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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

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

This research explores a selection of EU policies (such as the European Green Deal) and global trends and their potential land use impact on five case studies in the Netherlands. The assumption behind the research design is that based on the scope and anticipated realisation of EU policies and occurrence of global trends, the potential land use impact can be estimated. The study uses a qualitative foresight methodology, incorporating the uncertainty of future-oriented investigations. The reasoning and the identified causal links rely on estimates pertaining to economy, social change, and political decisions, as well as environmental impacts and technological advancements. The land use impact estimates are derived from this reasoning and different levels of uncertainty. The study differentiates between expansive and restrictive potential land use impacts. Expansive land use means increased demand for a certain type of land. Restrictive means that as a result of the policy or trend, a certain type of land use may no longer be necessary or may be converted to another type. Land use impacts that have different effects on different territories or are difficult to estimate clearly are categorised as inconclusive.

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

Enterococcus belongs to a group of microorganisms known as lactic acid bacteria (LAB), which constitute a broad heterogeneous group of generally food-grade microorganisms historically used in food preservation. Enterococci live as commensals of the gastrointestinal tract of warm-blooded animals, although they also are present in food of animal origin (milk, cheese, fermented sausages), vegetables, and plant materials because of their ability to survive heat treatments and adverse environmental conditions. The biotechnological traits of enterococci can be applied in the food industry; however, the emergence of enterococci as a cause of nosocomial infections makes their food status uncertain. Recent advances in high-throughput sequencing allow the subtyping of bacterial pathogens, but it cannot reflect the temporal dynamics and functional activities of microbiomes or bacterial isolates. Moreover, genetic analysis is based on sequence homologies, inferring functions from databases. Here, we used an end-to-end proteomic workflow to rapidly characterize two bacteriocin-producing Enterococcus faecium (Efm) strains. The proteome analysis was performed with liquid chromatography coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) for high-throughput and high-resolution characterization of bacterial proteins. Thus, we identified almost half of the proteins predicted in the bacterial genomes (>1100 unique proteins per isolate), including quantifying proteins conferring resistance to antibiotics, heavy metals, virulence factors, and bacteriocins. The obtained proteomes were annotated according to function, resulting in 22 complete KEGG metabolic pathway modules for both strains. The workflow used here successfully characterized these bacterial isolates and showed great promise for determining and optimizing the bioengineering and biotechnology properties of other LAB strains in the food industry.

Aim: Due to the lockdown caused by the Corona pandemic, the internship (PJ=practical year) seminars of the elective subject "General Practice" at Ruhr-University Bochum had to be transferred on short notice into online teaching formats via a digital platform. At the end of these new online course, the four students evaluated the comprising 16 teaching units.Methods: The seminars, each comprising four teaching units, took place in online blended-learning units and online events. After completing the seminar program, the four participants filled out a written questionnaire regarding the implementation of digital teaching, quality of teaching content, acceptance as well as advantages and disadvantages of the teaching format.Results: The acceptance of digital teaching was very high among students. Advantages and disadvantages of this teaching format compared to the previous face-to-face events became apparent; a positive assessment of the possibilities of the online format clearly prevailed, as competence-oriented, interactive aspects were very well implemented.Conclusion: Due to the need of switching to digital teachings formats, new, innovative perspectives have arisen for PJ teaching in Bochum as well as for the more distant second location Ostwestfalen-Lippe. This is particularly true with regard to centralised seminar offers despite decentralised training centres. When implementing "new" licensing regulations this creates an opportunity for general practice to include teaching practices in training throughout the country., Zielsetzung: Durch den coronabedingten Lockdown mussten die PJ-Seminare im Rahmen des Wahlfaches Allgemeinmedizin an der Ruhr-Universität Bochum kurzfristig über eine digitale Plattform in entsprechende Online-Lehrformate überführt werden. Am Ende wurde diese insgesamt 16 Unterrichteinheiten (UE) umfassende Online-Veranstaltung von den im PJ-Tertial befindlichen 4 Studierenden evaluiert.Methode: Die jeweils 4 UE umfassenden Seminare fanden im Online-Format in Form von Blended-Learning-Einheiten sowie reinen Online-Präsenzveranstaltungen durchgeführt. Nach Abschluss des Seminarprogramms erfolgte durch die 4 Teilnehmer*innen (TN) des PJ-Tertials eine schriftliche Evaluation mit Fragen zur Umsetzung der digitalen Lehre, zur Qualität der Lehrinhalte sowie zu Akzeptanz und zu Vor- und Nachteilen des Lehrformates.Ergebnisse: Die Akzeptanz der digitalen Lehre war bei den Studierenden sehr hoch. Es zeigten sich Vor- und Nachteile dieses Lehrformates gegenüber den bisherigen Präsenzveranstaltungen, wobei aber eine positive Bewertung der Möglichkeiten des Online-Formates deutlich überwog, da auch kompetenzorientierte, interaktive Aspekte sehr gut umgesetzt werden konnten. Schlussfolgerung: Durch die Notwendigkeit auf digitale Lehrformate umzustellen, haben sich für die PJ-Lehre am Standort Bochum sowie für den weiter entfernten Zweitstandort Ostwestfalen-Lippe neue, innovative Perspektiven ergeben. Dies gilt besonders auch im Hinblick auf zentrale Seminarangebote trotz dezentraler Ausbildungsstätten. Dadurch ergibt sich für die Allgemeinmedizin die Möglichkeit, bei der Umsetzung einer neuen Ärztlichen Approbationsordnung auch bundesweit PJ-Praxen in die Ausbildung mit einzubinden.

Some Listeria species are important human and animal pathogens that can be found in contaminated food and produce a variety of virulence factors involved in their pathogenicity. Listeria strains exhibiting multidrug resistance are known to be progressively increasing and that is why continuous monitoring is needed. Effective therapy against pathogenic Listeria requires identification of the bacterial strain involved, as well as determining its virulence factors, such as antibiotic resistance and sensitivity. The present study describes the use of liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to do a global shotgun proteomics characterization for pathogenic Listeria species. This method allowed the identification of a total of 2990 non-redundant peptides, representing 2727 proteins. Furthermore, 395 of the peptides correspond to proteins that play a direct role in Listeria pathogenicity; they were identified as virulence factors, toxins and anti-toxins, or associated with either antibiotics (involved in antibiotic-related compounds production or resistance) or resistance to toxic substances. The proteomic repository obtained here can be the base for further research into pathogenic Listeria species and facilitate the development of novel therapeutics for these pathogens

The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected

The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts

Streptococcus spp. are major mastitis pathogens present in dairy products, which produce a variety of virulence factors that are involved in streptococcal pathogenicity. These include neuraminidase, pyrogenic exotoxin, and M protein, and in addition they might produce bacteriocins and antibiotic-resistance proteins. Unjustifiable misuse of antimicrobials has led to an increase in antibiotic-resistant bacteria present in foodstuffs. Identification of the mastitis-causing bacterial strain, as well as determining its antibiotic resistance and sensitivity is crucial for effective therapy. The present work focused on the LC–ESI–MS/MS (liquid chromatography–electrospray ionization tandem mass spectrometry) analysis of tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2706 non-redundant peptides belonging to 2510 proteins was identified and analyzed. Among them, 168 peptides were determined, representing proteins that act as virulence factors, toxins, anti-toxins, provide resistance to antibiotics that are associated with the production of lantibiotic-related compounds, or play a role in the resistance to toxic substances. Protein comparisons with the NCBI database allowed the identification of 134 peptides as specific to Streptococcus spp., while two peptides (EATGNQNISPNLTISNAQLNLEDKNK and DLWC*NM*IIAAK) were found to be species-specific to Streptococcus dysgalactiae. This proteomic repository might be useful for further studies and research work, as well as for the development of new therapeutics for the mastitis-causing Streptococcus strains.