Fems Microbiology Letters最新文献

Arbuscular mycorrhizal (AM) fungi are fundamental to planetary health, enhancing plant nutrient uptake, stabilizing soils, and supporting biodiversity. Due to their prevalence and ecological importance, AM fungi are critical to achieving the environmental targets within the United Nations (UN) Sustainability Development Goals (SDGs) framework, including SDG 15: Life on Land. Despite these fungi engaging in the most widespread and ancient plant-microbe symbiosis, many fundamental aspects of the biogeography of AM fungi remain poorly resolved. This limits our ability to understand and document these fungal species' contributions to preserving terrestrial life on Earth. Using the largest global dataset of AM fungal eDNA sequences, we highlight that > 70% of ecoregions have no available data generated from soil using AM fungal specific metabarcoding. Drawing attention to these severe data gaps can optimize future sampling efforts in key habitats. Filling these gaps and developing a more complete picture on the biogeographic distributions of AM fungal species will help to clarify their contributions to environmental targets.

Taniborbactam (TAN) is an investigational β-lactamase inhibitor in clinical development combined with cefepime for the treatment of bacterial infections caused by broad-spectrum β-lactamase-expressing bacteria. Its spectrum of inhibition encompasses all classes of β-lactamases, including clinically important metallo-β-lactamases (MBLs) NDM-1 and VIM-2. However, TAN lacks a significant inhibition of imipenemase-type β-lactamases. Rare TAN-resistant New Delhi metallo-β-lactamase (NDM) or Verona integron-encoded metallo-β-lactamase (VIM) variants (namely NDM-9, NDM-30, and VIM-83) have been identified. The NitroSpeed Taniborbactam NP test was developed to rapidly assess the β-lactamase inhibitory activity of TAN against various β-lactamases, particularly serving as an efficient tool for identifying compounds with potential activity against different types of MBLs. The test is based on the hydrolysis of (i) nitrocefin (to determine the presence or absence of β-lactamase), (ii) ertapenem (to confirm the presence or the absence of carbapenemase), and (iii) TAN (to assess whether the carbapenemase is inhibited by TAN). The test was validated using a collection of 134 genetically characterized clinical isolates (103 Enterobacterales and 31 Pseudomonas aeruginosa). The NitroSpeed Taniborbactam NP test is simple, easy to perform, and provides results within ≤15 min. When evaluated against a broad set of β-lactamases, the test demonstrated 100% sensitivity, specificity, and accuracy.

Bacterial biofilms mediate chronic and recurrent bacterial infections that are extremely difficult to treat by currently available standards of care. In nature, these encased bacterial communities are typically comprised of more than one genus or species. Specifically, in the airway, nontypeable Haemophilus influenzae (NTHI) predominates and is commonly isolated with one or more of the following co-pathogens with which it forms unique relationships: methicillin-resistant Staphylococcus aureus, Burkholderia cenocepacia, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Moraxella catarrhalis. We recently showed that dual-genera biofilms comprised of NTHI plus a co-pathogen are disrupted when the biofilm matrix is destabilized by a pathogen-directed strategy that uses a humanized monoclonal antibody directed against the protective domains of bacterial DNABII proteins found at vertices of crossed strands of eDNA within the biofilm matrix. We also recently showed that a peptide synthesized from the host innate immune effector High Mobility Group Box 1 (HMGB1), called mB Box-97syn, competitively inhibits binding of the bacterial DNABII proteins to eDNA, which thereby also destabilizes single-species biofilms to release biofilm-resident bacteria into a transient yet highly vulnerable state that is more effectively cleared by the host innate immune system and/or antibiotics. Here, we expanded upon these studies to assess the ability of host-augmenting mB Box-97syn to both disrupt two-genera biofilms formed by NTHI plus a common co-pathogen, and prevent their formation. Disruption of established two-genera biofilms ranged from 57% to 88%, whereas prevention of two-genera biofilm formation ranged from 65% to 80% (P = .002 to P < .0001). The sobering recalcitrance of chronic and recurrent respiratory tract infections, combined with growing global concern of antimicrobial resistance (AMR), demands development of more effective management and prevention options. Ideally, novel treatment strategies would both target the pathogens and augment the host's natural abilities to eradicate them. Herein, we provide additional data to support continued development of the latter concept via demonstration of mB Box-97syn's efficacy against polymicrobial biofilms.

Nitrogen is important for fungal growth and development, and the GATA transcription factor AreA has been widely studied as a key regulator of nitrogen catabolite repression (NCR) in many fungi. However, AreB, another GATA transcription factor in the NCR pathway, remains less studied, and its role in Aspergillus flavus is still unclear. In this study, we characterized areB in A. flavus and investigated its role in regulating nitrogen utilization, fungal growth, and aflatoxin production. The areB gene produces three transcripts, with areB-α being the most abundantly expressed, particularly under nitrogen-limited conditions. Gene expression analysis via qPCR confirmed that areB acts as a negative regulator of NCR, as its deletion led to the upregulation of NCR-related genes under nitrogen-limiting conditions. Gene function analysis of areB revealed that its deletion impaired hyphal growth, reduced conidia production, and delayed conidial germination. Additionally, deletion of areB led to increased aflatoxin production, particularly under less favorable nitrogen sources, while overexpression of areB reduced aflatoxin levels. Furthermore, areB influenced sclerotia formation in a nitrogen-source-dependent manner. These findings reveal the multifaceted role of areB in nitrogen regulation, fungal development, and secondary metabolism, offering insights for controlling aflatoxin contamination and fungal growth.

The peptidoglycan stem peptides of the hyperthermophile Thermotoga maritima contain an unusual D-lysine (D-Lys) alongside the usual D-alanine and D-glutamate. We identified a Lys racemase that catalyzes racemization between L-Lys and D-Lys, and a diaminopimelate (Dpm) epimerase that catalyzes epimerization between LL-Dpm and meso-Dpm. Herein, we characterized a Dpm decarboxylase (TM1517) that catalyzes the conversion of meso-Dpm to L-Lys. TM1517 displayed high decarboxylase activity toward meso-Dpm but no activity toward LL-Dpm. D-Lys was not detected in the decarboxylation of meso-Dpm. The pH and temperature dependencies and kinetic parameters of decarboxylase activity were determined. Although other amino acid metabolizing activities of TM1517 were investigated, TM1517 did not exhibit any activities. Therefore, TM1517 is a Dpm decarboxylase associated with L- and D-Lys biosynthesis in T. maritima.

Stenotrophomonas maltophilia is an emerging global opportunistic pathogen that causes nosocomial infections. We demonstrated that the superoxide stress-sensing transcriptional regulator SoxR directly modulated the expression of an operon encompassing sodA1 (encoding manganese-containing superoxide dismutase) and fre (encoding putative flavin reductase) by directly binding to the operator site, which was located between the -35 and -10 motifs of the sodA1 promoter. It is known that upon exposure to the superoxide generators/redox-cycling drugs, the SoxR, which is bound to the operator site, became oxidized. This oxidation causes a conformational change of SoxR to an active form, enabling the upregulation of sodA1-fre gene expression. A ΔsodA1 was constructed, and the mutant showed enhanced sensitivity to the redox-cycling drugs, including menadione, plumbagin, and methyl viologen (paraquat), relative to its parental strain K279a. Thus, sodA1 may play a role in the survival of S. maltophilia under superoxide stress during either its saprophyte stage (e.g. exposure to redox-cycling drugs) or host-pathogen interactions.

The GH11 xylanase XynCDBFV, derived from Neocallimastix patriciarum, is widely used in various industries. However, its relatively low thermostability limits its potential. In this study, two computational approaches-Rosetta Cartesian_ddG and the deep learning-based tool Pythia-were employed to identify key residues affecting XynCDBFV thermostability. Both methods highlighted residues D57 and G201 as promising targets. Site-saturation mutagenesis at these positions yielded 18 variants with improved thermostability. Notably, three D57 variants (D57N/S/T) exhibited a 10°C increase in optimal temperature and retained 3.4%-21.7% higher residual activity than the wild type after 1-h incubation at 80°C. Five G201 variants (G201A/C/F/I/V) showed 5°C/10°C enhancements in optimal temperatures, with 10.1%-22.6% improved residual activity. These findings validate D57 and G201 as pivotal sites influencing thermostability. However, combining beneficial mutations from both sites led to reduced thermostability due to negative epistatic interactions. Comparative analysis revealed that while Rosetta Cartesian_ddG offers broader screening, it suffers from a high false discovery rate. In contrast, Pythia provides a balanced trade-off between precision and speed. This study offers a robust framework for enzyme thermostability enhancement and underscores the value of integrating computational predictions with experimental validation in protein engineering.

Helicobacter pylori is a significant human pathogen associated with gastric diseases, yet the contribution of plasmids to its pathogenicity remains largely unexplored. In this study, we combined plasmid network analysis, dereplication, functional annotation, and phylogenetic approaches to provide a comprehensive genomic and functional characterization of the H. pylori plasmidome using publicly available plasmid sequences. Of 322 plasmids analyzed, we identified 158 high-confidence plasmid sequences, representing 76 non-redundant plasmids (NR-plasmids). Notably, several sequences previously annotated as plasmids were reclassified as Integrative and Conjugative Elements. NR-plasmids were enriched in genes encoding Filamentation induced by cAMP (Fic) family proteins, which clustered into two distinct phylogenetic groups. Conserved motif analysis suggests that these two Fic protein types may form a novel toxin-antitoxin (TA) system, with Type-2 proteins potentially suppressing Type-1 activity, analogous to the TA mechanism described in Campylobacter fetus subsp. venerealis. Additionally, we identified genes encoding ATP-binding cassette (ABC) and major facilitator superfamily efflux pumps, as well as the virulence-associated protein D (VapD), which may contribute to antimicrobial resistance and host colonization, respectively. Our findings reveal the genomic and functional diversity of the H. pylori plasmidome and highlight the need for experimental validation to clarify its role in pathogenicity, antimicrobial resistance, and bacterial adaptation.

Salmonella contamination in chicken is a food safety problem that is widely concerned by all countries around the world. Based on the "One Health" concept, this study systematically collected samples from animals, the environment and workers across 5 stages of the broiler production chain (breeding farms, hatcheries, commercial broiler farms, slaughterhouses, retail) in China, to investigate the prevalence of Salmonella. Meanwhile, based on whole genome sequencing and risk assessment technology, combined with MLST, cgMLST traceability analysis was conducted to clarify the critical control points and transmission factors associated with Salmonella contamination. The results showed that the prevalence rate of Salmonella in the broiler production chain was 10.22% (469/4589). The broiler production chain encompassed 11 serotypes of Salmonella, with S.Enteritidis ran through the entire production chain. Fourteen types of ST were detected from 99 representative strains, and the dominant types were ST11, ST198 and ST1543. ST11 covered the samples from animals, environment and workers in all stages of broider production chain, and was further divided into 14 cgST types. Analysis using @RISK software revealed that the Spearman correlation coefficients for slaughterhouses and hatcheries were 0.54 and 0.26, respectively. These research findings are expected to comprehensively guide chicken production and provide effective strategies for preventing and controlling Salmonella contamination in the broiler production chain.

Phosphoenolpyruvate carboxylase encoded by ppc catalyzes the anaplerotic reaction of oxaloacetate in the tricarboxylic acid (TCA) cycle in Escherichia coli. Deletion of ppc does not prevent the cells from replenishing oxaloacetate via the glyoxylate shunt, but the ppc-deletion strain almost did not grow on glucose. In the present study, we obtained evolved strains by deleting both ppc and mutS to increase the mutation rate and investigated the mechanisms for improving growth by analyzing the mutated genes. Genome resequencing revealed that the evolved strains have non-synonymous mutations in icd encoding isocitrate dehydrogenase (ICDH). The introduction of icd mutations rescued the growth defects caused by ppc deletion. ICDH activity was strongly reduced by the amino acid substitutions G205D or N232S. The evolved strains appeared to suppress the competitive pathway for increasing the glyoxylate shunt flux. In metabolic engineering, the deletion of iclR, which encodes a repressor of the aceBAK operon, has been used to activate the glyoxylate shunt. The growth rate of the ΔppcΔiclR strain slightly increased, but it was still much lower than that of the Δppc + icdG205D strains. This finding suggests that iclR deletion is not sufficient to enhance glyoxylate shunt flux and that inactivation of the competitive pathway by icd mutations is more effective.