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Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic—that is, obligately lytic and not recently descended from a temperate ancestor—they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.

•This study depicts the thanatomicroniome succesional changes in soil on a daily basis.•Microbial changes were monitored quantitatively and qualitatively along decomposition.•Its potential use in forensic cases as a quantitative approach to estimate PMI.•A drastic growth of Firmicutes is observed from bloat stage to advanced decay.•Firmicutes growth curve is proposed to estimate PMI under Tennessee summer conditions. Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization. Three donated individuals to the University of Tennessee FAC were studied. Soil samples around the body were taken from the placement of the donor until advanced decay/dry remains stage. Bacterial DNA extracts were obtained from the samples, HTS techniques were applied and bioinformatic data analysis was performed. The three cadavers showed similar overall successional changes. At the beginning of the decomposition process the soil microbiome consisted of diverse indigenous soil bacterial communities. As decomposition advanced, Firmicutes community abundance increased in the soil during the bloat stage. The growth curve of Firmicutes from human remains can be used to estimate time since death during Tennessee summer conditions.

Mangroves are ecosystems with unique characteristics due to the high salinity and amount of organic matter that house a rich biodiversity. Fungi have aroused much interest as they are an important natural source for the discovery of new bioactive compounds, with potential biotechnological and pharmacological interest. This review aims to highlight endophytic fungi isolated from mangrove plant species and the isolated bioactive compounds and their bioactivity against protozoa, bacteria and pathogenic viruses. Knowledge about this type of ecosystem is of great relevance for its preservation and as a source of new molecules for the control of pathogens that may be of importance for human, animal and environmental health.

Background Streptococcus dysgalactiae is the main cause of neonatal polyarthritis in sheep and is also an important agent in ovine mastitis. However, the main sources of contamination by this pathogen have not been studied in depth. Case presentation A polyarthritis outbreak in 2-3-day-old lambs with an incidence rate of approximately 40%, was reported in a sheep farm focused on sheep’s milk and lamb’s meat. The problem persisted over three consecutive lambing cycles. The pathogen was identified as S. dysgalactiae by 16 S rRNA sequencing of joint fluid. Its genome was isolated and sequenced as S. dysgalactiae MLST 454. The main antibiotic resistance genes and virulence factors were determined. The water supply, milking system, and pasteurisation efficiency were tested by standard plate count methods as well as 16 S rRNA sequencing techniques. High levels of contamination were found in the milking system and colostrum, with the presence of Streptococcus spp. and S. dysgalactiae . The implementation of enhanced pasteurization and more rigorous decontamination of the milking system were sufficient to control the problem on the farm. Conclusions This study reveals the role of the milking system contamination in facilitating the spread of bacteria, such as S. dysgalactiae and provides evidence for the existence of an oral pathway of infection via colostrum.

To characterize the ecological and genomic architecture of temperate bacteriophages in Escherichia coli isolated from Brazilian broiler chickens, we analyzed 63 femur-derived genomes, most fulfilling molecular avian pathogenic E. coli (APEC) criteria, and tested whether temperate phage regions are enriched for antimicrobial resistance genes (ARGs), virulence factors, plasmid markers, and other mobilome components. Diversity was summarized using incidence-based richness estimators and bootstrap confidence intervals, and positional enrichment was assessed using permutation-based statistical analysis. We detected 1164 phage-like elements, including 188 medium- and high-quality phages, of which 93.6% were temperate. Median temperate diversity per genome was three phage genera and three temperate regions. At the population level, 19 temperate genera were observed, with a Chao2 estimate of 21.2, indicating near-saturated genus-level diversity. Positional mobilome analysis showed significant enrichment of insertion sequences within temperate regions (p < 0.05), while ARGs, virulence factors, and plasmid markers were not significantly enriched inside temperate phage coordinates (p > 0.05). The surrounding genomic neighborhood (±20 kb) accumulated mobile elements but showed no significant enrichment. CRISPR spacer matches further supported ongoing host–phage interactions. Overall, temperate phages are widespread and ecologically structured in Brazilian broiler-associated E. coli, but they are not preferential hotspots for ARG, virulence, or plasmid gene enrichment; instead, they are chiefly associated with insertion-sequence enrichment.

Outbreaks related to foodborne diseases are a major concern among health authorities, food industries, and the general public. Escherichia coli (E. coli) is a pathogen associated with causing multiple outbreaks in the last decades linked to several ready to eat products such as meat, fish, dairy products, and vegetables. The ingestion of contaminated food with pathogenic E. coli can cause watery diarrhea, vomiting, and persistent diarrhea as well as more severe effects such as hemorrhagic colitis, end-stage renal disease, and, in some circumstances, hemolytic uremic syndrome. Essential oils (EOs) are natural compounds with broad-spectrum activity against spoilage and pathogenic microorganisms and are also generally recognized as safe (GRAS). Particularly for E. coli, several recent studies have been conducted to study and characterize the effect to inhibit the synthesis of toxins and the proliferation in food systems. Moreover, the strategy used to apply the EO in food plays a crucial role to prevent the development of E. coli. This review encompasses recent studies regarding the protection against pathogenic E. coli by the use of EO with a major focus on inhibition of toxins and proliferation in food systems.

Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.

Quantitative Polymerase Chain Reaction (qPCR) is a molecular technique that has become a gold standard in various disciplines, including environmental microbiology, due to its high sensitivity and specificity. In recent years, it has been extensively used in wastewater-based epidemiology to monitor the prevalence of different viruses in the population. In this study, we evaluated whether the no inclusion of a standard curve in each single experiment to reduce time and costs could have an impact on the accuracy of the results. Thirty independent RT-qPCR standard curve experiments using quantitative synthetic RNA material were conducted for seven different viruses, which include two targets of the novel SARS-CoV-2, hepatitis A and E, noroviruses genogroups I and II, human astrovirus, and rotavirus. Results showed that although all the viruses presented adequate efficiency rates (>90%), variability was also observed between them, independently of the viral concentration tested. NoVGII was the virus that presented the higher inter-assay variability in terms of efficiency while showing better sensitivity. In terms of heterogeneity in results, the two targets of SARS-CoV-2 showed the highest rates, being N2 the gene that presented the largest variability (CV 4.38–4.99%) and the lowest efficiency (90.97%). These findings indicate that including a standard curve in every experiment is recommended to obtain reliable results.

Certain members of the Coronaviridae family have emerged as zoonotic agents and have recently caused severe respiratory diseases in humans and animals, such as SARS, MERS, and, more recently, COVID-19. Antivirals (drugs and antiseptics) capable of controlling viruses at the site of infection are scarce. Microalgae from the Chlorellaceae family are sources of bioactive compounds with antioxidant, antiviral, and antitumor activity. In the present study, we aimed to evaluate various extracts from Planktochlorella nurekis in vitro against murine coronavirus-3 (MHV-3), which is an essential human coronavirus surrogate for laboratory assays. Methanol, hexane, and dichloromethane extracts of P. nurekis were tested in cells infected with MHV-3, and characterized by UV-vis spectrophotometry, nuclear magnetic resonance (NMR) spectroscopy, ultraperformance liquid chromatography-mass spectrometry (UPLC-MS), and the application of chemometrics through principal component analysis (PCA). All the extracts were highly efficient against MHV-3 (more than a 6 Log unit reduction), regardless of the solvent used or the concentration of the extract, but the dichloromethane extract was the most effective. Chemical characterization by spectrophotometry and NMR, with the aid of statistical analysis, showed that polyphenols, carbohydrates, and isoprene derivatives, such as terpenes and carotenoids have a more significant impact on the virucidal potential. Compounds identified by UPLC-MS were mainly lipids and only found in the dichloromethane extract. These results open new biotechnological possibilities to explore the biomass of P. nurekis; it is a natural extract and shows low cytotoxicity and an excellent antiviral effect, with low production costs, highlighting a promising potential for development and implementation of therapies against coronaviruses, such as SARS-CoV-2.

Respiratory infections are a major public health threat. Significant global mortality is caused by influenza viruses, the new SARS-CoV-2 virus, and the Respiratory Syncytial Viruses (RSVs). Wastewater-based epidemiology (WBE) has recently emerged as a valuable tool for monitoring these pathogens, providing insights into their evolution, transmission patterns, and co-circulation within populations. This study aimed to track influenza viruses (A and B), the new SARS-CoV-2 virus, and the Respiratory Syncytial Viruses (RSVs) (type A and B) during the pandemic period (from October 2020 to October 2021) in a middle-size Spanish city (Valladolid) and its surrounding areas. Viral concentration was performed using an aluminum-based precipitation method, followed by RNA extraction and RT-qPCR quantification targeting the N1 and N2 regions of the SARS-CoV-2 nucleocapsid gene, the N gene for both RSV-A and RSV-B, and the M and non-structural protein genes for influenza A and B, respectively. The results demonstrated the utility of WBE in predicting increases in clinical cases of SARS-CoV-2, as evidenced by a high correlation (r > 0.5). For RSV-A, the findings aligned with previous studies. Interestingly, particularly considering the length and period of analysis, influenza A, influenza B, and RSV-B viruses were not observed during the study period. In addition, the prevalence of RSV-A decreased during the SARS-CoV-2 pandemic, likely due to the implementation of non-pharmaceutical interventions. In conclusion, this study reaffirms that WBE provides critical epidemiological insights, complements clinical surveillance, and supports public health authorities in making informed and timely decisions.