MicrobiologyOpen最新文献

Olive pomace (OP) is a sludge arising from the production of olive oil, generated in increasing amounts in Portugal. The management of this toxic waste stream is complex and the number of processing plants is limited. In this study, OP was incorporated as a feed component for rearing black soldier fly larvae (BSFL) under industrial conditions. Larvae were reared inside a climate-controlled room with regulated temperature and humidity. The rearing cycle lasted 13 days, after which larvae were harvested. In addition to assessing bioconversion efficiency and larval proximate composition, the resulting frass was examined for its fertilizer potential. Frass was analyzed for plant nutrient content and microbial profile in three forms: fresh, heat-treated (70°C for 1 h), and pelletized. The inclusion of OP in the diets reduced waste-to-biomass conversion efficiency (21.5%_DM to approximately 13.3%_DM) but did not affect the proximate composition of the larval biomass, which consistently contained around 43%_DM crude protein and 20%_DM crude fat. Neither the presence of OP nor the applied post-treatments altered the nutrient composition of frass, which contained on average 3.5% total N, 2.6% P₂O₅, and 5.9% K₂O. However, at the highest inclusion level (84%), the abundance of bacterial and fungal groups was significantly reduced. The predominant phyla in the frass were Actinobacteria, Bacteroidota, Firmicutes, Proteobacteria, Ascomycota and Basidiomycota, and the dynamics of microbial communities were influenced by specific micronutrients. The presence of OP led to a significant reduction of potentially pathogenic bacteria and fungi in the frass, indicating a sanitizing effect attributable to this material.

Emerging evidence suggests that OBSCN, a giant cytoskeletal protein gene, plays multifaceted roles in cancer progression, yet its impact on gastric cancer (GC) remains poorly understood. Through integrative analysis of multi-omics datasets, we observe a close relationship between OBSCN expression and outcome of immunotherapy. Besides, elevated expression of OBSCN strongly associated with adverse disease free survival (DFS). Tumor-resident microbes, such as Fusobacterium, can impact the expression of microRNAs (miRNAs) targeting OBSCN. In terms of genomic alterations, mutational status of OBSCN is substantially associated with the alpha- and beta-diversity of intratumoral microbiome and patients with mutated OBSCN exhibit elevated higher tumor mutational burden (TMB) and better response to immunotherapy. Furthermore, machine learning models based on the OBSCN mutation-related gene signatures (OMRGS) achieve outstanding performance in prediction of response to immune checkpoint inhibitors. In summary, our findings position OBSCN as a novel molecular nexus linking genomic alterations, intratumoral microbiome dysbiosis, and immune infiltration in GC, providing a rationale for future biomarker-driven therapeutic strategies.

The rise in azole resistance among Nakaseomyces glabratus and Pichia kudriavzevii in recurrent vulvovaginal candidiasis presents a growing public health challenge. This study investigated the expression of antifungal resistance-related genes (ERG11, CDR1, CDR2, and MDR1) in clinical resistant (CR) and clinical and laboratory resistant (CLR) strains of these yeasts. Cervicovaginal samples from patients with recurrent infections were collected, microscopically examined, and cultured. Yeast species were identified phenotypically and genotypically, followed by drug sensitivity testing. Total RNA was extracted, reverse transcribed to complementary DNA, and real-time polymerase chain reaction was used to quantify target gene expression, comparing results to drug-sensitive controls. Non-Candida albicans species constituted 29% (45 cases) of the isolates, with N. glabratus (68%) and P. kudriavzevii (17%) being the dominant species. Other species included Candida parapsilosis, Meyerozyma guilliermondii, Candida orthopsilosis, Saccharomyces cerevisiae, and Rhodotorula mucilaginosa. Coinfections with P. kudriavzevii/C. albicans and N. glabratus/C. albicans were also observed. Ketoconazole, itraconazole, and 5-flucytosine demonstrated the best antifungal activity against most species. However, some N. glabratus isolates were resistant to miconazole, clotrimazole, and amphotericin B, while all P. kudriavzevii isolates resisted clotrimazole. Overexpression of the CDR1 gene was noted in N. glabratus (CR, 21.53 ± 1.26; CLR, 84.96 ± 0.67), and the ERG11 and CDR1 genes in P. kudriavzevii (ERG11 for CR, 28.56 ± 2.16; CDR1 for CLR, 35.89 ± 0.35). These results indicate that even in cases where an isolate is classified as susceptible by drug susceptibility testing, elevated gene expression may persist, and treatment should not be discontinued.

The emergence and dissemination of aquatic pathogens pose significant risks to farmed species. Francisella halioticida, initially reported in abalones and Yesso scallops, was recently isolated from mussels in France, with some isolates showing high virulence. This study aimed to characterize and compare several F. halioticida isolates from mussels using phenotypic and genotypic approaches. Phenotypic analysis was performed using growth curves, biochemical profiles (API strips), and morphology assessed by electron microscopy. Genetic analysis has been performed through whole-genome comparison using classification methods and virulence markers seeking. Phenotypic analyses highlighted similarities among FR22 isolates and notable differences with FR21 and AG1. Notably, AG1 displayed distinct features. Antibiotic resistance profiling revealed the species' capacity to withstand multiple antimicrobial agents with various modes of action. Complete, circular genomes were assembled and compared using targeted and untargeted approaches. These analyses confirmed the affiliation of FR22 isolates with the F. halioticida species, while FR21 and AG1 taxonomy need to be further investigated. Virulence factor screening revealed the presence of secretion system components (types I, IV, and VI) in all isolates. A novel variant of the Francisella Pathogenicity Island (FPI) was described, shared by all virulent isolates. However, this FPI was absent in the low virulence isolate FR22b. In conclusion, this study discriminates against F. halioticida isolates and proposes new hypotheses on their virulence, contributing to improved detection tools and expanding our understanding of this emerging aquatic pathogen.

The rise of antibiotic-resistant bacteria has intensified the search for alternative antibacterial strategies. Bacteriophage (phage) therapy is gaining attention as a promising approach, utilizing phage-derived proteins such as holins and endolysins to combat bacterial infections. In this study, the endolysin (UE-lysin) and holin (UE-holin) genes from Escherichia phage UE-M6 were characterized, and their antimicrobial activity was evaluated. In silico analysis revealed that UE-lysin has a modular architecture, with the N-terminal enzymatic activity domain that contains an N-acetylmuramidase of the glycoside hydrolase family GH108, and the C-terminal cell wall-binding domain that contains the peptidoglycan binding family PG_binding_3 domain. UE-holin was predicted to belong to class II holins, featuring two transmembrane helices. Furthermore, the genes encoding the UE-lysin and UE-holin were cloned and their expression optimized in Escherichia coli BL21 (DE3). The purified recombinant UE-lysin (27 kDa) and UE-holin (15 kDa) exhibited antibacterial activity against the E. coli host strain PSU-5266 (UE-17). The addition of the outer membrane permeabilizer ethylenediaminetetraacetic acid further enhanced their activity. Notably, the combined application of UE-holin and UE-lysin demonstrated greater antibacterial efficacy than either enzyme alone, highlighting a synergistic effect. Furthermore, UE-lysin and UE-holin exhibited high lytic activity against E. coli, Bacillus, and Staphylococcus aureus strains, underscoring their potential as candidates for treating both Gram-negative and Gram-positive bacterial infections.

Therapeutically utilized phages should optimally be produced in defined bacterial strains that are free of prophages and virulence factors. However, phage–host interactions in these production strains may be very different from clinical strains. Here, we characterized a lytic Staphylococcus aureus–specific phage vB_SauP_EBHT (EBHT), which had a dramatic change in its host specificity when produced in alternative host 19A2 compared with the original isolation host DSM 104437, even though there were no changes in the phage genome, proteome, structure, or adsorption efficiency. The reason for the altered host range was revealed to be based on different methylation patterns of the EBHT genome by host restriction–modification (R-M) systems in the two hosts. Even though the alternative host 19A2 produced a higher burst size, the host range of the produced phages was narrower. Together, these results illustrate that the most efficient production host may not necessarily be the most optimal one and that bacterial R-M systems should be considered when selecting the optimal phage-production host.

Pseudomonas aeruginosa is found in 48%–52% of chronic wound biofilms, where its resistance to antimicrobials and host immunity presents a major clinical challenge. Although hypochlorous acid (HOCl) is known to be an effective antimicrobial, its mechanism of action remains unclear because standard experimental conditions often produce a mixture of HOCl and hypochlorite (OCl⁻), making it difficult to isolate the effects of HOCl. Here, we use proteomic profiling to investigate the effects of a pure, stable HOCl gel on P. aeruginosa biofilms in a physiologically relevant chronic wound model. We applied HOCl gel (5.7 mM, pH 6) to mature P. aeruginosa biofilms established in a wound-mimicking flow model. Proteins were analyzed using tandem mass tag (TMT)-based quantitative proteomics, identifying 1,878 proteins. HOCl treatment significantly reduced biofilm viability and altered the abundance of 330 proteins. We observed substantial depletion of proteins involved in biosynthesis, virulence, antibiotic resistance, and biofilm formation, alongside enrichment of stress response proteins. These findings indicate a shift toward survival phenotypes and weakened pathogenicity. Our data reveal that HOCl disrupts multiple pathways essential for P. aeruginosa survival and virulence. Crucially, our experimental design eliminates confounding factors that can lead to unintentional testing of mixed HOCl and OCl⁻ species, allowing us to assess the specific effects of HOCl. These findings call for a re-evaluation of HOCl research methodologies and reiterate the importance of realistic infection models in antimicrobial testing.

Acinetobacter baumannii is a multi-drug resistant Gram-negative coccobacillus. It is responsible for high mortality among patients in the intensive care unit. Reported A. baumannii virulence factors include the thioredoxin system which plays a critical role in gene regulation and protein reduction. The Type IV pilus (T4P) is a well-known bacterial virulence factor that is associated with adhesion and molecular exchange. Previously, our laboratory revealed the role of A. baumannii thioredoxin A (TrxA) in pathogenesis by studying a trxA deletion mutant that downregulates T4P gene expression. TrxA, a potent disulfide bond reducer, might affect the assembly of pili by targeting T4P component proteins, including PilA, the major pilin protein of T4P which contains multiple cysteine residues required for disulfide bond formation. Using a transposon library derived from the AB5075 clinical isolate, we phenotypically characterized a pilA mutant strain and compared its pathogenesis to the wild type (WT) strain as well as another trxA mutant. Whole genome sequencing was conducted to confirm the disruption of trxA and pilA genes in the corresponding mutant strains of AB5075. Alteration of bacterial surface appendages in ΔtrxA and ΔpilA was visualized by Scanning electron microscopy. Like ΔtrxA, the T4P mutant ΔpilA had marked reduction of surface pili. Bacterial attachment to excised intestinal surfaces was greatly reduced for ΔtrxA and ΔpilA. Attenuation of ΔtrxA and ΔpilA in pathogenesis was further confirmed using a mouse sepsis model. Collectively, this characterized ΔpilA deficiency in A. baumannii resulted in attenuation of virulence making it a potential therapeutic target.

The evolutionary profile of hepatitis B virus (HBV) quasispecies may influence the clinical course of chronic hepatitis B (CHB), but few studies have characterized quasispecies according to hepatitis B e antigen (HBeAg) status. In this study, we analyzed 289 full-length HBV clones from 19 treatment-naïve CHB patients with long-term infection (> 10 years), comprising nine HBeAg-positive and ten HBeAg-negative, using molecular cloning and Sanger sequencing. Compared with HBeAg-positive patients, HBeAg-negative patients displayed higher quasispecies diversity (mean intrapatient sequence divergence 1.09% vs. 0.44%) and more complex phylogenetic structures. They also exhibited a greater number of positively selected sites, with 70.8% located within known T- or B-cell epitope regions, predominantly in the surface (S), polymerase (Pol), and X regions. Classical basal core promoter (BCP) and precore (PreC) mutations were detected in 52.8% of HBeAg-negative clones, often coexisting with wild-type strains. In patients lacking these classical BCP/preC mutations but showing sustained viremia, intrahost recombination was observed. Moreover, overlapping reading frames, particularly +1 frameshifts in Pol/S region, demonstrated asymmetric distribution patterns. In patients harboring deletion mutations, intact quasispecies were also maintained. Collectively, these findings reveal multiple adaptive strategies that sustain HBV replication and immune escape in HBeAg-negative patients, providing mechanistic insights for disease monitoring and therapeutic interventions.

The gut microbiome of breeder hens plays a pivotal role in reproductive efficiency, egg quality, and progeny development. Its composition is shaped by host factors such as age and genetics, as well as environmental influences, including diet and management practices. Importantly, the breeder gut microbiome is not only dynamic but also responsive to targeted interventions that can enhance intestinal health, metabolic function, and laying performance. Vertical transmission of maternal microbes through the cloaca and egg components provides offspring with a foundational microbial community, with the yolk sac serving as a critical reservoir for early colonisers that influence gut maturation, immunity, and growth. Emerging evidence further demonstrates that maternal nutritional strategies can programme the gut microbiota of progeny and intestinal development, highlighting the breeder microbiome as both a determinant and mediator of transgenerational performance. These insights underscore the potential of microbiome-focused approaches to improve reproductive success and sustainability in poultry production.