Most food products are highly perishable as they constitute a rich nutrient source for microbial development. Among the microorganisms contaminating food, some present metabolic activities leading to ...spoilage. In addition to hygienic rules to reduce contamination, various treatments are applied during production and storage to avoid the growth of unwanted microbes. The nature and appearance of spoilage therefore depend on the physiological state of spoilers and on their ability to resist the processing/storage conditions and flourish on the food matrix. Spoilage also relies on the interactions between the microorganisms composing the ecosystems encountered in food. The recent rapid increase in publicly available bacterial genome sequences, as well as the access to high-throughput methods, should lead to a better understanding of spoiler behavior and to the possibility of decreasing food spoilage. This review lists the main bacterial species identified as food spoilers, their ability to develop during storage and/or processing, and the functions potentially involved in spoilage. We have also compiled an inventory of the available genome sequences of species encompassing spoilage strains. Combining in silico analysis of genome sequences with experimental data is proposed in order to understand and thus control the bacterial spoilage of food better.
•The main food bacterial spoilers associated to the type of spoilage was reviewed.•Some metabolic activities of spoilers regarding the type of spoilage were addressed.•Available genomes of bacterial species encompassing spoiler strains were listed.
The spoilage potential of eight bacterial groups/species (Serratia spp., Hafnia alvei, Brochothrix thermosphacta, Carnobacterium maltaromaticum, Shewanella baltica, Lactococcus piscium, ...Photobacterium phosphoreum, “other Enterobacteriaceae” containing one strain of Moellerella sp., Morganella sp. and Pectobacterium sp.) isolated from spoiled raw salmon fillets stored under modified atmosphere packaging (MAP) was evaluated by inoculation into sterile raw salmon cubes followed by storage for 12days at 8°C. Microbial growth and sensory changes were monitored during the storage period. The dominant spoilage bacteria were C. maltaromaticum, H. alvei and P. phosphoreum. In order to further characterize their spoilage potential and to study the effect of their interactions, each of these 3 specific spoilage organisms (SSO) and two mixed-cultures, C. maltaromaticum/H. alvei and C. maltaromaticum/P. phosphoreum were tested in the sterile salmon model system using a combination of complementary methods: molecular (PCR-TTGE), sensory, chemical and conventional microbiological analyses. It was concluded that, in the mixed-culture inoculated samples, the dominant species determined the spoilage characteristics. The volatile fraction of P. phosphoreum inoculated samples was analyzed by solid-phase microextraction (SPME) followed by gas chromatography coupled to mass spectrometry (GC–MS). Among the specific volatile compounds present on P. phosphoreum spoiled inoculated samples, acetic acid was correlated with sensory analysis and can be proposed as a raw salmon spoilage marker.
► Spoilage potential of 8 bacterial groups isolated from spoiled salmon was evaluated. ► Specific spoilage organisms were identified among these bacterial groups. ► Spoilage abilities and bacterial interactions of 3 dominant spoilers were further characterized. ► On mixed-culture inoculated samples, spoilage characteristics are imposed by the dominant species.
The development of a multi-omics approach has provided a new approach to the investigation of microbial communities allowing an integration of data, which can be used to better understand the ...behaviour of and interactions between community members. Metagenomics, metatranscriptomics, metaproteomics and metabolomics have the potential of producing a large amount of data in a very short time, however an important challenge is how to exploit and interpret these data to assist risk managers in food safety and quality decisions. This can be achieved by integrating multi-omics data in microbiological risk assessment.
In this paper we identify limitations and challenges of the multi-omics approach, underlining promising potentials, but also identifying gaps, which should be addressed for its full exploitation. A view on how this new way of investigation will impact the traditional microbiology schemes in the food industry is also presented.
•Omics represent valuable tools to produce behavioural and interactions data in microbial communities.•NGS produces data about ecology (metataxonomics), gene presence (metagenomics) and its transcription (metatranscriptomics).•Metagenomic libraries can allow the reconstruction of pathogens genome then used for Genome Scale Metabolic Models (GSMM).•Integrating omics data into MRA will have an impact in food safety, but also to better control spoilage processes.
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.
Strain SMXD51, isolated from chicken ceca and identified as Lactobacillus salivarius, produced a component that inhibits the growth of Gram-positive and Gram-negative bacteria and especially ...Campylobacter jejuni. The active peptide from the cell-free supernatant of Lb. salivarius SMXD51 was purified in three steps: (i) precipitation with 80% saturated ammonium sulfate, (ii) elution on a reversed phase SPE UPTI-CLEAN cartridge using different concentrations of acetonitrile, (iii) final purification by reversed phase HPLC on a C18 column. The mode of action of this peptide of 5383.2 Da was identified as bactericidal, and its amino acid composition was established. This new bacteriocin SMXD51 appears potentially very useful to reduce Campylobacter in poultry prior to processing.
► Lactobacillus salivarius SMXD51 produces a bacteriocin active against Campylobacter jejuni. ► This bacteriocin was purified to homogeneity. ► Its amino acid composition and molecular mass suggest that it is a new bacteriocin. ► Salivaricin SMXD51 inhibits food-borne pathogens (Listeria monocytogenes, Campylobacter…). ► Salivaricin SMXD51 exhibited a bactericidal and non bacteriolytic mode of action.
In order to characterise the spoilage related to microbiota of raw salmon, a combination of culture-dependent and -independent methods, including PCR–TTGE, was used to analyse 3 raw salmon batches ...stored for 3 days at chilled temperature in modified atmosphere packaging (MAP) (50% CO2/50% N2) or under vacuum. Sensory evaluation, microbiological enumeration and chemical analysis were performed after 3, 7 and 10 days of storage. At the onset of spoilage, 65 bacterial isolates were picked from the plates. Thus, 13 different genera or species were identified by phenotypic and molecular tests: Serratia spp., Photobacterium phosphoreum, Yersinia intermedia, Hafnia alvei, Buttiauxella gaviniae, Pseudomonas sp., Carnobacterium maltaromaticum, Carnobacterium divergens, Lactococcus piscium, Lactobacillus fuchuensis, Vagococcus carniphilus, Leuconostoc gasicomitatum and Brochothrix thermosphacta. The PCR–TTGE profiles and band identification enabled a shift of the dominant populations during the storage to be visualised for all the batches, probably due to the temperature change and the packaging. At the beginning of storage, Pseudomonas sp. dominated the raw salmon microbiota while in the following days (7 and 10), P. phosphoreum and L. piscium were identified as the main bacterial groups. This study enhances the knowledge of MAP and vacuum-packed raw salmon spoilage microbiota.
► 13 different bacterial taxa were identified by phenotypic and molecular tests. ► A shift of the dominant microflora during storage was brought to light. ► The dominant bacterial populations displayed by PCR–TTGE were identified.
Microbial food spoilage is responsible for significant economic losses. Brochothrix thermosphacta is one of the major bacteria involved in the spoilage of meat and seafood. Its growth and metabolic ...activities during food storage result in the production of metabolites associated with off-odors. In this study, we evaluated the genotypic and phenotypic diversity of this species. A collection of 161 B. thermosphacta strains isolated from different foods, spoiled or not, and from a slaughterhouse environment was constituted from various laboratory collections and completed with new isolates. A PCR test based on the rpoB gene was developed for a fast screening of B. thermosphacta isolates. Strains were typed by MALDI-TOF MS, rep-PCR, and PFGE. Each typing method separated strains into distinct groups, revealing significant intra-species diversity. These classifications did not correlate with the ecological origin of strains. The ability to produce acetoin and diacetyl, two molecules associated with B. thermosphacta spoilage, was evaluated in meat and shrimp juices. The production level was variable between strains and the spoilage ability on meat or shrimp juice did not correlate with the substrate origin of strains. Although the B. thermosphacta species encompasses ubiquitous strains, spoiling ability is both strain- and environment-dependent.
•There is significant diversity between B. thermosphacta strains.•Diversity is not related to the ecological origin of the isolates.•The ability to produce acetoin and diacetyl depends on strains and food matrices.
Seafood and fishery products are very perishable commodities with short shelf-lives owing to rapid deterioration of their organoleptic and microbiological quality. Microbial growth and activity are ...responsible for up to 25% of food losses in the fishery industry. In this context and to meet consumer demand for minimally processed food, developing mild preservation technologies such as biopreservation represents a major challenge. In this work, we studied the use of six lactic acid bacteria (LAB), previously selected for their properties as bioprotective agents, for salmon dill gravlax biopreservation. Naturally contaminated salmon dill gravlax slices, with a commercial shelf-life of 21 days, were purchased from a French industrial company and inoculated by spraying with the protective cultures (PCs) to reach an initial concentration of 10
log CFU/g. PC impact on gravlax microbial ecosystem (cultural and acultural methods), sensory properties (sensory profiling test), biochemical parameters (pH, TMA, TVBN, biogenic amines) and volatilome was followed for 25 days of storage at 8°C in vacuum packaging. PC antimicrobial activity was also assessed
against
. This polyphasic approach underlined two scenarios depending on the protective strain.
SF1944,
EU2229 and
EU2249, were very competitive in the product, dominated the microbial ecosystem, and displayed antimicrobial activity against the spoilage microbiota and
The strains also expressed their own sensory and volatilome signatures. However, of these three strains,
SF1944 did not induce strong spoilage and was the most efficient for
growth control. By contrast,
CD264,
MIP2551 and
SF1044 were not competitive, did not express strong antimicrobial activity and produced only few organic volatile compounds (VOCs). However,
CD264 was the only strain to extend the sensory quality, even beyond 25 days. This study shows that
SF1944 and
CD264 both have a promising potential as bioprotective cultures to ensure salmon gravlax microbial safety and sensorial quality, respectively.
The microbiota of fresh French pork sausages were characterised in five batches of comminuted pork meat that were equally divided into two formulations either containing the acid-based preservatives ...lactate and acetate, or no preservatives. Conventional microbiological analysis and high-throughput 16S rDNA amplicon sequencing methods were performed on meat batches packed under modified atmosphere (70% oxygen and 30% carbon dioxide) during chilled storage. In addition, meat pH and colour, and gas composition of the packages were monitored until the end of the shelf-life. During storage, the population of mesophilic and lactic acid bacteria increased from 4 log CFU/g to 8 log CFU/g after 15 days of chilled storage, both with and without preservatives. Despite similar changes of the physical and chemical parameters, such as pH and package gas composition, spoilage was delayed in the meat containing the preservatives, suggesting that lactate and acetate are effective against spoilage. Metagenetic analysis showed that at the end of the shelf-life, the species distribution differed between both the formulations and the batches. Lactic acid bacteria were shown to dominate both with and without preservatives; however, samples containing no preservatives were characterised by the presence of an increased population of Brochothrix spp. and Pseudomonas spp. whereas, Leuconostoc mesenteroides/pseudomesenteroides and Lactobacillus curvatus/graminis were more abundant in the meat with preservatives.
•The microbiota of two formulations of fresh pork sausages were characterized.•The evolution of pH, gas content of the package was similar between formulations.•The removal of lactate and acetate induced faster spoilage.•The microbiota were dominated by Lactic Acid Bacteria and Brochothrix spp.•Brochothrix spp. and Pseudomonas spp. were more abundant in absence of preservatives.
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics ...techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
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