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Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.

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.

Emerging contaminants (ECs) include endocrine-disrupting compounds, pharmaceuticals (lipid regulators, antibiotics, diuretics, non-steroid anti-inflammatory drugs, stimulant drugs, antiseptics, analgesic, beta blockers), detergents, disinfectants, and personal care products. The residues from these compounds have become a concerning because of their bioactive presence on environmental matrices, especially water bodies. The development of technologies, aiming the secure and efficient removal of these compounds from the environment or event to remove them before they achieve the environment, is necessary. In these context, the present review is about promising eco-friendly, low-cost and specially applied, including biological processes using microalgae, bacteria, enzymes produced by fungi, and adsorbent materials such as those recycled from other processes waste. The processes where revised considering the removal mechanism and the efficiency rate.

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.

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.

The literature is full of studies reporting environmental and health issues related to using traditional pesticides in food production and storage. Fortunately, alternatives have arisen in the last few decades, showing that organic agriculture is possible and economically feasible. And in this scenario, fungi may be helpful. In the natural environment, when associated with plants, these microorganisms offer plant-growth-promoting molecules, facilitate plant nutrient uptake, and antagonize phytopathogens. It is true that fungi can also be phytopathogenic, but even they can benefit agriculture in some way—since pathogenicity is species-specific, these fungi are shown to be useful against weeds (as bioherbicides). Finally, plant-associated yeasts and molds are natural biofactories, and the metabolites they produce while dwelling in leaves, flowers, roots, or the rhizosphere have the potential to be employed in different industrial activities. By addressing all these subjects, this manuscript comprehensively reviews the biotechnological uses of plant-associated fungi and, in addition, aims to sensitize academics, researchers, and investors to new alternatives for healthier and more environmentally friendly production processes.

Yeasts are the most used microorganisms for biotechnological purposes. Although they have been mainly recognized for their application in the beverage and bioethanol industries, these microorganisms can be efficiently employed in pharmaceutical and food production companies. In these industrial sectors, yeasts are highly desirable for their capacity to produce bioactive compounds from simple substrates, including wastes. In this review, we present the state of the art of bioactive compound production in microbial cell factories and analyze the avenues to increase the productivity of these molecules, which benefit human and environmental health. The article addresses their vast biological activities, from preventing to treating human diseases and from pre to postharvest control on agroindustrial streams. Furthermore, different yeast species, genetically engineered or not, are herein presented not only as biofactories of the referred to compounds but also as their targets. This comprehensive analysis of the literature points out the significant roles of biodiversity, bioprospection, and genome editing tools on the microbial production of bioactive compounds and reveals the value of these approaches from the one health perspective.

Background/Objectives: Antimicrobial resistance (AMR) poses a significant threat to global health and the economy, with projected costs ranging from$300 billion to $ 1 trillion annually and an estimated 10 million deaths per year by 2050. The food chain, from primary production to retail, represents a critical entry point for antimicrobial resistant bacteria into communities. This underscores the need for a coordinated “One Health” approach, integrating efforts in animal production, environmental health, and human healthcare to address this global concern. This study aimed to characterize the global resistome in Spanish primary production by sequencing 6222 bacterial genomes from animal origin. Methods and Results: Whole genome sequencing was performed on bacterial isolates collected from various farms and analyzed using a validated bioinformatic pipeline. The analysis revealed a diverse range of bacterial species, with Enterobacteriaceae being the most prevalent family. Escherichia coli was the most common species, followed by Salmonella enterica and Pseudomonas aeruginosa. This study identified 1072 antimicrobial resistance genes coding for 43 different classes of resistance, potentially conferring resistance to 81 antimicrobials. Additionally, 79 different plasmid types were detected, highlighting the potential for horizontal gene transfer. Conclusions: The resistome analysis revealed genes conferring resistance to various antibiotic classes, as well as antiseptics, disinfectants, and efflux pump-mediated resistance. This comprehensive characterization of AMR genes circulating in bacteria from primary production provides crucial insights into the ecology of AMR in Spanish livestock.

The discovery of biomolecules has been the subject of extensive research for several years due to their potential to combat harmful pathogens that can lead to environmental contamination and infections in both humans and animals. This study aimed to identify the chemical profile of endophytic fungi, namely Neofusicoccum parvum and Buergenerula spartinae, which were isolated from Avecinnia schaueriana and Laguncularia racemosa. We identified several HPLC-MS compounds, including Ethylidene-3,39-biplumbagin, Pestauvicolactone A, Phenylalanine, 2-Isopropylmalic acid, Fusaproliferin, Sespendole, Ansellone, Calanone derivative, Terpestacin, and others. Solid-state fermentation was conducted for 14–21 days, and methanol and dichloromethane extraction were performed to obtain a crude extract. The results of our cytotoxicity assay revealed a CC50 value > 500 μg/mL, while the virucide, Trypanosoma, leishmania, and yeast assay demonstrated no inhibition. Nevertheless, the bacteriostatic assay showed a 98% reduction in Listeria monocytogenes and Escherichia coli. Our findings suggest that these endophytic fungi species with distinct chemical profiles represent a promising niche for further exploring new biomolecules.

Renewable energy can assist the management of the effects of population growth and rapid economic development on the sustainability of animal husbandry. The primary aim of renewable energy is to minimize the use of fossil fuels via the creation of environmentally friendly energy products from depleted fossil fuels. Digesters that treat swine manure are extensively used in treatment systems; and inclusion of swine carcasses can increase the organic loading rate (OLR) thereby improving biogas yield and productivity on farms. However, the characteristics of the components including animal residues, proteins, lipids, remains of undigested feed items, antimicrobial drug residues, pathogenic microorganisms and nutrient contents, are complex and diverse. It is therefore necessary to manage the anaerobic process stability and digestate purification for subsequent use as fertilizer. Efficient methane recovery from residues rich in lipids is difficult because such residues are only slowly biodegradable. Pretreatment can promote solubilization of lipids and accelerate anaerobic digestion, and pretreatments can process the swine carcass before its introduction onto biodigesters. This review presents an overview of the anaerobic digestion of swine manure and carcasses. We analyze the characteristics of these residues, and we identify strategies to enhance biogas yield and process stability. We consider energy potential, co-digestion of swine manure and carcasses, physical, chemical, and biological pretreatment of biomass, sanitary aspects of swine manure and co-digestates and their recycling as fertilizers.