Characterization and evaluation of the spoilage potential of Lactococcus piscium isolates from modified atmosphere packaged meat

Insights on the virulence and genomic features of Lactococcus garvieae isolated from giant freshwater prawn Macrobrachium rosenbergii (de Man 1879)

Giant freshwater prawn (Macrobrachium rosenbergii (MR)) is a significant aquafarm species commercially cultured in Taiwan. Intensive farming practices have led to the outbreak of Lactococcus garvieae (LG), which causes Lactococcosis in MR. Recently, LG has re-emerged and the number of mortalities in prawn farms has increased in Taiwan. However, there is no preventative strategy described and a lack of knowledge on virulence factors and pathogenesis from LG in MR. The most virulent strain of L. garvieae from M. rosenbergii was screened in vivo among seven isolates selected for infectivity testing injecting 0.1 mL of 108 CFU/mL bacterial concentration. Among the seven isolates screened, L. garvieae 109-6 resulted in 100% mortality within 3 days post-infection. Furthermore, 109-6 L. garvieae LD50 dosage from in MR was found to be 106 CFU/mL. Subsequently, the most virulent strain 109-6 was sequenced using MinIon Nanopore sequencing. Results indicated that the LG genome yielded a protein-coding of 3857 with 59 tRNA and 16 rRNA and no plasmid. Interestingly, the distribution of subsystems in the annotated genome revealed genes related to virulence, defence, and disease among LG 50 genes. Altogether, the virulent strain and its genome data revealed distinctive features of LG, which hinted toward its pathogenicity and could facilitate for better preventive strategies.

Characteristics of changes in volatile organic compounds and bacterial communities in physically preserved pigeon breast meat

To understand the relationship between changes in aroma and bacteria in pigeon breast meat (PBM) during preservation, bacterial communities and volatile compounds in PBM were analyzed using high-throughput sequencing and gas chromatography-ion mobility spectrometry. Analyses of total viable bacteria counts revealed that modified atmospheric packaging (MAP) and electron beam irradiation (EBI) could be used to extend the shelf-life of PBM to 10 d and 15 d, respectively. Furthermore, Lactococcus spp. and Psychrobacter spp. were the dominant bacterial genera of the MAP and EBI groups, respectively. The results of the study revealed 91 volatile organic compounds, one of which, butanal, was the most intense volatile organic compound while being an important source of aroma differences between the physical preservation techniques. Alpha-terpinolene, acetoin-M, gamma-butyrolactone, 1-hexanol-M, and 2,6-dimethyl-4-heptanone may be markers of PBM spoilage. During preservation, the MA group (treatment with 50 % CO2 + 50 % N2) demonstrated greater stabilization of PBM aroma. A Spearman correlation analysis showed that Lactococcus spp., Psychrobacter spp., and Pseudomonas spp. were the dominant bacterial genera of PBM during preservation and were closely related to an increase in the intensity of anisole, 2-methyl-3-furanthiol, and 5-methyl-2-furanmethanol, respectively. Lactococcus spp. and Psychrobacter spp. play crucial roles in the sensory degradation of PBM. In this study, we analyzed the changes in bacterial genera and volatile organic compounds of PBM under different physical preservation techniques to identify a suitable method for preserving PBM and evaluating its freshness.

Transcriptome responses of Lactococcus paracarnosus to different gas compositions and co-culture with Brochothrix thermosphacta

Lactococcus (Lc.) paracarnosus and the phylogenetically closely related Lc. carnosus species are common members of the microbiota in meat stored under modified atmosphere and at low temperature. The effect of these strains on meat spoilage is controversially discussed. While some strains are known to cause spoilage, others are being studied for their potential to suppress the growth of spoilage and pathogenic bacteria. In this study, Lc. paracarnosus DSM 111017T was selected based on a previous study for its ability to suppress the growth of meat spoilers, including Brochothrix thermosphacta. The mechanism by which this bioprotective strain inhibits competing bacteria and how it contributes to spoilage are not yet known. To answer these two questions, we investigated the effect of four different headspace gas mixtures (simulated air (21 % O2/79 % N2); HiOx-MAP (70 % O2/30 % CO2); nonOx-MAP (70 % N2/ 30 % CO2); simulated vacuum (100 % N2) and the presence of Brochothrix (B.) thermosphacta TMW 2.2101 on the growth and transcriptional response of Lc. paracarnosus DSM 111017T when cultured on a meat simulation agar surface at 4 °C. Analysis of genes specifically upregulated by the gas mixtures used revealed metabolic pathways that may lead to different levels of spoilage metabolites production. We propose that under elevated oxygen levels, Lc. paracarnosus preferentially converts pyruvate from glucose and glycerol to uncharged acetoin/diacetyl instead of lactate to counteract acid stress. Due to the potential production of a buttery off-flavour, the strain may not be suitable as a protective culture in meat packaged under high‑oxygen conditions. 70 % N2/ 30 % CO2, simulated vacuum- and the presence of Lc. paracarnosus inhibited the growth of B. thermosphacta TMW 2.2101. However, B. thermosphacta did not affect gene regulation of metabolic pathways in Lc. paracarnosus, and genes previously predicted to be involved in B. thermosphacta growth suppression were not regulated at the transcriptional level. In conclusion, the study indicates that the gas mixture used in packaging significantly affects the metabolism and spoilage potential of Lc. paracarnosus and its ability to inhibit B. thermosphacta growth.

Changes in the Microbiome in Yak Mastitis: Insights Based on Full-Length 16S rRNA Sequencing

Mastitis is an inflammation of the mammary gland that can be caused by various factors, including biological, chemical, mechanical, or physical. Microbiological culture, DNA techniques, and high-throughput next-generation sequencing have been used to identify mastitis-causing pathogens in various animal species. However, little is known about microbiota and microbiome changes linked to yak milk mastitis. This study aimed to characterize the milk microbiota of healthy and mastitis-infected yaks using full-length 16S rRNA sequencing. The results showed that the bacterial microbiota comprises 7 phyla, 9 classes, 20 orders, 39 families, 59 genera, and 72 species. Proteobacteria and Firmicutes were the predominant microbial communities, with lower abundances of Bacteroidota, Actinobacteriota, Acidobacteriota, and other minor groupings also observed. Proteobacteria dominated the clinical and subclinical mastitis groups (95.36% and 89.32%, respectively), in contrast to the healthy group (60.17%). Conversely, Firmicutes were more common in the healthy group (39.7%) than in the subclinical and clinical mastitis groups (10.49% and 2.92%, respectively). The predominant organisms found in the healthy group were Leuconostoc mesenteroides, Lactococcus piscium, Carnobacterium maltaromaticum, and Lactococcus raffinolactis. Low abundances of Staphylococcus aureus species were found in both subclinical and clinical mastitis groups, with Moraxella osloensis and Psychrobacter cibarius dominating the subclinical mastitis group and Pseudomonas fluorescens dominating the clinical mastitis group. An alpha diversity study revealed that the healthy group had a higher microbial diversity than the clinical and subclinical mastitis groups. According to beta-diversity analysis, the principal coordinate analysis identified that mastitis-infected samples significantly differed from healthy ones. The milk microbiota of healthy yaks is more varied, and specific prominent taxa within various groups can act as marker microorganisms for mastitis risk. The genera Leuconostoc and Lactococcus are promising candidates for creating probiotics.

Effects of Modified Atmosphere Packaging with Various CO2 Concentrations on the Bacterial Community and Shelf-Life of Smoked Chicken Legs

The effects of modified atmosphere packaging (MAP) with various CO₂ concentrations on the bacterial community and shelf-life of smoked chicken legs during 25 d of storage at 4 °C were evaluated herein. Four treatments were stored in pallets (PAL) and MAP under 20% (M20), 60% (M60), and 100% (M100) CO₂, respectively. The results indicated that the MAP treatments provided the legs with higher redness and hardness and lower yellowness, luminance, and lipid oxidation, compared with the PAL treatment. In addition, the MAP treatments effectively inhibited the growth of viable bacteria, delayed bacterial spoilage, and extended the shelf-life of the samples. The M60 and M100 treatments had a better inhibition effect on bacteria. In terms of bacterial community, Carnobacterium, Pseudomonas, Brochothrix, and Lactococcus were the most predominant genera in the 25 d-stored MAP samples, with Carnobacterium maltaromaticum, Pseudomonas fragi, Shewanella baltica, and Lactococcus piscium being the dominant species. However, while the inhibition effects of the M60 and M100 treatments on the bacterial community at Day 25 were similar, the outer package of the M100 treatment collapsed. Overall, the M60 treatment may be a promising approach to improving the quality and extending the shelf-life of smoked chicken legs.

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.

Analysis of Microbial Diversity and Dynamics During Bacon Storage Inoculated With Potential Spoilage Bacteria by High-Throughput Sequencing

Staphylococcus xylosus, Leuconostoc mesenteroides, Carnobacterium maltaromaticum, Leuconostoc gelidum, and Serratia liquefaciens were investigated for their roles in in the spoilage of sterilized smoked bacon. These five strains, individually and in combination, were applied as starters on sliced bacon at 4–5 log₁₀ CFU/g using a hand-operated spraying bottle and stored for 45 days at 0–4°C. Dynamics, diversity, and succession of microbial community during storage of samples were studied by high-throughput sequencing (HTS) of the V3–V4 region of the 16S rRNA gene. A total of 367 bacterial genera belonging to 21 phyla were identified. Bacterial counts in all the inoculated specimens increased significantly within the first 15 days while the microbiota developed into more similar communities with increasing storage time. At the end of the storage time, the highest abundance of Serratia (96.46%) was found in samples inoculated with S. liquefaciens. Similarly, for samples inoculated with C. maltaromaticum and L. mesenteroides, a sharp increase in Carnobacterium and Leuconostoc abundance was observed as they reached a maximum relative abundance of 97.95 and 81.6%, respectively. Hence, these species were not only the predominant ones but could also have been the more competitive ones, potentially inhibiting the growth of other microorganisms. By analyzing the bacterial load of meat products using the SSO model, the relationships between the microbial communities involved in spoilage can be understood to assist further research.

Lactococcosis a Re-Emerging Disease in Aquaculture: Disease Significant and Phytotherapy

Lactococcosis, particularly that caused by Lactococcus garvieae, is a major re-emerging bacterial disease seriously affecting the sustainability of aquaculture industry. Medicinal herbs and plants do not have very much in vitro antagonism and in vivo disease resistance towards lactococcosis agents in aquaculture. Most in vitro studies with herbal extractives were performed against L. garvieae with no strong antibacterial activity, but essential oils, especially those that contain thymol or carvacrol, are more effective. The differences exhibited by the bacteriostatic and bactericidal functions for a specific extractive in different studies could be due to different bacterial strains or parts of chemotypes of the same plant. Despite essential oils being shown to have the best anti-L. garvieae activity in in vitro assays, the in vivo bioassays required further study. The extracts tested under in vivo conditions presented moderate efficacy, causing a decrease in mortality in infected animals, probably because they improved immune parameters before challenging tests. This review addressed the efficacy of medicinal herbs to lactococcosis and discussed the presented gaps.

The pathogenic and spoilage bacteria associated with red meat and application of different approaches of high CO2 packaging to extend product shelf-life

With the fast-global development of packaging techniques, the potential antimicrobial effect of CO₂, as a safe, cheap and readily available gas, makes it the integral component for packaging of meat products. The associated spoilage and/or pathogenic bacteria on raw meat may respond in different ways to elevated CO₂ concentrations. The growth of some aerobic Gram-negative bacteria such as Pseudomonas spp. is significantly inhibited but some LAB bacteria may be allowed to grow faster and dominate the product. The antimicrobial efficacy of enriched CO₂ packaging is attributed to the rate of CO₂ solubility in the product which is itself affected by the level of headspace CO₂, product pH, temperature and the ratio of headspace gas to product (G:P). This review, first, explores the varied range of beef and sheep meat spoilage and pathogenic bacteria and the intrinsic and extrinsic parameters that may influence the pattern of microbial growth and meat spoilage rate during storage. Then, the antimicrobial mechanism of elevated CO₂ packaging will be discussed and the different approaches of achieving enriched CO₂ packaging i.e. the traditional technique of flushing a desired gas mixture and/or using the new commercially developed CO₂ emitters will then be compared in terms of their strengths, limitations and technical mode of action.

Application of a path-modelling approach for deciphering causality relationships between microbiota, volatile organic compounds and off-odour profiles during meat spoilage

Microbiological spoilage of meat is considered as a process which involves mainly bacterial metabolism leading to degradation of meat sensory qualities. Studying spoilage requires the collection of different types of experimental data encompassing microbiological, physicochemical and sensorial measurements. Within this framework, the objective herein was to carry out a multiblock path modelling workflow to decipher causality relationships between different types of spoilage-related responses: composition of microbiota, volatilome and off-odour profiles. Analyses were performed with the Path-ComDim approach on a large-scale dataset collected on fresh turkey sausages. This approach enabled to quantify the importance of causality relationships determined a priori between each type of responses as well as to identify important responses involved in spoilage, then to validate causality assumptions. Results were very promising: the data integration confirmed and quantified the causality between data blocks, exhibiting the dynamical nature of spoilage, mainly characterized by the evolution of off-odour profiles caused by the production of volatile organic compounds such as ethanol or ethyl acetate. This production was possibly associated with several bacterial species like Lactococcus piscium, Leuconostoc gelidum, Psychrobacter sp. or Latilactobacillus fuchuensis. Likewise, the production of acetoin and diacetyl in meat spoilage was highlighted. The Path-ComDim approach illustrated here with meat spoilage can be applied to other large-scale and heterogeneous datasets associated with pathway scenarios and represents a promising key tool for deciphering causality in complex biological phenomena.

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

BACKGROUND

Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C.

RESULTS

We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures.

CONCLUSIONS

The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.

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

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

Microbiomes in the Context of Refrigerated Raw Meat Spoilage

Meat spoilage is a complicated biological phenomenon taking place over the course of time. Several factors influence it, mainly external factors related to packaging and storage temperature but also internal ones related to contamination diversity and product ingredients. We conducted genomic studies of specific spoilage organisms (SSO) and investigated the spoilage microbiomes providing information about the factors that make a specific organism a competitive SSO, as well as the interactions between certain SSO and the most active species and pathways in packaged raw meat. Our studies showed that spoilage microbiomes are diverse, but certain aspects, such as oxygen content or added marinades, shape this diversity strongly. We have also characterized a new spoilage-associated pathway, i.e., heme-dependent respiration capability, in Leuconostoc gelidum subsp. gasicomitatum. The microbiome studies we conducted explain why this species has become a competitive SSO. It is a fast grower and gains advantage for its growth if oxygen is present in the packages. Since the contamination of psychrotrophic lactic acid bacteria is difficult to avoid in meat manufacture, leuconostocs cause spoilage problems from time to time especially in marinated products or those packaged under high-oxygen–containing atmospheres.

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.

Microbiota encompassing putative spoilage bacteria in retail packaged broiler meat and commercial broiler abattoir

It is well established, that certain bacteria within the Brochothrix, Carnobacterium, Lactobacillus, Lactococcus, and Leuconostoc genera have an important role in the spoilage of chill stored poultry meat packaged in modified atmosphere. However, little is known about the role of microorganisms that are difficult to culture and the microbiota during poultry spoilage. We combined traditional cultivation and culture-independent 16S rRNA amplicon sequencing to investigate the microbiota encompassing putative bacteria of whole broiler meat, packaged in modified atmosphere, during and exceeding shelf-life. Samples were taken from 6 flocks during independent slaughter days. Additional samples were analysed from the production line. There was a significant difference in the microbial community structure of 80%O₂/20%CO₂ retail packaged broiler meat during different times of shelf-life, mainly due to an increase of species within the Brochothrix, Carnobacterium, Vagococcus, and Janthinobacterium genera. These genera were already detected four to eight days after slaughter. However, no significant difference between flocks with respect to the microbiota encompassing putative spoilage bacteria was observed when examined in retail packaged broilers, slaughtered at the same abattoir on different days. Our study also showed that lactic acid bacteria within the Vagococcus genus can constitute a dominating part of the later shelf-life microbiota in fresh whole broiler meat packaged in 80%O₂/20%CO₂ modified atmosphere. A single operational taxonomic unit (OTU) assigned as Janthinobacterium lividum, an occasional spoiler of meat products, was identified as a major part of the microbiota in late shelf life broiler meat and swab samples in the cooling facility at the slaughter house production line. The combination of traditional cultivation and culture-independent methods provided a great insight into the microbiota of broiler meat during shelf-life and identified a potential point of contamination in the production line for cold tolerant Janthinobacterium.

Microbiomes Associated With Foods From Plant and Animal Sources

Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.

Mapping the dominant microbial species diversity at expiration date of raw meat and processed meats from equine origin, an underexplored meat ecosystem, in the Belgian retail

Although equine meats and their derived smoked or fermented products are popular in some regions of the world, they only form a minor fraction of the global meat consumption. The latter may explain why their associated bacterial communities have not received much attention. In the present study, 69 different samples of equine meats and meat products were investigated. The samples consisted of raw meat from horses (17 samples) and zebra (7), as well as non-fermented but smoked (24) and fermented (21) horse meat products. After purchase, all samples were stored at 4 °C and analysed at expiration date. Besides an estimation of the total microbial counts, specific attention was paid to the identification of lactic acid bacteria (LAB) and catalase-positive cocci, in particular the group of coagulase-negative staphylococci (CNS), involved, due to their technological relevance in view of the elaboration of meat products. Samples that were loosely wrapped in butcher paper instead of vacuum- or modified-atmosphere packages were also screened for pseudomonads and enterobacterial species. In total, 1567 bacterial isolates were collected, subjected to (GTG)₅-PCR fingerprinting of genomic DNA, and identified by multiple gene sequencing (based on the 16S rRNA, pheS, rpoA, rpoB, and/or tuf genes). Overall, the bacterial species diversity consisted mostly of LAB but was contingent on the type of product. Raw meat was dominated by Carnobacterium divergens, Lactobacillus sakei, Lactococcus piscium, and Leuconostoc gelidum, with zebra meat being particularly rich in lactococci. Smoked and fermented horse meat products contained mostly Lb. sakei and, to a lesser degree, Lactobacillus curvatus. In addition, several catalase-positive cocci (mostly Staphylococcus equorum), Anoxybacillus sp., Brevibacterium sp., Brochothrix thermosphacta, and the enterobacterial species Hafnia alvei were found.

Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition

Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities.IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.

The Evolution of gene regulation research in Lactococcus lactis

Lactococcus lactis is a major microbe. This lactic acid bacterium (LAB) is used worldwide in the production of safe, healthy, tasteful and nutritious milk fermentation products. Its huge industrial importance has led to an explosion of research on the organism, particularly since the early 1970s. The upsurge in the research on L. lactis coincided not accidentally with the advent of recombinant DNA technology in these years. The development of methods to take out and re-introduce DNA in L. lactis, to clone genes and to mutate the chromosome in a targeted way, to control (over)expression of proteins and, ultimately, the availability of the nucleotide sequence of its genome and the use of that information in transcriptomics and proteomics research have enabled to peek deep into the functioning of the organism. Among many other things, this has provided an unprecedented view of the major gene regulatory pathways involved in nitrogen and carbon metabolism and their overlap, and has led to the blossoming of the field of L. lactis systems biology. All of these advances have made L. lactis the paradigm of the LAB. This review will deal with the exciting path along which the research on the genetics of and gene regulation in L. lactis has trodden.

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail

Sliced cooked poultry products are susceptible to bacterial spoilage, notwithstanding their storage under modified-atmosphere packaging (MAP) in the cold chain. Although the prevailing bacterial communities are known to be mostly consisting of lactic acid bacteria (LAB), more information is needed about the potential variation in species diversity within national markets. In the present study, a total of 42 different samples of sliced cooked poultry products were collected in the Belgian retail and their bacterial communities were analysed at expiration date. A total of 629 isolates from four different culture media, including plate count agar for the total microbiota and de Man-Rogosa-Sharpe (MRS), modified MRS, and M17 agar as three selective agar media for LAB, were subjected to (GTG)₅-PCR fingerprinting and identification by gene sequencing. Overall, Carnobacterium, Lactobacillus, and Leuconostoc were the dominant genera. Within each genus, the most encountered isolates were Carnobacterium divergens, Lactobacillus sakei, and Leuconostoc carnosum. When comparing samples from chicken origin with samples from turkey-derived products, a higher dominance of Carnobacteria spp. was found in the latter group. Also, an association between the dominance of lactobacilli and the presence of added plant material and lactate salts was found.

Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia

The consumption of yellow-feathered broiler has been advocated for purchasing with chilled meat rather than live broilers in Asia due to the outbreaks of animal influenza. Here, the microbial community of chilled yellow-feathered broiler response to modified-air packaging (MAP, 80% CO2/20% N2) and penetrated-air packaging (PAP, air-filling) during storage was revealed by a combination of whole-metagenome shotgun sequencing and traditional isolation methods, and the volatile organic compounds and proteolytic activity of representative dominant isolates were also accessed. The results revealed that MAP prolonged shelf life from 4 to 8 days compared to PAP, when the numbers of total viable counts and lactic acid bacteria reached more than 7 log CFU/g. Aeromonas, Acinetobacter, Escherichia, and Streptococcus occupied the bacteria communities in initial broiler carcasses. MAP dramatically increased the bacteria diversity during storage compared to PAP. Clear shifts of the dominant bacteria species were obviously observed, with the top genera of Aeromonas, Lactococcus, Serratia, and Shewanella in MAP, whereas the microbial communities in PAP were largely dominated by Pseudomonas. The isolates of Pseudomonas from PAP carcasses and Aeromonas from MAP carcasses displayed strong proteolytic activities. Meanwhile, the principal component analysis based on the volatile organic compounds indicated that the metabolic profiles greatly varied between each treatment, and no link between the natural odor of spoilage meat in situ and the volatile odor of the dominant isolates incubated in standard culture was found. These data could lead to new insights into the bacteria communities of yellow-feathered broiler meat during storage and would benefit the development of novel preservative approaches.

The Microbial Community Dynamics during the Vitex Honey Ripening Process in the Honeycomb

The bacterial and fungal communities of vitex honey were surveyed by sequencing the 16S rRNA gene and the internal transcribed spacer region of ribosomal DNA. Vitex honey samples were analyzed at different stage of ripening; the vitex flower was also analyzed, and the effect of the chemical composition in the experimental setup was assessed. The results confirmed the presence of dominant Bacillus spp. as the dominant bacterial in honey, and yeast related genera was the main fungal in the honey, respectively. Lactococcus and Enterococcus were detected for the first time in honey. The proportion of most of the fungal community decreased during the honey ripening process. Multivariate analyses also showed that the fungal community of 5, 10, and 15 days honey samples tended to cluster together and were completely separated from the 1 day honey sample. The change in the fungal community showed a correlation with the variation in the chemical components, such as moisture and phenolic compounds. Together, these results suggest that ripening of honey could change its microbial composition, and decrease the potential risk of microbiology.

Lactococcus piscium: a psychrotrophic lactic acid bacterium with bioprotective or spoilage activity in food-a review

The genus Lactococcus comprises 12 species, some known for decades and others more recently described. Lactococcus piscium, isolated in 1990 from rainbow trout, is a psychrotrophic lactic acid bacterium, probably disregarded because most of the strains are unable to grow at 30°C. During the last 10 years, this species has been isolated from a large variety of food: meat, seafood and vegetables, mostly packed under vacuum (VP) or modified atmosphere (MAP) and stored at chilled temperature. Recently, culture-independent techniques used for characterization of microbial ecosystems have highlighted the importance of Lc. piscium in food. Its role in food spoilage varies according to the strain and the food matrix. However, most studies have indicated that Lc. piscium spoils meat, whereas it does not degrade the sensory properties of seafood. Lactococcus piscium strains have a large antimicrobial spectrum, including Gram-positive and negative bacteria. In various seafoods, some strains have a protective effect against spoilage and can extend the sensory shelf-life of the products. They can also inhibit the growth of Listeria monocytogenes, by a cell-to-cell contact-dependent. This article reviews the physiological and genomic characteristics of Lc. piscium and discusses its spoilage or protective activities in food.

Exploring the Bacterial Diversity of Belgian Steak Tartare Using Metagenetics and Quantitative Real-Time PCR Analysis

Steak tartare is a popular meat dish in Belgium. It is prepared with raw minced beef and is eaten with sauce, vegetables, and spices. Because it contains raw meat, steak tartare is highly prone to bacterial spoilage. The objective of this study was to explore the diversity of bacterial flora in steak tartare in Belgium according to the source and to determine which bacteria are able to grow during shelf life. A total of 58 samples from butchers' shops, restaurants, sandwich shops, and supermarkets were collected. These samples were analyzed using 16S rDNA metagenetics, a classical microbiological technique, and quantitative real-time PCR (qPCR) targeting the Lactobacillus genus. Samples were analyzed at the beginning and at the end of their shelf life, except for those from restaurants and sandwich shops, which were analyzed only on the purchase date. Metagenetic analysis identified up to 180 bacterial species and 90 genera in some samples. But only seven bacterial species were predominant in the samples, depending on the source: Brochothrix thermosphacta, Lactobacillus algidus, Lactococcus piscium, Leuconostoc gelidum, Photobacterium kishitani, Pseudomonas spp., and Xanthomonas oryzae. With this work, an alternative method is proposed to evaluate the total flora in food samples based on the number of reads from metagenetic analysis and the results of qPCR. The degree of underestimation of aerobic plate counts at 30°C estimated with the classical microbiology method was demonstrated in comparison with the proposed culture-independent method. Compared with culture-based methods, metagenetic analysis combined with qPCR targeting Lactobacillus provides valuable information for characterizing the bacterial flora of raw meat.

Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage

Beef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, and Leuconostoc carnosum were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as Kocuria rhizophila, Staphylococcus xylosus, Leuconostoc carnosum, and Carnobacterium divergens, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisin-based antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life.

Packaging gas selects lactic acid bacterial communities on raw pork

AIMS

To study the effect of different CO2-rich packaging atmospheres on the composition of lactic acid bacterial communities proliferating on raw pork.

METHODS AND RESULTS

Raw pork loin was inoculated with a mixture of 14 lactic acid bacteria (LAB) strains previously associated with meat and packaged with four gas atmospheres: (i) 100% CO2 (ii) 80% N2 20% CO2 (iii) 80% N2, 20% CO2, 0·4% CO and (iv) 80% O2, 20% CO2. The colony counts of LAB, pH and composition of packaging gas were monitored every other day during the storage of 14 days at +6°C. The compositions of lactic acid bacterial communities on pork were evaluated after 7 days of storage with culture-independent, terminal restriction fragment length polymorphism analysis of 16S rRNA gene fragments. After 14 days of storage, the compositions of lactic acid bacterial communities were evaluated using identification of plate-grown LAB isolates by numerical ribopattern analysis. The results showed that (i) high concentration of CO2 in packaging atmosphere favoured Lactobacillus sp. (ii) high concentration of O2 favoured Leuconostoc spp. (iii) atmosphere with 80% N2, 20% CO2 favoured Lactococcus sp.

CONCLUSIONS

The composition of modified packaging atmosphere is a major factor selecting lactic acid bacterial communities proliferating on raw meat.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides an explanation for the compositions of lactic bacterial communities on modified atmosphere packaged raw meat observed in other studies. The results should be considered when attempting to manipulate LAB communities in raw meat, e.g. by protective cultures.

Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals

Mesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB. Pseudomonas spp., Enterobacteriaceae, Streptococcaceae, and Lactobacillus spp. constituted the most widespread operational taxonomic units (OTUs), whereas Leuconostoc gelidum was detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However, L. gelidum became the most predominant microbe at the end of the shelf life. The ability of L. gelidum to outgrow notorious, spoilage-related taxa like Pseudomonas, Brochothrix, and Lactobacillus underpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment.

Selection of bioprotective cultures for preventing cold-smoked salmon spoilage

Biopreservation is a natural technology of food preservation, which consists of inoculating food with microorganisms selected for their antibacterial properties. The objective of this study was to select lactic acid bacteria (LAB) to improve the quality of cold-smoked salmon (CSS). In this work, different strains representative of the 4 dominant species, identified in a previous study by pyrosequencing the 16S rRNA gene, were isolated and their spoiling potential in CSS blocks, sterilized by ionization, was assessed by twelve trained panelists along the vacuum storage at 8°C. Photobacterium phosphoreum, Brochothrix thermosphacta and Serratia proteamaculans released strong off-odors whereas the spoiling potential of Carnobacterium divergens was weaker. The spoiling capacity of Lactococcus piscium EU2241, Leuconostoc gelidum EU2247, Lactobacillus sakei EU2885, Staphylococcus equorum S030674 and 4 commercial starters was tested by the same method and 2 strains were eliminated due to off-odor production. The effect of the 6 selected LAB against the 4 specific spoiling organisms (SSOs) selected was tested by challenge tests in sterile CSS blocks. The protective effect of the LAB differed from one SSO to another and no correlation could be established between the sensory improvement, SSO inhibition, and the implantation or acidification of protective cultures (PCs). All the PCs except L. piscium reduced the off-odors released by P. phosphoreum although some of them had no effect on its growth. S. equorum, which did not grow in CSS, favored the implantation of P. phosphoreum but prevented its off-odor formation. L. piscium was the only strain that prevented the spoilage of B. thermosphacta and S. proteamaculans although it did not grow very well and did not acidify the product. L. gelidum EU2247 inhibited the growth of these 2 SSOs and lowered the pH but had no effect on the sensory quality. Finally, L. piscium was tested in 2 naturally contaminated products, with a positive effect on 1 batch. This effect was not correlated with the microbial ecosystem as determined by acultural and cultural techniques. Based on these results, the selection strategy is discussed.

Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47

Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered.

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.

Prolonged shelf life and reduced drip loss of chicken filets by the use of carbon dioxide emitters and modified atmosphere packaging

Modified atmosphere packaging containing CO2 is widely used for extending the shelf life of chicken meat. Active packaging by adding CO2 emitter sachets to packages of meat is an alternative to traditional modified atmosphere packaging. The purpose of the study was to investigate the shelf life of chicken filets under different CO2 concentrations at 4°C storage. The inhibition of microbial growth was proportional to the CO2 concentration. Storage in 100% CO2 both with and without a CO2 emitter sachet gave a microbiological shelf-life extension of 7 days compared with 60% CO2. Carnobacterium divergens, Carnobacterium sp., and Lactococcus sp. were the dominating species at the end of the storage period. During storage in pure CO2, the carbon dioxide dissolved in the meat and caused the collapse of the packages. The resulting squeeze of the meat lead to a severe increase in drip loss. The drip loss was reduced profoundly by using the CO2 emitting sachet in the packages. The addition of CO2 emitters can easily be implemented at industrial packaging lines without reduction in production efficiency.

Lactococcus formosensis sp. nov., a lactic acid bacterium isolated from yan-tsai-shin (fermented broccoli stems)

A coccal-shaped organism, designated 516T, was isolated from yan-tsai-shin (fermented broccoli stems), a traditional fermented food in Taiwan. 16S rRNA gene sequencing results showed that strain 516T had 98.9 % sequence similarity to that of the type strain Lactococcus garvieae NBRC 100934T. Comparison of three housekeeping genes, rpoA, rpoB and pheS, revealed that strain 516T was well separated from Lactococcus garvieae NBRC 100934T. DNA–DNA hybridization studies indicated that strain 516T had low DNA relatedness with Lactococcus garvieae NBRC 100934T (46.1 %). The DNA G+C content of strain 516T was 38.1 mol% and the major fatty acids were C16 : 0 (22.7 %), C19 : 0 cyclo ω8c (17.9 %) and summed feature 7 (29.0 %). Based on the evidence, strain 516T represents a novel species of the genus Lactococcus , for which the name Lactococcus formosensis sp. nov. is proposed. The type strain is 516T ( = NBRC 109475T = BCRC 80576T).

The effect of marination on lactic acid bacteria communities in raw broiler fillet strips

Marination with marinade containing salt, sugar, and acetic acid is commonly used in Finland to enhance the value of raw broiler meat. In this study, we investigated the effect of marination, marinade components and storage time on composition of bacterial communities in modified atmosphere-packaged (MAP) broiler fillet strips. The communities were characterized using two culture-independent methods: 16S rRNA gene fragment sequencing and terminal restriction fragment length polymorphism. In unmarinated broiler fillet strips, Lactococcus spp. and Carnobacterium spp. predominated at the early storage phase but were partially replaced by Lactobacillus spp. and Leuconostoc spp. when the chilled storage time was extended. In the marinated fillet strips, Lactobacillus spp. and Leuconostoc spp. predominated independent from the storage time. By mixing the different marinade components with broiler meat, we showed that marination changed the community composition and favored Leuconostoc spp. and Lactobacillus spp. by the combined effect of carbohydrates and acetic acid in marinade. Marination increased the maximum level of lactic acid bacteria in broiler meat and enhanced CO₂ production and acidification of meat during the chilled storage. Accumulation of CO₂ in package head-space due to the enhanced growth of Leuconostoc spp. in marinated meat may lead to bulging of packages, which is a spoilage defect frequently associated with marinated and MAP raw broiler preparations in Finland.