MicrobiologyOpen最新文献

The escalating prevalence of antibiotic resistance has become a major threat to the effectiveness of conventional antibiotics. Meanwhile, the development of novel antibiotics faces substantial challenges, including lengthy research cycles, high costs, and the rapid emergence of bacterial tolerance, making it difficult for new drugs to keep pace with bacterial evolution. In this context, molecular reversal strategies targeting antibiotic resistance genes have emerged as a promising avenue to overcome this impasse. Among them, the use of antibiotic adjuvants, agents that enhance the efficacy of existing antibiotics by inhibiting resistance gene function, preventing their horizontal transfer or modulating host defense has gained considerable attention. Furthermore, innovative approaches such as CRISPR-Cas gene editing, photodynamic therapy, nanotechnology, and ecological competition strategies have shown great potential in reversing antimicrobial resistance. Collectively, these strategies offer novel insights into addressing the global crisis of antibiotic resistance, paving the way for more effective clinical interventions and ensuring the sustained efficacy of current antibiotic therapies.

Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are well studied, microbial communities in cold terrestrial sulfur springs remain less understood. In this study, we used 16S rRNA gene sequencing to examine how sulfur availability and environmental conditions shape microbial assemblages across different biofilm types in a cold sulfur spring system at Blount Springs, Alabama (33.9301° N, 86.7928° W). Sulfur-oxidizing chemolithotrophs, including Sulfurovum and Halothiobacillus, represented the majority of the recovered reads in sulfur-rich white biofilms, while purple phototrophic biofilms were enriched with anoxygenic sulfur-oxidizing bacteria, such as Chromatium and Chlorobium. Nonsulfur biofilms from adjacent environments displayed greater microbial diversity, including a high abundance of photosynthetic diatoms, like, Melosira. Notably, Sulfurovum was abundant across both sulfur-rich and phototrophic niches, suggesting ecological flexibility and a central role in sulfur metabolism. These findings highlight the influence of sulfur chemistry and light availability in structuring microbial communities and contribute to a broader understanding of microbial adaptation and sulfur cycling in cold sulfur spring ecosystems.

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.

Expression of concern: A. Diop, E. Seck, G. Dubourg, N. Armstrong, C. Blanc-Tailleur, D. Raoult, and P.-E. Fournier, "Genome Sequence and Description of Gracilibacillus timonensis sp. nov. Strain Marseille-P2481^T, A Moderate Halophilic Bacterium Isolated from the Human Gut Microflora," MicrobiologyOpen 8, no. 2 (2019): e00638, https://doi.org/10.1002/mbo3.638. This Expression of Concern is for the above article, published online on 19 April 2018 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. In addition, a third party has reported that Figure 4a in this article has strong similarities with a figure published in an earlier article by the same authors. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.

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.

Feline calicivirus (FCV) is a primary cause of upper respiratory tract infections and oral ulcerative disease in cats and exhibits substantial genetic diversity that complicates prevention and control. In this study, we isolated the FCV-BJ616 strain, established a reverse-genetics system, and investigated its pathogenic mechanisms, thereby providing a foundation for antibody-based therapies and broad-spectrum vaccine development. The virus was purified by three rounds of plaque cloning, and its morphology was examined by electron microscopy. VP1 expression was confirmed by immunofluorescence and Western blotting. Using integrated systems-biology and reverse-genetics approaches, an infectious clone of rFCV-BJ616 was successfully assembled and rescued, exhibiting genetic stability comparable to that of the parental strain. In vivo infection experiments showed that rFCV-BJ616 retained wild-type virulence, causing persistent high fever, weight loss, and multiorgan pathology in infected cats. Proteomic analysis indicated that infection with FCV-BJ616 or rFCV-BJ616 markedly activated cytokine-mediated inflammatory signaling pathways. Both FCV-BJ616 and rFCV-BJ616 significantly upregulated the expression of IL-8, S100A8/A9, and TLR3, which are associated with acute inflammation and tissue damage. Furthermore, elevated IFN-β levels concomitant with STAT1 downregulation suggested a transient attenuation of antiviral signaling during early immune activation. These findings were corroborated by ELISA-based validation of serum cytokine profiles. Collectively, this study provides new insights into the molecular pathogenesis and evolution of FCV-BJ616 and establishes a robust reverse-genetics platform for precise genome manipulation and future vaccine development.

Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.

Stenotrophomonas maltophilia is a nosocomial and opportunistic microorganism with increasing antibiotic resistance rates. This study aimed to assess its biofilm production capacity, antibiotic resistance distribution, and the prevalence of biofilm- and resistance-related genes in clinical isolates. In this multiinstitutional study, 230 isolates were collected from hospitals across Iran between 2022 and 2024. Resistance trends were evaluated using disc diffusion and minimal inhibitory concentration E test methods, per Clinical and Laboratory Standards Institute guidelines. Crystal violet staining assessed biofilm production, while polymerase chain reaction (PCR) sequencing identified biofilm- and resistance-related genes. Real-time PCR was used to evaluate the relative expression of the smeD, smeE, and smeT genes, calibrated against TMP/SMX-sensitive control strains. Susceptibility rates to trimethoprim/sulfamethoxazole (TMP/SMX), levofloxacin, and minocycline were 97.39%, 93.47%, and 93.04%, respectively. TMP/SMX-resistant strains showed 19.8- and 16-fold higher expression of smeD and smeE, compared with sensitive isolates. The spgM gene was detected in all isolates, and 93.04% (n = 214) were biofilm producers, with most showing moderate-biofilm formation (n = 89, 38.70%). Additionally, the rpfF gene was closely associated with strong-biofilm formation (p ≤ 0.05). The L2, L1, smqnr, sul2, and sul1 resistance genes were identified in 214 (93.04%), 181 (78.69%), 135 (58.7%), 136 (59.1%), and 127 (55.2%) isolates, respectively. Our findings demonstrate that most isolates remain sensitive to TMP/SMX, while resistance to alternative antibiotics is rising. Moreover, biofilm production appears significantly associated with the rpfF gene.

Gallid alphaherpesvirus 1 (GaAHV-1), also referred to as infectious laryngotracheitis virus (ILTV), primarily targets the upper respiratory tract of chickens. This infection leads to significant economic setbacks worldwide in the poultry sector, driven by reductions in egg output, weight gain, and increased mortality rates. Even with the broad implementation of vaccination programs, ILTV outbreaks remain a challenge, as vaccine strains can revert to a virulent form under field conditions. This underscores the need to explore targeted therapeutic options, including a deeper understanding of GaAHV-1's nuclear trafficking mechanisms, critical for viral replication. The herpesvirus large tegument protein UL36 contains N-terminal nuclear localization signals (NLSs) that are essential for capsid routing to the nuclear pore complex (NPC). However, the mechanisms by which UL36 of GaAHV-1 mediates nuclear import remain poorly understood. In this study, we identified the NLS of GaAHV-1 UL36 and elucidated their binding mechanism with human nuclear import proteins. Using high-resolution crystal structures and quantitative assays, we mapped the specific residues and regions within UL36's N-terminal domain that facilitate binding to importin (IMP) α. Moreover, we revealed variations in binding affinities among different importin isoforms. Our biochemical and structural analyses demonstrate that the predicted N-terminal NLS of GaAHV-1 UL36 is critical for IMPα binding. These findings provide detailed molecular insights into the interaction between the GaAHV-1 large tegument protein and IMPs, paving the way for the development of targeted antiviral therapies.

Brucella-induced neuroinflammation represents a key mechanism in the development of neurobrucellosis. The objective of this investigation was to clarify the molecular pathways through which the BvrR contributes to neuroinflammation and cognitive dysfunction. Human microglial clone 3 (HMC3) cells were transfected with pcDNA3.1-BvrR-His to examine the effects of BvrR from Brucella abortus on endoplasmic reticulum (ER) function and the activation of activating transcription factor 2 (ATF2) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) p65. The role of phosphorylated inositol-requiring enzyme 1 (p-IRE1) in mediating BvrR-induced activation of ATF2 and NF-κB p65 was assessed by applying the IRE1 activator IXA4 and the IRE1 inhibitor GSK2850163, followed by evaluation with western blotting and RT-qPCR. Interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) concentrations in cell culture supernatants were quantified using ELISA. For in vivo analysis, HBAAV2/9-IBA-1-BvrR-6*HIS-ZsGreen was stereotactically delivered into the right hippocampus of mice. Expression of BvrR in HMC3 cells induced phosphorylation of IRE1 and expansion of the ER. This activation enhanced ATF2 and NF-κB p65 phosphorylation, facilitated their nuclear translocation, and significantly increased IL-6 and TNF-α expression at both the protein and mRNA levels. Inhibition of IRE1 with GSK2850163 suppressed these responses, whereas IRE1 activation with IXA4 reproduced the effects of BvrR. Findings indicate that BvrR from B. abortus activates IRE1, which subsequently stimulates ATF2 and NF-κB p65, leading to increased expression of IL-6 and TNF-α and the induction of inflammatory responses in HMC3 cells.