reinforce the paradigm that gut microbiota are divided into resident and transient components and suggest that depuration status should be taken into consideration when designing and interpreting future experiments.

Exploration of Infant Food Microbial Composition from Formal and Informal Settings Using Viable Counts and 16S rRNA Gene Amplicon Sequencing in Johannesburg, South Africa

Diarrhoea is a considerable agent of disease and loss of life in children below age five in South Africa. Soweto, South Africa is an urban township in Johannesburg, with most of its population living in informal settlements. Informal settlements in areas such as Soweto are often impoverished communities that do not get water easily, inadequate sanitation is pervasive, and poor hygiene common (risk factors for diarrhoeal diseases). Among the age groups, infants are most vulnerable to diarrhoeal infection, mainly through the ingestion of food and water. The presence of undesirable microbiota is a food safety and health challenge. This study investigated the microbiome of infant food samples collected from formal (n = 19) and informal (n = 11) households in Soweto. A non-culture-dependent technique was used to characterise the bacterial diversity and composition of the infant food samples. The results indicated that household type did not influence microbial diversity and composition in Soweto. South Africa. Firmicutes, Proteobacteria, Cyanobacteria, and Tenericutes dominated the phyla rank in food samples from formal and informal households. Potential pathogens of public health significance, including diarrhoeal disease agents such as Salmonella spp., E. coli, and Campylobacter spp., were detected within the foods. We concluded that the infant food samples showed rich bacterial diversity, and the presence of potential pathogens of public health significance suggests a disease risk that infants may face upon consuming the foods.

Changes in extractive components and bacterial flora in live mussels Mytilus galloprovincialis during storage at different temperatures

To estimate the quality of mussels during storage, the mortality, succinate dehydrogenase (SDH) activity, extractive components, viable bacterial count (VBC), and bacterial flora of live mussels were investigated. The hierarchical cluster analysis, based on extractive components and VBC, taste active value (TAV), and equivalent umami concentration (EUC), suggested that metabolite composition, bacterial, and taste changing patterns of samples stored at 5 and 10°C differed from those stored at 0°C. The mortality of mussels stored at 5 and 10°C was lower than those at 0°C. The gills of live mussels stored at 0°C for more than 7 days exhibited significantly lower SDH activity than those stored at 5 and 10°C. There was no significant difference in EUC among the samples stored at different temperatures, but a significantly higher TAV of Ala and succinic acid was observed in live mussels after 12 days of storage at 5 and 10°C than in those stored at 0°C. Next-generation sequencing analysis showed that samples stored at 5 and 10°C lost bacterial diversity, and their bacterial flora changed compared to that before storage. Considering these results, the most suitable storage condition to maintain high quality for live mussels is 5°C for less than 7 days.

Predator Presence Alters Intestinal Microbiota in Mussel

Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.

Response to Cold Adaption in Acinetobacter johnsonii XY27 from Spoiled Bigeye Tuna (Thunnus obesus): Membrane Protein Composition and Protein Biomarker Identification by Proteomics

Acinetobacter johnsonii is one of the major food-spoilage bacteria and can survive under cold stress. In this study, the membrane composition, membrane permeability, and energy transduction of A. johnsonii XY27 cultured at 4 and 30 °C were examined comparatively by flow cytometry combined with liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The Na⁺/K⁺ATPase activity, alkaline phosphatase and ATPase activity, fluorescence intensity, and cell viability in A. johnsonii XY27 increased with the decrease in cultivation temperature. The polyunsaturated fatty acid and monounsaturated fatty acids have a higher content in A. johnsonii XY27 cultured at 4 °C compared to that cultured at 30 °C, in which the contents of methyl palmitoleate, methyl myristoleate, and methyl oleate increased dramatically with decreasing temperature. Comparative proteomics analysis revealed that 31 proteins were downregulated and 4 proteins were upregulated, in which catalase-peroxidase 1 and cold shock proteins as biomarker proteins could effectively control A. johnsonii during cold adaptation.

Exploring the Dynamic of Bacterial Communities in Manila Clam (Ruditapes philippinarum) During Refrigerated Storage

Microorganism contamination is one of the most important factors affecting the spoilage and food safety of Manila clams. This study aimed to gain insights into bacterial composition and the dynamic change of bacterial communities on retailed Manila clam during refrigerated storage within the edible period. High-throughput sequencing was conducted to monitor the bacterial population with the prolongation of storage time of Day 0, Day 1, and Day 3. Result demonstrated that phyla of Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi composed the majority of bacterial communities during the whole observation process. Furthermore, the increase of Proteobacteria showed a positive correlation with the storage time, whereas Acidobacteriota and Chloroflexi continued to decline in storage. For genus annotation, none of genus obtained dominant population in storage. From Day 0 to Day 1, the genera of Streptomyces, Bradyrhizobium, and Mycobacterium significantly increased; meanwhile, 12 genera significantly decreased. Compared with samples at Day 0, a total of 15 genera significantly decreased with the reduced proportion ranging from 0.50 to 4.40% at Day 3. At the end of the storage, the genus Crossiella became the most redundant population. Both the richness and diversity decreased at the start of storage at Day 1, and then slightly increased at Day 3 was observed. Based on the result in this study, strategy targeting the increased bacteria could be tested to improve the consumption quality and safety of refrigerated clam.

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.

Evaluation of microbial contamination of different pork carcass areas through culture-dependent and independent methods in small-scale slaughterhouses

Routine evaluation of the slaughter process is performed by the enumeration of the aerobic colony count, Enterobacteriaceae and Salmonella spp. on the carcass through destructive or non-destructive methods. With non-destructive methods, bacteria are counted from a minimum area of 100 cm² in different sampling sites on the pork carcasses, and the results of these investigated areas are pooled to one value for the complete carcass evaluation (a total of 400 cm²). However, the composition of the bacterial community present on the different sampling areas remains unknown. The aim of the study was to characterize the microbial population present on four areas (ham, back, jowl and belly) of eight pork carcasses belonging to two different slaughterhouses through culture-dependent (Matrix-assisted laser desorption/ionization time-of-flight Mass Spectrometry MALDI-TOF MS, combined with 16S rRNA gene sequencing) and complementary culture-independent (16S rRNA amplicon sequencing) methods. The presence of Salmonella spp. and Y. enterocolitica was additionally assessed. Using MALDI-TOF MS, Staphylococcus, Pseudomonas, and Escherichia coli were found to dominate the bacterial cultures isolated from the 8 carcasses. Based on the 16S rRNA amplicon sequencing analyses however, no specific genus clearly dominated the bacterial community composition. By using this culture-independent method, the most abundant genera in microbial populations of the ham, back, jowl and belly were found to be similar, but important differences between the two slaughterhouses were observed. Thus, present data suggests that the indigenous bacterial population of individual animals is overruled by the microbial population of the slaughterhouse in which the carcass is handled. Also, our data suggests that sampling of only one carcass area by official authorities may be appropriate for the evaluation of the hygienic status of the carcasses and therefore of the slaughter process.

Characterization of the Volatiles and Quality of Hybrid Grouper and Their Relationship to Changes of Microbial Community During Storage at 4 °C

To investigate the effects of spoilage bacteria on aquatic product quality and volatile organic compounds (VOCs) in hybrid grouper (Epinephelus fuscoguttatus ♀×Epinephelus lanceolatus ♂), the physical conditions were evaluated, the chemical changes including color, total volatile base nitrogen (TVB-N), VOCs, and free amino acids (FFAs) were determined, and biological profiles were made through microbial community (total viable counts (TVC), 16S rRNA gene amplification sequencing, and next-generation sequencing (NGS) technology on hybrid grouper, which were stored at 4 °C for 10 days. The results showed that the whiteness and TVB-N of grouper increased throughout the storage period. The contents of glycine, alanine, and total free amino acid decreased with the microbial activity towards the end of the study period. At the end of storage, the TVC reached 9.0 log10 (CFU/g). Seventy eight strains of bacteria were isolated from the hybrid grouper, most of which were shown to be Pseudomonas spp., after 16S rRNA sequencing. The results of the NGS test showed that the diversity of dominant bacteria decreased with time; Pseudomonas azotoformans was the dominant spoilage bacteria at the end of storage. The VOCs of fish and bacteria in the grouper's spoilage process were presented in headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). Twenty eight compounds were identified in hybrid grouper, among which alcohol and aldehyde were used to characterize freshness, both of which were not only related to the overall flavor of the grouper, but were also affected by microbial activity. However, due to the complexity of microbial communities in aquatic products, the correlation between community changes and VOCs needs further research. This study provides insights into the correlation between VOCs and specific spoilage organisms (SSOs) through the analysis of the microbial community and VOCs.

Assessment of Spoilage Bacterial Communities in Food Wrap and Modified Atmospheres-Packed Minced Pork Meat Samples by 16S rDNA Metagenetic Analysis

Although several studies have focused on the dynamics of bacterial food community, little is known about the variability of batch production and microbial changes that occur during storage. The aim of the study was to characterize the microbial spoilage community of minced pork meat samples, among different food production and storage, using both 16S rRNA gene sequencing and classical microbiology. Three batches of samples were obtained from four local Belgian facilities (A–D) and stored until shelf life under food wrap (FW) and modified atmosphere packaging (MAP, CO₂ 30%/O₂ 70%), at constant and dynamic temperature. Analysis of 288 samples were performed by 16S rRNA gene sequencing in combination with counts of psychrotrophic and lactic acid bacteria at 22°C. At the first day of storage, different psychrotrophic counts were observed between the four food companies (Kruskal-Wallist test, p-value < 0.05). Results shown that lowest microbial counts were observed at the first day for industries D and A (4.2 ± 0.4 and 5.6 ± 0.1 log CFU/g, respectively), whereas industries B and C showed the highest results (7.5 ± 0.4 and 7.2 ± 0.4 log CFU/g). At the end of the shelf life, psychrotrophic counts for all food companies was over 7.0 log CFU/g. With metagenetics, 48 OTUs were assigned. At the first day, the genus Photobacterium (86.7 and 19.9% for food industries A and C, respectively) and Pseudomonas (38.7 and 25.7% for food companies B and D, respectively) were dominant. During the storage, a total of 12 dominant genera (>5% in relative abundance) were identified in MAP and 7 in FW. Pseudomonas was more present in FW and this genus was potentially replaced by Brochothrix in MAP (two-sided Welch’s t-test, p-value < 0.05). Also, a high Bray-Curtis dissimilarity in genus relative abundance was observed between food companies and batches. Although the bacteria consistently dominated the microbiota in our samples are known, results indicated that bacterial diversity needs to be addressed on the level of food companies, batches variation and food storage conditions. Present data illustrate that the combined approach provides complementary results on microbial dynamics in minced pork meat samples, considering batches and packaging variations.