Search Results (267)

Multidrug-resistant Acinetobacter baumannii is a major nosocomial pathogen for which bacteriophages are being explored as alternative antibacterial agents. In this study, we isolated and characterized AUBFM01, a lytic phage active against MDR A. baumannii, and performed an initial assessment of its interaction with PMA-differentiated THP-1 macrophages. AUBFM01 was evaluated by host range testing, adsorption and one-step growth assays, lytic activity, stability testing, biofilm disruption, whole-genome sequencing, and flow cytometry-based macrophage profiling. The phage showed rapid adsorption, a short latent period of approximately 30 min, and a burst size of about 165 phage particles per infected cell. It remained stable under moderate temperature and near-neutral pH conditions and significantly reduced preformed A. baumannii biofilm biomass in vitro. Genomic analysis identified a 41,354-bp double-stranded DNA genome lacking detectable lysogeny-associated genes, antibiotic resistance determinants, and known bacterial virulence factors. In THP-1 macrophages, AUBFM01 exposure was associated with reduced cell viability and with enrichment of a resting/intermediate-like CD86-defined phenotype among the remaining cells, including after endotoxin reduction. These findings identify AUBFM01 as a lytic anti-Acinetobacter phage with antibiofilm activity and notable macrophage-associated effects that warrant further mechanistic and safety investigation. Full article

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. Full article

Foodborne pathogens of Enterobacteriaceae are becoming an increasing global concern, with multidrug-resistant strains posing significant risks to food safety and public health, especially in high-risk products like dairy. This research focused on isolating, biologically characterizing, and genomically profiling new bacteriophages that target key Enterobacteriaceae members as potential biocontrol agents. Eight phages were isolated from wastewater using four bacterial hosts and analyzed through transmission electron microscopy, one-step growth analysis, adsorption kinetics, host range evaluation, whole-genome sequencing, comparative genomics, phylogenetic analysis, proteomic profiling, and virion assembly pathway characterization. All eight isolates exhibited icosahedral heads with contractile tails typical of Myoviridae morphology, demonstrated broad-spectrum lytic activity against 21 bacterial strains (infectivity: 47.6–95.2%), showed high adsorption efficiencies (84.75–99.98%), and had burst sizes ranging from 11 to 166 particles per cell. Genome sizes varied from 103 to 170 kb with coding densities between 92–96%. Importantly, none contained antimicrobial resistance genes, virulence factors, or lysogeny-associated elements, confirming their strictly lytic lifestyles and favorable biosafety profiles. Phylogenetic and comparative analyses indicated mosaic genomic structures influenced by horizontal gene transfer rather than host phylogeny. These findings provide a robust biological and genomic basis for evaluating these phages as potentially safe and effective alternatives to antibiotics in controlling foodborne Enterobacteriaceae, pending further in situ validation. Full article

Cronobacter sakazakii is a formidable foodborne pathogen that poses a severe, often fatal threat to neonates and immunocompromised individuals, with contaminated powdered infant formula as the primary transmission vehicle. Infections can lead to devastating conditions, such as meningitis, necrotizing enterocolitis, and sepsis, with alarmingly high mortality rates. Clinical management is hampered by the lack of standardized treatment guidelines and the emergence of antibiotic resistance. However, ongoing research into its molecular pathogenesis continually covers novel targets for intervention. In this review, we synthesize recent advances in our understanding of the sophisticated mechanisms that enable C. sakazakii to cause disease. We argue that its virulence hinges on a multi-faceted strategy, including efficient host invasion and tissue penetration via outer membrane proteins, sophisticated immune evasion tactics for intracellular survival, a repertoire of regulated virulence determinants, resilient biofilm formation, and robust stress response systems that ensure environmental persistence. As research continues to decipher these intricate host–pathogen interactions, we highlight promising future directions, including the development of rapid on-site diagnostics, the application of effective biocontrol strategies like phage therapy and probiotics, and the formulation of targeted therapeutic regimens. Ultimately, integrating these multifaceted insights is paramount to developing comprehensive strategies for preventing and controlling the global health burden imposed by C. sakazakii. Full article

The bacterium Yersinia enterocolitica serotype O:3 is targeted by two distinct agents, the bacteriophage φR1-37 and the bacteriocin-like enterocoliticin (a tailocin), which both utilize the lipopolysaccharide (LPS) outer core (OC) hexasaccharide as their primary host receptor. In order to understand this convergent recognition mechanism, we first characterized the enterocoliticin system, reporting the complete sequence of its large, biosynthetic gene cluster. Most of the 42 predicted gene products were functionally annotated by homology to known gene products. We then focused on identifying the receptor-binding proteins (RBPs) responsible for host attachment of both agents in order to elucidate a possible shared mechanism of binding. For phage φR1-37, the receptor binding complex was identified as the inseparable Gp298 tail fiber protein and its Gp297 trimerization chaperone, confirming its function as the RBP. Based on sequence identity with Gp298, the Orf39 gene product of the enterocoliticin cluster was predicted to be its corresponding RBP. An analytical comparison of the predicted RBPs revealed a highly conserved homologous region spanning 80–85 amino acid residues, which presents the only structural explanation for their identical receptor specificity. To resolve the binding mechanism, we generated high-confidence trimeric structural models for the Gp298 and Orf39 proteins using AlphaFold3-multimer. These models validated the high structural similarity of the RBP domains, despite global dissimilarity of the complete trimeric structures. Further docking simulations with a pentasaccharide ligand (generated by CarbBuilder) provided suggestive molecular models for the protein-carbohydrate interactions within the OC region. Intriguingly, a database search using the identified binding site motif revealed their wide and diverse presence in various phage tail proteins, suggesting that this motif is a specialized, common structure for carbohydrate recognition. This work identifies a conserved, novel sugar-binding motif as the molecular basis of host recognition for these key anti-Yersinia biologics. Full article

Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage–bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction–modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria–phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms. Full article

Background/Objectives: The gut microbiota is increasingly recognized as a key determinant of human health, playing a vital role in metabolism, immunity, and disease susceptibility. Dysbiosis, or microbial imbalance, is associated with gastrointestinal disorders such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and Clostridioides difficile infection (CDI), as well as extraintestinal conditions, including obesity, cardiovascular disease, and neuropsychiatric disorders. This review aims to provide an updated overview of emerging therapeutic strategies to modulate the gut microbiota to restore eubiosis and improve health outcomes. Methods: A narrative review of recent literature was conducted, focusing on preclinical and clinical studies investigating microbiota-targeted therapies. The review primarily covers innovative interventional approaches, including fecal microbiota transplantation (FMT), bacterial consortium transplantation (BCT), bacteriophage therapy and outer membrane vesicles (OMVs). Results: Evidence supports the role of probiotics, prebiotics, and synbiotics in remodeling microbial communities and improving host health, although their effects may be strain- and context-dependent. FMT has demonstrated high efficacy in the treatment of recurrent Clostridium difficile infections and is being studied for IBD, IBS and extraintestinal diseases, following the recent Food and Drug Administration approval of the first commercial FMT products. BCT offers a standardized alternative to donor-derived material, with early clinical successes such as FDA-approved SER-109. Phage therapy and OMVs represent promising frontiers, offering targeted microbial modulation and interactions with the immune system, although clinical data remain limited. Conclusions: Emerging gut microbiota modulation strategies offer new perspectives for precision medicine and could transform the prevention and treatment of many diseases, but further studies are needed to ensure their safety, standardization, and clinical application. Full article

Multidrug-resistant (MDR) Escherichia coli (E. coli) at the poultry–human interface motivates evaluating strictly lytic bacteriophages as targeted biocontrol candidates. A lytic E. coli phage (GADS24) was isolated from poultry waste in Saudi Arabia. Plaque formation and host range were assessed against 10 clinical E. coli isolates. Virion morphology was examined by transmission electron microscopy (TEM). Whole-genome sequencing (Illumina) and annotation (Prokka/RAST) were followed by comparative genomics (BLASTn 2.15.0, ANI JSpeciesWS: 2014–2025 Ribocon GmbH—Version: 5.0.3, dDDH GGDC: GGDC 3.0 and phylogenetic/proteomic analyses for taxonomic placement. GADS24 formed clear plaques and lysed 5 of 10 clinical E. coli isolates tested. TEM revealed an icosahedral capsid (~72.6 nm) and a contractile tail (~131.7 nm), consistent with Tevenvirinae/Mosigvirus morphology. The dsDNA genome is 168,896 bp (GC 43.8%) with 268 predicted ORFs and two tRNA genes (tRNA-Arg and tRNA-Met); no lysogeny-related genes were detected. The closest relative was Escherichia phage JN02 (98.44% ANI; 57.8% dDDH), supporting assignment to Mosigvirus while indicating a genome-resolved distinct lineage. The genome is available in GenBank (OQ703618). GADS24 represents a genome-resolved, strictly lytic Mosigvirus with in vitro biocontrol-relevant phenotyping against E. coli, supporting follow-up development for poultry-associated infection control and deeper phage–host interaction studies. Full article

Chronic Pseudomonas aeruginosa lung infections in cystic fibrosis (CF) represent one of the most treatment-refractory bacterial diseases, sustained by biofilm formation, metabolic dormancy, and adaptive antibiotic resistance evolution. While bacteriophage (phage) therapy has emerged as a promising alternative for multidrug-resistant (MDR) pathogens, clinical studies in CF have demonstrated transient reductions in bacterial burden without achieving complete eradication. This review integrates molecular, evolutionary, and immunological findings to explain the multifactorial barriers that limit phage therapeutic efficacy in chronic CF infections. We highlight three major obstacles: (i) bacterial dormancy and persistence within biofilms that restrict phage adsorption and replication; (ii) hypermutability and extensive genotypic diversification of CF-adapted P. aeruginosa, which accelerate phage resistance evolution and necessitate broad host-range coverage; and (iii) CF-specific immune constraints—including a dysfunctional innate immune system and phage-neutralizing humoral immunity—that reduce phage bioavailability and undermine sustained bacterial clearance. Emerging strategies to overcome these challenges include the discovery of dormant-targeting phages capable of replicating in metabolically quiescent cells, evolution-informed phage training to delay resistance evolution, and synthetic phage engineering approaches designed to disrupt biofilms and expand host-range coverage. In parallel, computational or artificial intelligence (AI)-guided frameworks for phage cocktail design and cystic fibrosis transmembrane conductance regulator (CFTR) modulator-mediated restoration of host immune function together offer a more integrated therapeutic paradigm that unites phage biology and host immune context. By unifying clinical outcomes with mechanistic, evolutionary, and immunological perspectives, this review outlines a next-generation framework for phage therapy in CF aimed at achieving more durable therapeutic outcomes. Full article

Antimicrobial resistance is a growing global health threat, necessitating alternatives to conventional antibiotics. Bacteriophages, viruses that specifically target bacteria, represent a promising option, and phage-loaded electrospun fibers have recently gained attention as wound dressings for localized phage therapy. However, the influence of phage morphology and scaffold design has been largely overlooked. This study investigates how phage morphology and structure, in conjunction with scaffold design and processing conditions, may influence the biological performance of electrospun scaffolds. A bilayer scaffold was developed comprising a supportive polycaprolactone (PCL)/gelatin (70:30) layer and a polyvinyl alcohol (PVA) top layer loaded with bacteriophages. Two phage types, short-tailed podovirus APTC-SL.1 and long-tailed myovirus APTC-Efa.20, were incorporated into PVA fibers to evaluate their antibacterial activity against Staphylococcus lugdunensis and Enterococcus faecalis, respectively. The fibers were characterized using XRD, FTIR, TGA, optical microscopy, SEM, TEM, wettability analysis, and in vitro degradation tests. Biological assessments included antimicrobial testing, phage viability, and phage release. The bilayer scaffold containing short-tailed phages preserved phage viability and produced clear zones of lysis against S. lugdunensis, with ≈8.15% viability retained after electrospinning and relatively controlled release, whereas long-tailed phages showed no antibacterial activity. These results suggest that phage structure and morphology, together with electrospinning conditions and scaffold architecture, may play an important role in maintaining phage functionality in wound dressing applications, while acknowledging that host–phage interactions may also contribute to the observed differences. Full article

Bt Cry toxins remain the cornerstone of transgenic crop protection against Lepidopteran pests, yet field-evolved resistance, particularly in invasive species such as Spodoptera frugiperda and Helicoverpa armigera, can threaten their long-term efficacy. This review presents a comprehensive and unified mechanistic framework that synthesizes current understanding of Bt Cry toxin modes of action and the complex, multilayered regulatory mechanisms of field-evolved resistance. Beyond the classical pore-formation model, emerging evidence highlights signal transduction cascades, immune evasion via suppression of Toll/IMD pathways, and tripartite toxin–host–microbiota interactions that can dynamically modulate protoxin activation and receptor accessibility. Resistance arises from target-site alterations (e.g., ABCC2/ABCC3, Cadherin mutations), altered midgut protease profiles, enhanced immune regeneration, and microbiota-mediated detoxification, orchestrated by transcription factor networks (GATA, FoxA, FTZ-F1), constitutive MAPK hyperactivation (especially MAP4K4-driven cascades), along with preliminary emerging findings on non-coding RNA involvement. Countermeasures now integrate synergistic Cry/Vip pyramiding, CRISPR/Cas9-validated receptor knockouts revealing functional redundancy, Domain III chimerization (e.g., Cry1A.105), phage-assisted continuous evolution (PACE), and the emerging application of AlphaFold3 for structure-guided rational redesign of resistance-breaking variants. Future sustainability hinges on system-level integration of single-cell transcriptomics, midgut-specific CRISPR screens, microbiome engineering, and AI-accelerated protein design to preempt resistance trajectories and secure Bt biotechnology within integrated resistance and pest management frameworks. Full article

Antibiotic resistance is arguably one of the greatest threats to global health today. The worldwide emergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae underscores the urgent need for alternative treatments. Bacteriophages (phages) are considered one of the most promising alternatives to address this crisis. In this review, we summarize current knowledge of phage–host interactions and highlight recent advances in phage therapy against K. pneumoniae, including phage cocktails, antibiotic combination therapy, and treatments based on phage-derived proteins. Despite their tremendous therapeutic potential, significant challenges remain. We therefore also discuss strategies to optimize phage research and recent innovations in the field. Full article

Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the ‘low–temperature–pathogen’ model and shifts focus to mucosal barrier dysfunction and host–microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host–microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention. Full article

Bulleidia extructa strain PP_925, isolated from the periodontal pocket of a patient with periodontitis, is a Gram-positive Bacillota with an unusually compact genome of 1.38 Mb. Phylogenomic analyses place PP_925 within Erysipelotrichales and show close relatedness of Bulleidia to Solobacterium and Lactimicrobium, as well as the existence of previously undescribed related clades. The metabolic repertoire of PP_925 is strongly reduced: it retains glycolysis, the phosphotransacetylase–acetate kinase pathway, and arginine catabolism but lacks the tricarboxylic acid cycle and most de novo biosynthetic pathways for amino acids, nucleotides, fatty acids, cofactors, and vitamins, implying reliance on salvage and cross-feeding. Phylogenetic inference indicates independent peptidoglycan losses in multiple mycoplasma Erysipelotrichia-related lineages, while PP_925 has retained an ancestral Gram-positive cell wall despite extensive genomic reduction. The genome preserves systems crucial for host interaction and adaptability, including a horizontally acquired tad locus encoding type IV pili, a comG competence system, and several adherence-associated virulence factors. Defense mechanisms are diverse and include a CRISPR-Cas II-A system, a type II restriction–modification module adjacent to Gao_Qat-like genes, and the Wadjet system in a genome without prophages; CRISPR spacers indicate repeated encounters with Bacillota phages. Comparative genomics of PP_925 and related strains reveals a small core genome with lineage-specific adhesion and defense modules, indicating recent shared ancestry combined with adaptive flexibility under substantial genome reduction. Full article

Bacteriophages, viruses that target bacteria, offer a promising alternative to antibiotics in the face of escalating bacterial resistance. Despite their discovery over a century ago, their widespread adoption has been impeded by regulatory challenges, limited funding, and the dominance of antibiotics. This review evaluates the current status of phage therapy by examining a comprehensive literature search, applying predefined inclusion and exclusion criteria. The review assesses selected scientific reports and clinical studies for their safety and efficacy profiles. Our findings indicate that advancements in phage therapy involve critical steps such as rapid bacterial detection, effective isolation, production, purification of phage preparations, and understanding their interactions with the host. Clinical studies generally show promising safety profiles with fewer adverse events compared to controls, and some trials suggest efficacy even at lower phage titers. Case reports further highlight phage therapy’s potential, demonstrating high success rates and minimal adverse events, although caution is advised due to potential biases. Despite promising results, significant research gaps remain, primarily due to the limited number of large-scale, well-designed clinical trials. Full article