MicrobiologyOpen最新文献

The ability of gut microbes to degrade host- and diet-derived glycans is central to microbiome ecology and host interactions, yet predicting these functions in silico remains challenging. Hyaluronan (HA), a glycosaminoglycan (GAG) abundant in host tissues and dietary supplements, is depolymerized by specialized polysaccharide utilization loci (PULs) in Bacteroides. Here, we combined comparative protein analysis, functional assays, and quantitative proteomics to evaluate the reliability of sequence-based predictions of HA utilization. Clustering of more than 3900 PL8 and GH88 protein sequences from 54 Bacteroides species did not distinguish known HA degraders from nondegraders, underscoring the limited predictive power of these enzymes alone. Experimental validation in Bacteroides acidifaciens DSM 111135 and Bacteroides thetaiotaomicron DSM 2079 confirmed HA degradation, as HA-derived fragments were identified by liquid chromatography–mass spectrometry. Proteomic profiling revealed coordinated induction of both canonical GAG-specific PULs-encoded proteins and noncanonical accessory proteins (BT4410/BT4411) in response to HA in both species. Incorporating such noncanonical components into comparative frameworks may improve prediction of glycan utilization potential and help link microbial genomic content to ecological function in the gut.

This study investigated the usefulness of the IR Biotyper, which types bacterial strains using Fourier transform infrared (FT-IR) spectroscopy, against extended-spectrum β-lactamase (ESBL)- and metallo-β-lactamase (MBL)-producing Enterobacterales. Sixty-six clinical isolates (20 ESBL-producing Klebsiella pneumoniae, 15 IMP-producing K. pneumoniae, and 31 IMP-producing Enterobacter cloacae complex isolates) were analyzed using the IR Biotyper, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome single-nucleotide polymorphism (wgSNP) analyses and the results were compared. Of the 20 ESBL-producing K. pneumoniae strains analyzed, the IR Biotyper detected three clusters. Of these clusters, two were determined as respective clusters by PFGE and wgSNP analyses, and the strains included in each cluster showed the same STs. The IR Biotyper detected three clusters in the analysis of 15 IMP-producing K. pneumoniae strains. Of these clusters, strains in the two clusters showed high concordance with PFGE, MLST, and wgSNP analyses. The IR Biotyper identified six clusters among the IMP-producing E. cloacae complex isolates. These results were fully concordant with those of PFGE, MLST, and wgSNP analyses in the two clusters. The range of adjusted Rand index was 0.734–0.967 between the IR Biotyper and PFGE and 0.658–0.857 between the IR Biotyper and MLST or wgSNP analyses. This study demonstrated the performance of IR Biotyper for the detection of clonal similarities in ESBL- and IMP-producing Enterobacterales and it might be useful for outbreak investigation.

Gut microbe cultivation is essential for studying host-microbiota interactions. Traditional cultivation methods often fail to recover microbial species at low abundance (< 0.1%). To overcome this limitation, we employed the bent-capillary-centrifugal-driven (BCCD) method to encapsulate and cultivate fecal microbes in microdroplets. Fecal bacterial cells were distributed into ~50 nL microdroplets via the BCCD generator, and the microdroplets were dispersed in the oil phase and further incubated under controlled conditions. The BCCD method significantly increased the frequency of microbes at low abundance. Compared to the plate-based method, BCCD-based cultivation produced distinct microbial community structures and exhibited significantly lower temporal variation during cultivation (p < 0.05). Lineage-specific effect size (LEfSe) analysis revealed that BCCD-based cultivation enriched 29 low-abundant bacterial genera, whereas the plate-based method enriched 26. Using this method, we isolated 1,049 bacterial strains representing 123 species and 58 genera, including 8 novel species. Among the isolated and cultivated genera, 62.1% (36/58) were microbes of low abundance in the original fecal sample, and 41.4% (12/29) of the BCCD-specific enriched genera were successfully obtained. Notably, comparison with four major gut microbial culture studies revealed 45 species were exclusively recovered in this work. Taken together, the results demonstrated that our BCCD-based cultivation method effectively enriched and facilitated the isolation and cultivation of microbes at low abundance and novel gut bacterial species.

To identify potential therapeutic strategies for relapsed or refractory lymphoma (R/RL) by examining differences in gut microbiota composition and metabolic profiles between patients with R/RL and those with primary, treatment-naïve lymphoma (PL), using fecal microbiota analysis and metabolomics. A total of 21 patients with lymphoma were enrolled at the Department of Lymphoma and Oncology, Shanxi Bethune Hospital, between November 2023 and December 2024. The cohort included 14 patients with R/RL and 7 with PL, who served as the control group. Pretreatment fecal samples and clinical data were collected from all participants. Gut microbiota profiling was conducted using 16S rDNA sequencing, including alpha diversity, beta diversity, species composition, and differential abundance. Untargeted metabolomics was employed to identify and analyze differentially expressed metabolites between the groups. Patients with R/RL exhibited increased relative abundances of Actinobacteriota and Alphaproteobacteria and decreased levels of Erysipelotrichales, Morganellaceae, Faecalibacterium, Clostridium, Klebsiella, and Ruminococcus. Seven metabolites were significantly upregulated in the R/RL group (p < 0.05): 3-amino-4-methylpentanoic acid (p = 0.028), 2-hydroxybutyric acid (p = 0.020), UDP-N-acetylglucosamine (UDP-N-AG) (p = 0.011), pantothenic acid (p = 0.037), isoleucine (p = 0.028), glycine (p = 0.044), and alanine (p = 0.025). Literature review and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated enhanced central carbon metabolism and amino acid metabolism in cancer. Alterations in gut microbiota and metabolic activity may contribute to the pathophysiology of R/RL. Therapeutic modulation of the gut microbiota, including the use of fecal microbiota transplantation, may improve the intestinal immune microenvironment in this patient population. The present work is hypothesis-generating and requires large-scale validation.

Diarrheagenic Escherichia coli (DEC) is a leading cause of pediatric diarrhea, with antimicrobial resistance (AMR) complicating treatment. This study analyzed 350 E. coli isolates (175 DEC and 175 non-DEC) to determine molecular pathotypes, resistance patterns, and therapeutic targets. Polymerase chain reaction and 16S ribosomal RNA sequencing identified enteropathogenic E. coli as the most prevalent DEC pathotype (35%), followed by enterotoxigenic E. coli (25%), enterohemorrhagic E. coli (15%), enteroinvasive E. coli (10%), and diffusely adherent E. coli (20%). Phylogenetic analysis confirmed distinct clustering between DEC and non-DEC strains, revealing their evolutionary relationships. Antimicrobial susceptibility testing showed high resistance to ampicillin (87.6%), trimethoprim-sulfamethoxazole (75.5%), and erythromycin (100%), while carbapenems and colistin retained effectiveness. Functional analysis using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated enhanced metabolic and immune-related functions in DEC strains, differentiating them from non-DEC strains. Machine learning and bioinformatics-driven drug discovery identified Alatamide and Isosativan as potential therapeutic compounds, exhibiting strong binding affinities and structural stability against DEC virulence targets through molecular docking and molecular dynamics simulations. This study provides critical insights into the epidemiology, genetic diversity, and resistance patterns of DEC and non-DEC strains. The integration of bioinformatics and machine learning offers a promising strategy for discovering alternative treatments. Continuous AMR surveillance, responsible antibiotic use, and further experimental validation of identified drug candidates are essential to managing E. coli-associated diarrheal infections in pediatric populations and mitigating the global burden of multidrug-resistant pathogens.

Antimicrobial resistance is a critical global health crisis, driving renewed interest in natural alternatives like honey. Australia's diverse native flora offers unique opportunities for producing bioactive honeys, yet their antimicrobial potential remains underexplored. This study aimed to systematically evaluate the antimicrobial activity and chemical composition of Australian honeys from post-bushfire New South Wales landscapes and to identify key drivers of bioactivity and their therapeutic potential. Antimicrobial activity was assessed against Staphylococcus aureus and Escherichia coli using broth microdilution methods, measuring both total activity and non-peroxide activity. Comprehensive chemical profiling included bioactive compounds, quality parameters, sugars, organic acids, amino acids, volatiles, and secondary metabolites, assessed using standardized methodologies and ¹H-Nuclear Magnetic Resonance spectroscopy. Statistical analyses included correlation analysis, LASSO regression modeling, and principal component analysis. Most honeys exhibited strong antimicrobial activity, with 77% achieving MICs of ≤ 10% (w/w) against both pathogens, and 25% achieving ≤ 5% (w/w) against at least one pathogen. Honeys produced from mixed flora had consistently high levels of antibacterial activity, while monofloral honeys were much more variable. H₂O₂ was the strongest single factor associated with antibacterial potency, explaining 45%-46% of the variability in MIC values among samples. Including additional chemical parameters in multivariate models improved the ability to predict antibacterial strength, explaining up to 59% of the variation for S. aureus, and 73% for E. coli. The superior performance of mixed-flora samples challenges conventional assumptions favoring monofloral products and supports biodiversity-focused beekeeping practices, providing a foundation for developing Australian honeys as therapeutic alternatives while supporting sustainable industry recovery.

Estragole, a prime compound present in the essential oils (EOs) of Ocimum tenuiflorum and Tagetes lucida, shows significant antimicrobial activity against WHO priority bacterial pathogens. This study evaluated the bactericidal effects of estragole, both in its chemically pure form and when isolated from the EOs of these plants, when used alone and in combination with the antibiotics meropenem and tobramycin against multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria. Antibacterial activity was evaluated using the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) methods. The interaction of estragole with the selected antibiotics was analyzed using the checkerboard method, where the fractional inhibitory concentration index (FICI) was calculated. Results showed that estragole has inherent bactericidal properties, with MICs of no more than 256 μg/mL, indicating significant activity regardless of the bacteria's resistance profile. Combinations with meropenem and tobramycin exhibited pronounced synergy, achieving reductions in the MIC of up to 16-fold in over 88% of the bacteria tested. An additive or partially synergistic effect was evident in only around 11% of cases. These results highlight the potential of estragole as a therapeutic adjuvant capable of enhancing the efficacy of conventional antibiotics, reducing the required doses and the associated side effects and toxicities. Furthermore, this study emphasizes the beneficial potential of phytochemical-antibiotic combinations as an innovative strategy to address the growing threat posed by antimicrobial resistance.

During the quorum-sensing (QS)-active state, the Gram-negative phytopathogenic Ralstonia pseudosolanacearum strain OE1-1 activates the transcriptional regulator PhcA, regulating the QS-dependent genes including ralfuranone production-related genes such as ralA and major exopolysaccharide EPS I production-related genes such as xpsR encoding the transcriptional regulator XpsR, which are responsible for OE1-1 virulence. Ralfuranone affects the regulation of more than 80% (QS/Ral-dependent genes) of QS-dependent genes, indicating the ralfuranone-mediated feedback regulation of QS. To elucidate the mechanisms underlying the regulation of QS/Ral-dependent genes, we analyzed the transcriptomes of phcA-deletion (ΔphcA) and ralfuranone-deficient (ΔralA) mutants, as well as strain OE1-1 by RNA-sequencing. We found a novel TetR/AcrR family transcriptional regulator (RalT)-encoding gene (ralT); the expression level of ralT reduced significantly in ΔralA but not ΔphcA relative to expression level in strain OE1-1, and RalT negatively regulated ralT. A transcriptome analysis of the ralT-deletion mutant (ΔralT) showed that the ralT-deletion reduced the expression levels of 89.4% of positively QS/Ral-dependent genes including ralA and xpsR, while enhanced 44.6% of negatively QS/Ral-dependent genes. The transcript levels of these genes were positively correlated between ΔralT and ΔphcA or ΔralA, suggesting contribution of RalT to the regulation of some QS/Ral-dependent genes. However, the ralT-deletion enhanced EPS I production, suggesting that RalT represses the XpsR-independent factor(s), which is regulated PhcA and contributes to the EPS I production. Furthermore, ΔralT exhibited enhanced virulence, compared with strain OE1-1. Collectively, results of the present genetic study suggest that RalT contributes to the exquisite fine-tuning of OE1-1 virulence.

Vaginitis, a common gynecological ailment among women, poses a considerable health challenge with high recurrence rates even after conventional treatment. Vaginitis includes more common forms, such as bacterial vaginosis, vulvovaginal candidiasis, and Trichomonas vaginalis (TV), and less common forms, including senile vaginitis, infantile vaginitis, viral vaginitis, and mixed vaginitis. Conventional treatment approaches for vaginitis involve medications, such as metronidazole and clindamycin; however, long-term use of these agents raises concerns about adverse reactions, disruption of the vaginal ecosystem, and antibiotic resistance. Bioactive compounds from Traditional Chinese Medicine (TCM), known for their lower toxicity and multifaceted biological activity, are effective for treating vaginitis with fewer side effects and a focus on restoring a healthy vaginal microecology. TCM decoctions exhibit internal effectiveness, while local TCM treatments utilize external medications and modalities, such as irrigation and fumigation sitz baths. This review offers insights to guide vaginitis treatment and provides a theoretical foundation for the development and application of herbal therapies for vaginitis.

Pseudomonas aeruginosa poses a significant therapeutic challenge in pediatric patients with cystic fibrosis (CF) due to increasing multidrug resistance (MDR) and carbapenem resistance, underscoring the need for surveillance to guide treatment strategies. In this study, sputum and throat swab samples were collected from inpatient and outpatient CF children with pulmonary infection at the Children's Medical Center in Tehran, Iran. Isolates were identified using standard culture and biochemical methods, followed by antimicrobial susceptibility testing. Carbapenemase production was assessed phenotypically and by molecular detection of resistance genes, and genetic diversity was also evaluated using Random Amplified Polymorphic DNA (RAPD)–polymerase chain reaction (PCR). A total of 117 P. aeruginosa isolates were recovered (prevalence 17.41%), of which 94.9% were nonsusceptible to at least one antimicrobial agent. Carbapenem-resistant P. aeruginosa (CRPA) and MDR isolates accounted for 24.8% and 23.1% of isolates, respectively. Carbapenemase gene coexistence was significantly associated with MDR (ρ = 0.227, p = 0.014) and CRPA (ρ = 0.314, p = 0.001). Metallo-β-lactamase production was detected in 13.7% of isolates, while blaVIM was the most frequently identified carbapenemase gene (59%). RAPD–PCR demonstrated marked genetic heterogeneity, grouping isolates into 24 distinct clusters. Overall, the substantial burden of MDR and CRPA identified at this tertiary pediatric center highlights an urgent need for stricter antimicrobial stewardship, enhanced infection control measures, and ongoing surveillance to mitigate resistance spread and preserve therapeutic effectiveness in this vulnerable population. These findings warrant multicenter investigation to determine whether similar patterns exist across other Iranian pediatric CF facilities.