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The current proceedings summarize the presentations delivered during the third International Electronic Conference on Microbiology (ECM 2025), which was held online from 1 to 3 April 2025, via the SciForum platform. This virtual event brought together researchers from around the world to share recent advances in microbiological sciences. The ECM 2025 highlighted recent developments across a broad spectrum of microbiological research, including antimicrobial resistance, gut microbiota, infectious diseases, and environmental microbiomes. Participants shared their work through online presentations and abstracts, with selected submissions invited for full publication. The event fostered global collaboration, promoted open-access science, and showcased innovative tools for studying and managing microbial systems in health, agriculture, and industry. The multidisciplinary program was organized into several thematic sessions: S1. Gut Microbiota and Health Disease. S2. Foodborne Pathogens and Food Safety. S3. Antimicrobial Agents and Resistance. S4. Emerging Infectious Diseases. S5. Microbiome and Soil Science. S6. Microbial Characterization and Bioprocess. S7. Microbe–Plant Interactions. This conference report presents summaries of the contributions made by participating authors over the three-day event. Full article

Steak tartare is a ready-to-eat (RTE) meat product, prepared with finely chopped or ground raw beef, with a rich culinary history and increasing consumption trend in the last years. Yet, its microbiological safety and technological challenges remain largely under-investigated. This review analyses the regulations, the safety, and technological advances in steak tartare manufacturing, focusing on microbiological risks due to potential contamination by pathogens like Salmonella spp., Listeria monocytogenes, and Escherichia coli O157:H7. From this perspective, the outbreaks associated with the consumption of raw meat products have confirmed the importance of good hygiene practice and process control, currently based on the presence of nitrite in the formulation and accurate cold chain management. Recently, the EU regulations have set stricter limits for the use of nitrites and nitrates in meat products, and this evolution has increased the interest in natural alternatives. The scientific literature indicates that plant-based antimicrobials, high-pressure processing (HPP), and novel starter cultures can be promising tools to improve raw meat safety and shelf life. This review analyses the possible options for nitrite replacement, which might involve combined interventions with natural antimicrobials, starter cultures, and packaging solutions. Future studies need to address the microbial behaviour and dynamics in nitrite-free formulations, including safety validation by challenge testing with foodborne pathogens. In this respect, steak tartare could be a model for innovation in the meat industry. However, considering the challenges that must be faced, collaboration across disciplines will be essential to meet regulatory constraints and consumer expectations while ensuring product quality and safety. Full article

Vibrio parahaemolyticus is a prevalent pathogen responsible for foodborne diseases in coastal regions. Understanding its dynamic relationship with various meteorological and marine factors is crucial for predicting outbreaks of bacterial foodborne illnesses. This study analyzes the occurrence of V. parahaemolyticus-induced foodborne illness in Zhejiang Province, China, from 2014 to 2018, using an 8-day time unit based on the temporal characteristics of marine products. The detection rate of V. parahaemolyticus exhibited a distinct cyclical pattern, peaking during the summer months. Meteorological and marine factors showed varying lag effects on the detection of V. parahaemolyticus, with specific lag periods as follows: sunshine duration (3 weeks), air temperature (3 weeks), total precipitation (8 weeks), relative humidity (7 weeks), sea surface temperature (1 week), and sea surface salinity (8 weeks). The SARIMAX model, which incorporates both marine and climatic factors, was developed to facilitate short-term forecasts of V. parahaemolyticus detection rates in coastal cities. The model’s performance was evaluated, and the actual values consistently fell within the 95% confidence interval of the predicted values, with a mean absolute error (MAE) of 0.047, indicating high accuracy. This framework provides both theoretical and practical insights for predicting and preventing future foodborne disease outbreaks. These findings can support food industry stakeholders—such as seafood suppliers, restaurants, regulatory agencies, and healthcare institutions—in anticipating high-risk periods and implementing targeted measures. These include enhancing cold chain management, conducting timely seafood inspections, strengthening cross-contamination controls during seafood processing, dynamically adjusting market surveillance intensity, and improving hygiene practices. In addition, hospitals and local health departments can use the model’s forecasts to allocate medical resources such as beds, medications, and staff in advance to better prepare for seasonal surges in foodborne illness. Full article

The human microbiome plays a critical role in health and disease, with recent innovations in microbiome research offering groundbreaking insights that could reshape the future of healthcare. This study explored emerging methodologies, such as long-read sequencing, culturomics, synthetic biology, machine learning, and AI-driven diagnostics, that are transforming the field of microbiome–host interactions. Unlike traditional broad-spectrum approaches, these tools enable precise interventions, such as detecting foodborne pathogens and remediating polluted soils for safer agriculture. This work highlights the integration of interdisciplinary approaches and non-animal models, such as 3D cultures and organ-on-a-chip technologies, which address the limitations of current research and present ethical, scalable alternatives for microbiome studies. Focusing on food safety and environmental health, we examine how microbial variability impacts pathogen control in food chains and ecosystem resilience, integrating socioeconomic and environmental factors. The study also emphasizes the need to expand beyond bacterial-focused microbiome research, advocating for the inclusion of fungi, viruses, and helminths to deepen our understanding of therapeutic microbial consortia. The combination of high-throughput sequencing, biosensors, bioinformatics, and machine learning drives precision strategies, such as reducing food spoilage and enhancing soil fertility, paving the way for sustainable food systems and environmental management. Hence, this work offers a comprehensive framework for advancing microbiome interventions, providing valuable insights for researchers and professionals navigating this rapidly evolving field. Full article

Next-Generation Sequencing (NGS) technology was applied to evaluate Food Safety Management System (FSMS) performance in seafood-processing factories by exploring microbiome diversity alongside traditional methods for detecting foodborne pathogens. A total of 210 environmental swabs collected from processing zones in six factories underwent 16S rRNA amplicon sequencing. FSMS-certified factories exhibited significantly higher species richness, with alpha diversity p-values of 0.0036 for observed ASVs, 0.0026 for Faith’s PD and 0.032 for Shannon. Beta diversity analysis also revealed significant differences, with p-values of 0.001 for Bray–Curtis, unweighted UniFrac and Jaccard. Pathogens like Listeria monocytogenes, Salmonella spp. and Bacillus cereus were present in “uncertified” factories but absent in the “certified” factories. The “certified” factories had a significantly higher proportion of lactic acid bacteria (LAB) genera (70.22%) compared to “uncertified” factories (29.78%). The LAB genera included Streptococcus, Lactococcus, Lactobacillus and others. NGS has demonstrated superior capability by providing comprehensive microbiome detection, including the unculturable microorganisms and insights into microbial diversity, so it lacks the limitations that come with traditional culturing. These findings highlight the potential for leveraging beneficial microbes in bioremediation and pathogen control to enhance FSMS effectiveness in seafood-processing environments. Full article

Food safety is a significant global and local concern due to the threat of foodborne pathogens to public health and food security. Bacterial biofilms are communities of bacteria adhered to surfaces and represent a persistent contamination source in food environments. Their resistance to conventional antimicrobials exacerbates the challenge of eradication, driving the search for alternative strategies to control biofilms. Unconventional or “green” antimicrobial agents have emerged as promising solutions due to their sustainability and effectiveness. These agents include bacteriophages, phage-derived enzymes, plant extracts, and combinations of natural antimicrobials, which offer novel mechanisms for targeting biofilms. This approach aligns with the “One Health” concept, which underscores the interconnectedness of human, animal, and environmental health and advocates for integrated strategies to address public health challenges. Employing unconventional antimicrobial agents to manage bacterial biofilms can enhance food safety, protect public health, and reduce environmental impacts by decreasing reliance on conventional antimicrobials and mitigating antimicrobial resistance. This review explores the use of unconventional antimicrobials to combat foodborne pathogen biofilms, highlighting their mechanisms of action, antibiofilm activities, and the challenges associated with their application in food safety. By addressing these issues from a “One Health” perspective, we aim to demonstrate how such strategies can promote sustainable food safety, improve public health outcomes, and support environmental health, ultimately fostering a more integrated approach to combating foodborne pathogen biofilms. Full article

Foodborne diseases (FBDs) represent a significant public health concern, particularly in regions like Central America and the Caribbean (CAC), where surveillance gaps due to a lack of resources, knowledge, and technical abilities hinder control over outbreaks. This review investigates the bacterial pathogens responsible for FBDs, their prevalence, management challenges, and prevention strategies. This systematic review followed PRISMA guidelines, focusing on bacterial FBDs in CAC from 2000 to 2024. PubMed and Google Scholar were used as primary databases, supported by other sources to identify relevant studies. Inclusion criteria encompassed studies focusing on bacterial pathogens, prevalence, risk factors, and surveillance practices. Out of the 509 studies initially identified, 35 met the inclusion criteria. The most prevalent pathogens were Salmonella spp., Escherichia coli, Campylobacter spp., and Aliarcobacter spp., with contamination often associated with poultry, eggs, and vegetables. Key challenges included inadequate surveillance systems, limited resources, and inconsistent reporting practices. A more significant investment in pathogen monitoring, documentation, and education, along with technologies like whole-genome sequencing (WGS), is crucial. Institutional and governmental funding is vital to improve surveillance and strengthen regional risk analysis. Full article

Background/Objectives: Gut microbiota is essential for maintaining host immune homeostasis and has been confirmed to be closely related to some intestinal and extraintestinal diseases. Bacteroides, as the dominant bacterial genus in the human gut, has attracted great attention due to its excellent metabolic activity, but there are few studies on Bacteroides dorei species. In our previous study, a gut commensal strain, Bacteroides dorei RX2020 (B. dorei), was isolated from healthy human feces and exhibited superior flavonoid metabolic activity, prompting further analysis of its uncharacterized genomic features, probiotic potential, safety, and immunomodulatory activity. Results: The results showed that B. dorei exhibited intrinsic probiotic functionalities with preserved genomic and phenotypic stability, demonstrated safety profiles in murine models through in vivo assessments, and conferred antagonistic activity against enteric foodborne pathogens via competitive exclusion. The strain also demonstrated abundant metabolic activity and was involved in the metabolism of tryptophan and bile acids (BAs). Moreover, B. dorei can promote the production of IFNβ by dendritic cells (DCs) to inhibit the replication of influenza virus in epithelial cells, which may be achieved by regulating host metabolism. Conclusions: This study reveals the potential of B. dorei as next-generation probiotics (NGPs), contributing to a broader understanding and application of these novel probiotics in health and disease management. Full article

Cronobacter sakazakii is a food-borne pathogen that can thrive in various environments, including the human body. The human body’s physiological temperature exceeds that of the environment (22–30 °C), necessitating adaptations to heat stress during this transition. Managing heat stress is crucial when transitioning from the environment to the human body. In this study, we explored the effect of human body temperature on the growth of planktonic C. sakazakii, as well as its acid resistance, osmotic stress resistance, autoaggregation, and cell surface hydrophobicity. Our study demonstrated that human body temperature facilitated the growth, acid resistance, and osmotic resistance of C. sakazakii, compared to 28 °C. The relationship between human body temperature and phenotypes was studied by comparing gene expression at human and environmental temperatures (37 to 28 °C) using high-throughput sequencing. The results revealed up-regulation in the expression of 626 genes, including genes involved in arginine and proline metabolism, carbon fixation pathways, and nitrogen metabolism. Further analysis showed that human body temperature is essential for the environmental stress resistance of C. sakazakii. It boosts denitrification, betaine transport, and universal stress proteins, supporting membrane integrity and osmoprotectant transport. This study enhances our understanding of the strategies employed by C. sakazakii during its adaptation to the human body. Full article

Biosensors are innovative and cost-effective analytical devices that integrate biological recognition elements (bioreceptors) with transducers to detect specific substances (biomolecules), providing a high sensitivity and specificity for the rapid and accurate point-of-care (POC) quantitative detection of selected biomolecules. In the meat production chain, their application has gained attention due to the increasing demand for enhanced food safety, quality assurance, food fraud detection, and regulatory compliance. Biosensors can detect foodborne pathogens (Salmonella, Campylobacter, Shiga-toxin-producing E. coli/STEC, L. monocytogenes, etc.), spoilage bacteria and indicators, contaminants (pesticides, dioxins, and mycotoxins), antibiotics, antimicrobial resistance genes, hormones (growth promoters and stress hormones), and metabolites (acute-phase proteins as inflammation markers) at different modules along the meat chain, from livestock farming to packaging in the farm-to-fork (F2F) continuum. By providing real-time data from the meat chain, biosensors enable early interventions, reducing the health risks (foodborne outbreaks) associated with contaminated meat/meat products or sub-standard meat products. Recent advancements in micro- and nanotechnology, microfluidics, and wireless communication have further enhanced the sensitivity, specificity, portability, and automation of biosensors, making them suitable for on-site field applications. The integration of biosensors with blockchain and Internet of Things (IoT) systems allows for acquired data integration and management, while their integration with artificial intelligence (AI) and machine learning (ML) enables rapid data processing, analytics, and input for risk assessment by competent authorities. This promotes transparency and traceability within the meat chain, fostering consumer trust and industry accountability. Despite biosensors’ promising potential, challenges such as scalability, reliability associated with the complexity of meat matrices, and regulatory approval are still the main challenges. This review provides a broad overview of the most relevant aspects of current state-of-the-art biosensors’ development, challenges, and opportunities for prospective applications and their regular use in meat safety and quality monitoring, clarifying further perspectives. Full article

Clostridioides difficile is the leading cause of antibiotic-associated diarrhea in hospitalized patients. In recent years, the incidence of C. difficile infection (CDI) has increased globally, with a notable rise in community-associated CDI (CA-CDI). The presence of the microorganism in animals, the environment, and food suggests that these sources may contribute to the spread of the infection in the community. This review applies a One Health approach, integrating human, animal, and environmental health, to provide a comprehensive strategy for understanding and managing this pathogen. Findings reveal the widespread dissemination of C. difficile in animals, the environment, and food. The predominant PCR ribotypes identified were RTs 078 and 014/020, followed by RTs 126, 001, 002, 009, 010, and 033. C. difficile strains exhibited resistance to multiple antimicrobial agents, including clindamycin, erythromycin, fluoroquinolones, cephalosporins, and tetracyclines. Discriminative typing methods, such as whole-genome sequencing, revealed clonal relationships between C. difficile strains from humans and animals, indicating either direct transmission or a common environmental source of infection. The high genetic similarity between isolates from the environment and humans indicates potential environmental contamination. Additionally, clusters of C. difficile strains found in food and humans indicate a possible foodborne transmission route. This review summarizes the current knowledge on the role of Clostridioides difficile within the One Health framework. Full article

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen and known to reside naturally in cattle. The application of untreated biological soil amendments of animal origin on fresh produce fields results in unique food safety challenges. It is critical to identify farm manure management practices to mitigate pre-harvest pathogen contamination. The objective of this study was to quantify the prevalence and level of STEC in cattle manure in the Mid-Atlantic region of the United States. A total of 161 bovine manure samples were collected from 13 cattle farms between 2016 and 2018. The samples were enriched with non-selective and selective media and quantified following a Most-Probable Number (MPN) assay. Among the recovered STEC isolates, PCR was performed to determine the presence of stx, eae, and rfbE. Clermont PCR was performed to identify phylogenetic groups of isolates. Of the 13 farms, 11 had STEC populations between <1.0 and >5.6 log MPN/g. Farm, humidity, and sampling year significantly (p < 0.05) influenced STEC populations in bovine manure. Of the 108 isolates, 50% were stx+ and 14% eae+. Phylogenetic group analysis revealed that 46% of the isolates belonged to group A, 19% to B1, 7% to B2, and 28% to D. Group D had the highest prevalence of stx+ and eae+ and group B1 had the lowest prevalence. Results suggest STEC geographical distribution in the Mid-Atlantic region is farm-specific, and climatic conditions can be critical for its survival and dissemination. Full article

Allyl isothiocyanate (AITC) is a low-molecular-weight natural chemical predominantly obtained from the autolysis of sinigrin, a glucosinolate found in cruciferous vegetables like mustard, horseradish, and wasabi. AITC has sparked widespread interest due to its various biological actions, which include strong antioxidant, anti-inflammatory, antibacterial, and anticancer capabilities. This compound offers promising potential in several fields, particularly in food preservation, medicine, and enhancing food quality through natural means. AITC’s effectiveness against a broad spectrum of microorganisms, including foodborne pathogens and spoilage agents, makes it an attractive natural alternative to synthetic preservatives. The potential to extend the shelf life of perishable foods makes AITC an important tool for food production, meeting rising customer demand for natural additives. In addition to its antimicrobial effects, AITC demonstrates significant anti-inflammatory activity, reducing levels of pro-inflammatory cytokines and modulating key signaling pathways, which could make it valuable in managing chronic inflammatory conditions. Furthermore, emerging research highlights its potential in cancer prevention and treatment, as AITC has been demonstrated to induce apoptosis and inhibit cell increase in several cancer cell lines, offering a natural approach to chemoprevention. This review delves into the chemical structure, metabolism, and bioavailability of freshly produced AITC, providing a comprehensive overview of its beneficial properties. Challenges related to AITC’s volatility, dosage optimization, and regulatory considerations are also discussed, alongside future research directions to enhance the stability and efficacy of AITC-based formulations. The findings underscore AITC’s role as a versatile bioactive compound with known potential to support human health and the sustainable food industry. Full article

Foodborne viruses such as human norovirus (HuNoV) and hepatitis A virus (HAV) are the major causes of foodborne illnesses worldwide. These viruses have a low infectious dose and are persistent in the environment and food for weeks. Ready-to-eat (RTE) low moisture foods (LMFs) undergo minimal pathogen reduction processes. In recent years, multiple foodborne HAV outbreaks involving hundreds of individuals were associated with the consumption of dates, indicating that they could be important vehicles for foodborne infection. There is no standard method for the extraction and detection of foodborne viruses from dates, but herein we have compared the efficiency of three different protocols based on the ISO 15216 method in the extraction of murine norovirus (MNV) from whole Medjool dates and successfully employed the best performing method in the extraction of HAV, HuNoV GI, and GII and determined the limit of detection (LOD₉₅) of 61, 148, and 184 genomic equivalent (gEq) per 25 g, respectively. Finally, we tested the adopted method on various varieties of dates including pitted ones and reported the detection of HuNoV GI and GII from four naturally contaminated date varieties. This ISO 15216 protocol could be employed for surveillance purposes and outbreak management related to dates. Full article

The overuse of antibiotics in animal husbandry has driven the search for alternative strategies to combat zoonotic pathogens. Foodborne zoonotic diseases caused by pathogenic bacteria pose a significant threat to human health, and therefore food safety should be a priority. This study investigates the in vitro inhibitory effects of chicken egg yolk immunoglobulin Y (IgY) on the growth and viability of three major foodborne pathogens: Campylobacter jejuni, Salmonella spp., and Escherichia coli. IgY was isolated from immunized hen egg yolks using a modified water dilution method, and its antigen-specificity confirmed through agglutination assays. Growth inhibition was evaluated across multiple doses and time points, revealing a dose-dependent bacteriostatic effect against all tested pathogens. A single dose of IgY (0.5 mg/mL) significantly reduced C. jejuni counts by up to 7 log, while repeated doses were required for Salmonella spp. and E. coli. These findings highlight egg yolk immunoglobulin’s potential as a source of sustainable, effective, ethical, readily available, and inexpensive antibiotic substitutes in livestock management. Future research will focus on validating these results in vivo and exploring large-scale production of IgY for practical application in animal healthcare. Full article