MicrobiologyOpen最新文献

The Cape Floristic Region, a biodiversity hotspot in South Africa, is characterised by acidic, nutrient-poor soils and distinctive fynbos vegetation. Despite the ecological importance and metabolic versatility of Acidobacteriota, their diversity and functional roles in fynbos soils remain poorly understood. This study investigated the diversity and abundance of Acidobacteriota in two nature reserves, Jonkershoek and Kogelberg, and the influence of soil abiotic factors and enzyme activities on their distribution and composition at the subdivision (SD) level. A total of 26 bulk soil samples were collected, and the V1–V9 regions of the 16S rRNA gene were sequenced using the Oxford Nanopore platform. The mean relative abundance of Acidobacteriota ranged from 1.5% to 36.25%. Subdivision 1 was the most dominant, with relative abundances of 66.96 ± 8.96% in Kogelberg Nature Reserve and 30.35 ± 0.15% in Jonkershoek Nature Reserve (p = 0.001). Other prevalent SDs included SDs 2, 3, and 5, with this study being the first to report the presence of SDs 22 and 17 in fynbos soils. Beta-diversity analysis revealed distinct community compositions between the two reserves, driven by soil pH, moisture content, available phosphate, electrical conductivity, and enzyme activities (p = 0.001). Several positive and negative correlations between Acidobacteriota SDs and soil properties were also identified. Overall, this study highlights the high diversity of Acidobacteriota in fynbos soils and their close associations with soil abiotic properties, underscoring the need for cultivation-based research to elucidate their ecological roles in these oligotrophic environments.

This systematic review and meta-analysis compared bacterial semi-quantification of respiratory samples from the BIOFIRE FILMARRAY Pneumonia (PN) Panels with quantitative and semi-quantitative culture methods (qCMs). Fourteen studies comprising 1,654 samples were included. Across both bronchoalveolar lavage-like and endotracheal aspirate-like specimens, the BIOFIRE PN Panel reported consistently higher bacterial loads than qCMs, with pooled mean differences of 1.17 and 0.95 log, respectively. Discrepancies decreased as culture-reported bacterial burden increased. The concordance rate in identifying the predominant pathogen was 94%, supporting the panel's clinical relevance. However, differential reporting at lower bacterial loads suggests that existing culture-based thresholds may not translate directly to molecular diagnostics. These findings highlight the need for pathogen- and method-specific interpretive thresholds to optimize the diagnostic utility of semi-quantitative molecular results and inform antimicrobial stewardship decisions.

The present study reports the isolation and molecular identification of Streptomyces sp. strain WSN-2 using 16S rRNA gene sequencing and BLASTn analysis (GenBank Accession No. MN128377), followed by its application in the green synthesis of silver nanoparticles (AgNPs). Biomass filtrate of Streptomyces sp. WSN-2 efficiently reduced silver ions to form stable AgNPs, confirmed by a characteristic UV-Vis surface plasmon resonance (SPR) peak at 423 nm. Structural and morphological characterization using FTIR, SEM, TEM, and EDX revealed spherical nanoparticles with a smooth texture and well-dispersed arrangement. TEM analysis indicated particle size predominantly between 50 and 60 nm (overall range 0.83–100 nm), while the zeta potential of –22.9 mV confirmed moderate colloidal stability. EDX spectra displayed strong elemental silver absorption peaks at 3-4 keV, indicating crystalline Ag formation. The biosynthesized AgNPs exhibited strong antimicrobial activity against wide range of pathogenic microbes. Maximum antibacterial growth inhibition zones were observed against S. typhi (24 ± 1.53 mm), followed by E. coli (23 ± 1.25 mm), B. subtilis (23 ± 1.73 mm), and P. aeruginosa (22 ± 1.53 mm). Antifungal assays revealed highest antifungal activity against A. flavus (16 ± 1.15 mm), and notable inhibition of A. niger (16 ± 1.25 mm), A. fumigatus (15 ± 1.70 mm), and F. oxysporum (14 ± 1.53 mm). MIC values ranged from 8.00 ± 0.05 µg/mL for P. aeruginosa to 18.000.07 µg/mL for A. fumigatus. The AgNPs also demonstrated remarkable antioxidant potential, achieving 65.2% H₂O₂ scavenging activity at 50 µg/mL, surpassing L-ascorbic acid (45.1%). These findings highlight Streptomyces sp. WSN-2 as a promising biogenic source for the synthesis of stable AgNPs with significant antibacterial, antifungal, and antioxidant potential.

Microbial degradation of lignin is important to carbon cycling. The gut microbiome of wood-feeding Hypomeces squamosus Fabricius has been shown to degrade lignin efficiently. However, the specific degradation mechanisms remain incompletely understood. In this study, we investigated the mechanism of lignin degradation using omics comparative analysis, focusing on differentially expressed genes and metabolic pathways in the gut microbiome of insects fed with a lignin-rich diet. The dominant genus taxon was Pantoea (29.82%), which was predominant in insects fed with high lignin-containing Iris ensata Thunberg, whereas Wolbachia and Enterobacter were predominant in insects fed with cabbage leaves (MHS_K group). Furthermore, expression levels of carbohydrate-active enzymes from the auxiliary activities (AAs) families in the MHS_I group were 1.18 times higher than those in the MHS_K group. These mainly included lignin peroxidase and manganese peroxidase of the AA2 family, vanillyl-alcohol oxygenase of the AA4 family, and 1,4-benzoquinone reductase of the AA6 family. Expression levels of multiple genes encoding aromatic compound-degrading genes (2303 accounted for 75.76% of the total upregulated genes) were found, including about 0.03% was related to lignin degradation. Genes MHS-HN_11398_2 (protocatechuate 2,3-dioxygenase) and MHS-HN_4821_1 (muconolactone d-isomerase) were enriched in the MHS_I group. Three lignin-degrading pathways were found: ortho-cleavage and meta-cleavage of catechol, as well as ring-opening of protocatechuate. This study provides a comprehensive and theoretical evidence of the gut microbiome roles of H. squamosus Fabricius in lignin degradation.

Antimicrobial resistance continues to rise globally, with biofilm-associated infections intensifying the clinical burden through persistent tolerance to antibiotics and evasion of immune responses. Biofilms, structured microbial communities embedded in a protective extracellular matrix, underlie many chronic and recurrent infections, including endocarditis, urinary tract infections, cystic fibrosis lung disease, and device-related infections. Conventional antibiotics often fail in these contexts, and the discovery pipeline for novel agents remains limited. Nanotechnology has therefore emerged as a promising alternative, offering unique physicochemical features that enable enhanced penetration into biofilm matrices, improved drug stability, and targeted delivery of therapeutic agents. Diverse nanosystems, including metallic, polymeric, lipid-based, and ligand-functionalized platforms, have shown encouraging results in vitro and in vivo, demonstrating superior biofilm disruption and bacterial eradication compared with conventional therapies. Nevertheless, translating these advances into clinical practice remains challenging. Key barriers include complex and costly synthesis, scalability under good manufacturing practices, limited drug loading efficiencies, variability of preclinical biofilm models, regulatory uncertainties, and the risks of nanoparticle (NP)-induced toxicity, unpredictable biodistribution, and potential resistance development. Moreover, the dynamic interactions between NPs, host fluids, and biofilm extracellular matrices complicate pharmacokinetic and pharmacodynamic predictability. Addressing these obstacles requires coordinated efforts to refine manufacturing processes, standardize biofilm models, and implement nanospecific regulatory frameworks. With careful optimization, nanomedicine holds the potential to redefine the therapeutic landscape for biofilm-related infections.

Front cover caption: The cover image is based on the article Genomic and Metabolic Characterization of a Potentially Novel Paenibacillus Species Isolated as a Laboratory Contaminant Growing on Medium Supporting Cotton Tissue Culture by Sanjay Antony Babu et al., 10.1002/mbo3.70107.

Front cover caption: The cover image is based on the article Diarrheagenic and ESBL Potential of Escherichia coli From Publicly Shared Common Touch Surfaces by S.M. Lutful Kabir et al., 10.1002/mbo3.70125.

Coagulase-negative staphylococci (CNS) and Mammaliicoccus species recently reclassified from the Staphylococcus sciuri group, are increasingly recognized as opportunistic pathogens in dairy animals and humans. This study investigated phylogenetic diversity and antimicrobial resistance in raw caprine milk from Sudan by integrating conventional bacteriological methods, molecular sequencing, and antimicrobial susceptibility testing. Raw goat milk samples were cultured, and presumptive CNS isolates were identified using phenotypic tests (novobiocin, oxidase, urease, and carbohydrate fermentation) following the standard Staphylococcus identification flow chart. PCR amplification of the elongation factor Tu (tuf) gene and the methicillin-resistance gene (mecA) enabled molecular confirmation and assessment of antimicrobial resistance. Sequenced tuf amplicons (~370 bp) were analyzed by BLAST and aligned in MEGA 12 for maximum-likelihood phylogenetic reconstruction. Staphylococcus simulans and Mammaliicoccus lentus were isolated in this study; antimicrobial susceptibility testing revealed that S. simulans, but not M. lentus, was methicillin-resistant and carried the mecA gene. Partial tuf gene sequencing confirmed 99.6%–99.7% identity with reference strains of the respective species. Phylogenetic analysis revealed that the isolated S. simulans formed a distinct branch within the global clusters. Meanwhile, M. lentus was found to be closely related to the global strains, showing only minor divergence. This study reports the presence of S. simulans and M. lentus in caprine milk from Sudan using both phenotypic and genotypic identification methods. This underscores the importance of integrating traditional laboratory methods with molecular techniques for precise species identification. The identification of methicillin-resistant S. simulans highlights the need for ongoing monitoring of CNS in raw milk.

Antibiotic-resistant bacteria represent a major global challenge as increasing infections become recalcitrant to standard treatments. A lack of novel therapeutics entering the market in the past 30 years further exacerbates this issue and highlights the importance of identifying and validating novel antibiotic targets. In this study, we explored prospective therapeutic targets by examining two metabolites in the lysine biosynthesis pathway, meso-diaminopimelate (DAP) and lysine, within the critically listed pathogen Pseudomonas aeruginosa. These metabolites are involved in bacterial cell wall and protein synthesis; therefore, enzymes present in this pathway represent potential targets for novel therapeutics. To elucidate the validity of these targets, we generated for the first time, gene deletion mutants of the P. aeruginosa DHDPR- and DAPDC-encoding genes using a two-step allelic exchange method. Both the mutants resulted in a lethal phenotype that could be rescued by supplementation with meso-DAP and/or lysine. We subsequently characterized the mutants' pathogenicity in a Galleria mellonella infection model. The DHDPR mutant was unable to provide a lethal infection in this model. Given the importance of these metabolites to membrane and cell wall synthesis, we investigated membrane permeability utilizing a fluorescent probe assay and transmission electron microscopy. Due to their increased membrane permeability, these mutants exhibited greater sensitivity to antibiotics commonly used against Pseudomonas infections. Overall, this study highlights that targeting the lysine biosynthesis pathway could enhance bacterial susceptibility to existing antibiotics, supporting its development as an adjuvant strategy to potentiate current treatments and extend their clinical utility.

Aptamers, short nucleic acid sequences with high specificity and affinity for their targets, are promising candidates for diagnostic applications due to their ability to detect a wide range of pathogens. We present a fluorescent bioimaging approach for detecting Pseudomonas aeruginosa, based on aptamer F23. Conjugated with fluorescent dye, its detection efficacy was evaluated on 15 Gram-negative and -positive bacteria, including fixed and live cells, as homogeneous and heterogeneous populations. We developed an automated, open-access software for quantifying microscopy images. Its high sensitivity enables accurate quantification of bacteria labeled with aptamers. For example, it successfully detected 1122 P. aeruginosa cells labeled with aptamer F23 out of a total of 1123 P. aeruginosa cells in a single image. With 200,000 analyzed bacteria, we demonstrated that the aptamer effectively detects various reference and clinical strains of P. aeruginosa, while failing to detect Gram-positive Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus epidermidis, and Corynebacterium striatum, as well as Gram-negative Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli. This aptamer is therefore a promising tool to distinguish P. aeruginosa from different strains of the skin microbiota. However, our quantitative method also revealed partial labeling to other bacterial cells, highlighting the issue of refining aptamer selection to improve selectivity.