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Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and identified as the main pathogens. The present study describes the characterization of 18 Pseudomonas strains, isolated from fish products using shotgun proteomics. The bacterial proteomes obtained were further analyzed to identify the main functional pathway proteins involved. In addition, this study revealed the presence of 1015 non-redundant peptides related to virulence factors. An additional 25 species-specific peptides were identified as putative Pseudomonas spp. biomarkers. The results constitute the largest dataset, described thus far for the rapid identification and characterization of Pseudomonas species present in edible fish; furthermore, these data can provide the basis for further research into the development of new therapies against these harmful pathogens

This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage

The presence of biogenic amines (histamine, tyramine, putrescine, and cadaverine) in seafood is a significant concern for food safety. This review describes for the first time a shotgun quantitative proteomics strategy to evaluate and compare foodborne strains of bacteria that produce biogenic amines in seafoods. This approach recognized 35,621 peptide spectrum matches, belonging to 20,792 peptides, and 4621 proteins. It allowed the determination of functional pathways and the classification of the strains into hierarchical clusters. The study identified a protein–protein interaction network involving 1160 nodes/10,318 edges. Proteins were related to energy pathways, spermidine biosynthesis, and putrescine metabolism. Label-free quantitative proteomics allowed the identification of differentially regulated proteins in specific strains such as putrescine aminotransferase, arginine decarboxylase, and l-histidine-binding protein. Additionally, 123 peptides were characterized as virulence factors and 299 peptide biomarkers were selected to identify bacterial species in fish products. This study presents the most extensive proteomic repository and progress in the science of food biogenic bacteria and could be applied in the food industry for the detection of bacterial contamination that produces histamine and other biogenic amines during food processing/storage

Food authentication and food allergy profiling are relevant topics that must be carefully considered by authorities, food production and manufacturing industries, and customers. Precise, sensitive, and efficient detection procedures are crucial for authenticating food and identifying allergens. In this paper, we present a current review of advanced proteomic approaches for food authentication and allergen profiling. We discuss three proteomics strategies, namely, discovery proteomics, targeted proteomics, and proteomics-based systems biology, used to authenticate food and profile allergens. This review includes a selection of the most representative papers published in this field in the last few years. Furthermore, we discuss future directions and potential opportunities in this field

In seafood, the Biogenic Amines (BAs) histamine, cadaverine, tyramine, putrescine, spermidine, and spermine are used as indicators for food spoilage. BAs are low-molecular-weight nitrogenous compounds principally generated by microbial decarboxylation of free amino acids or deamination/amination or transamination of aldehydes and ketones. The present investigation evaluates biogenic amine-producing bacteria responsible for the production of BAs in seafood by shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also contribute to improving food quality and safety with the development of new treatments for food intoxication and for tracking microbial sources in foodstuffs

Nos produtos do mar, as aminas bioxénicas (BAs) histamina, cadaverina, tiramina, putrescina, espermidina e espermina úsanse como indicadores do deterioro dos alimentos. As BAs son compostos nitroxenados de baixo peso molecular xerados principalmente pola descarboxilación microbiana de aminoácidos libres ou desaminación/aminación ou transaminación de aldehídos e cetonas

La globalización ha generado redes de distribución más complejas y fragmentadas, que conllevan una mayor probabilidad de introducción y reemergencia de microorganismos alterantes y patógenos en alimentos. Tradicionalmente, los agentes microbiológicos patógenos y alterantes en alimentos se han identificado mediante métodos de aislamiento, y consecuente caracterización morfológica, fisiológica y bioquímica. Estos métodos son tediosos y precisan varios días para ser completados, por lo que no responden a las nuevas necesidades de una industria alimentaria global. Los nuevos desafíos en el control de la inocuidad alimentaria requieren de métodos de detección y caracterización precoz, no solo para reducir la morbilidad y la mortalidad relativas a las ETA, sino también para evitar pérdidas económicas tanto al productor como al distribuidor de alimentos. Por tanto, el principal objetivo de esta Tesis Doctoral ha sido desarrollar y optimizar protocolos de identificación y caracterización de bacterias alterantes y patógenos en alimentos, usando tecnologías de última generación (ómicas). Específicamente, el trabajo se ha centrado en el género Enterococcus debido a su naturaleza dual, y a un patógeno emergente como Raoultella ornithinolytica. Para ello se desarrollaron metodologías analíticas sensibles y precisas, basadas en la genómica y en la proteómica.

Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs

This study focused on the quality loss inhibition of fish muscle during refrigerated storage. Two parallel experiments were carried out that were focused on the employment of pitaya (Stenocereus thurberi) extracts in biodegradable packing films. On the one hand, a pitaya–gelatin film was employed for hake (Merluccius merluccius) muscle storage. On the other hand, a pitaya–polylactic acid (PLA) film was used for Atlantic mackerel (Scomber scombrus) muscle storage. In both experiments, fish-packing systems were stored at 4 °C for 8 days. Quality loss was determined by lipid damage and microbial activity development. The presence of the pitaya extract led to an inhibitory effect (p < 0.05) on peroxide, fluorescent compound, and free fatty acid (FFA) values in the gelatin–hake system and to a lower (p < 0.05) formation of thiobarbituric acid reactive substances, fluorescent compounds, and FFAs in the PLA–mackerel system. Additionally, the inclusion of pitaya extracts in the packing films slowed down (p < 0.05) the growth of aerobes, anaerobes, psychrotrophs, and proteolytic bacteria in the case of the pitaya–gelatin films and of aerobes, anaerobes, and proteolytic bacteria in the case of pitaya–PLA films. The current preservative effects are explained on the basis of the preservative compound presence (betalains and phenolic compounds) in the pitaya extracts