Fems Microbiology Letters最新文献

{"title":"An engineered peptide derived from the innate immune effector high-mobility group box 1 disrupts and prevents dual-genera biofilms formed by common respiratory tract pathogens.","authors":"Jaime D Rhodes, Tyler J Kelly, Steven D Goodman, Lauren O Bakaletz","doi":"10.1093/femsle/fnaf029","DOIUrl":"10.1093/femsle/fnaf029","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of crystal violet staining, microscopy with image analysis, and quantitative PCR to examine biofilm dynamics.","authors":"So-Yeon Jeong, Ji Won Lee, Eun Ji Kim, Chi Won Lee, Tae Gwan Kim","doi":"10.1093/femsle/fnae115","DOIUrl":"10.1093/femsle/fnae115","url":null,"abstract":"<p><p>Crystal-violet staining, microscopy with image analysis, and quantitative PCR (qPCR) were compared to examine biofilm dynamics. Biofilms of 30 polycultures comprising 15 bacterial species were monitored for 14 days. Collectively, qPCR (representing population) revealed a different growth pattern compared to staining (biomass) and microscopy (colonization): biomass and colonization gradually increased over time, whereas population increased rapidly for the first seven days and leveled off. Temporal forms were categorized into two growth patterns: continuous increase (CI) and non-continuous increase. Staining and microscopy showed similar odds of detecting the CI pattern (27 and 23 polycultures, respectively) across polycultures, greater than that of qPCR (14 polycultures) (P < 0.05). All three methods revealed the identical patterns for 13 polycultures. Staining with microscopy, staining with qPCR, and microscopy with qPCR found the same patterns in 22, 15, and 19 polycultures, respectively. Additionally, staining was quantitatively agreed with microscopy (P < 0.05; R2 > 0.50), whereas neither staining nor microscopy strongly agreed with qPCR (P < 0.05; R2 ≤ 0.22). Collectively, staining was more compatible with microscopy than qPCR in characterizing biofilm dynamics and quantifying biofilms owing to the difference between population growth and biofilm expansion. The concurrent use of qPCR with biomass estimations allows for accurate and comprehensive biofilm quantification.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The NitroSpeed Taniborbactam NP test as a rapid test for detection of β-lactamase-mediated susceptibility to taniborbactam.","authors":"Otávio Hallal Ferreira Raro, Soraya Herrera-Espejo, Maxime Bouvier, Auriane Kerbol, Laurent Poirel, Patrice Nordmann","doi":"10.1093/femsle/fnaf044","DOIUrl":"https://doi.org/10.1093/femsle/fnaf044","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":"372 ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12065395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibiofilm activity of Clitoria ternatea flowers anthocyanin fraction against biofilm-forming oral bacteria.","authors":"Allimalar Sathiaseelan, Keang Peng Song, Hock Siew Tan, Wee Sim Choo","doi":"10.1093/femsle/fnaf035","DOIUrl":"10.1093/femsle/fnaf035","url":null,"abstract":"<p><p>This study investigated the antibiofilm effects of Clitoria ternatea flowers anthocyanin fraction (AF) on Streptococcus mutans, Actinomyces viscosus, and Aggregatibacter actinomycetemcomitans. AF was obtained using column chromatography, and liquid chromatography-mass spectrometry was employed for its characterization and identification. The crystal violet assay and scanning electron microscopy analysis revealed significant inhibition of early biofilm formation and destruction of preformed biofilms after AF treatment (0.94-15 mg ml-1). Antiadhesion assay on acrylic teeth demonstrated that AF effectively hampered sucrose dependent and independent attachment. Importantly, growth curve and pH drop assays showed that AF inhibited pH reduction for all bacteria tested without hindering bacterial growth. Furthermore, the tetrazolium-based cytotoxicity assay indicated no toxicity towards normal human gingival fibroblasts at 0.78-12.5 mg ml-1. These findings suggest C. ternatea anthocyanins are promising antibiofilm agents for oral biofilm control, acting during both initial formation and on mature biofilms.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contributions of hemolytic proteins in virulent Aeromonas hydrophila to motile Aeromonas septicemia disease of channel catfish (Ictalurus punctatus).","authors":"Dunhua Zhang, Jun Feng, Yi Wang, Craig A Shoemaker, Allison A Wise, Benjamin H Beck","doi":"10.1093/femsle/fnae108","DOIUrl":"10.1093/femsle/fnae108","url":null,"abstract":"<p><p>Hemolytic proteins are a major group of virulence factors in pathogenic Aeromonas hydrophila. Six genes encoding presumable hemolytic proteins were revealed from the genome of virulent A. hydrophila (vAh) that caused severe disease in channel catfish. The aim of this study was to assess the contribution of these hemolytic proteins to the virulence of this bacterium. Genes coding for following six proteins were investigated: aerolysin (Arl), 21-kDa hemolysin (Hly1), thermostable hemolysin (Hly2), phospholipase/lecithinase-related hemolysin (Hly3), membrane-associated hemolysin III (Hly4), and cytolysin-associated hemolysin (Hly5). Individual genes were deleted from the bacterium using CRISPR-Cas9 mediated methods. Assessment showed that deletion of Arl gene (Δarl) completely abolished hemolytic activity of this mutant while Δhly1-Δhly5 mutants had the same activity as the wild vAh. Extracellular proteins (ECPs) of the Δarl mutant caused significantly (p < 0.01) less cell death in vitro with viability increased by approximately 20%, compared to the wild vAh. ECPs of mutants Δhly1-Δhly5 remained the same cell toxicity as the wild vAh. A second deletion of hly5 from the Δarl mutant further lowered the cell toxicity of the ECP of the mutant (Δarl + Δhly5). Assays in vivo showed that both Δarl and Δhly5 mutants caused less fish mortality with reduction of 57% and 16%, respectively, compared to the wild vAh; the Δarl + Δhly5 mutant caused the least mortality with approximately 87% of reduction; and other mutants had the same virulence as the wild vAh. Analyses of SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and Western blotting evidently indicate that both Arl and Hly5 proteins formed hexamer-like stable structures post secretion from the bacterium. Arl and Hly5 apparently had synergistic action in cytotoxicity and causing disease and were the major virulence factors among the six hemolytic proteins analyzed in this study.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The GATA factor AreB regulates nitrogen metabolism, fungal development, and aflatoxin production in Aspergillus flavus.","authors":"Qing-Qing Zhi, Zhen-Long Wang, Pei-Bo Yuan, Lei He, Zhu-Mei He","doi":"10.1093/femsle/fnae110","DOIUrl":"10.1093/femsle/fnae110","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functionally important components of the transcription elongation complex involved in Rho-dependent termination.","authors":"Ajay Khatri, Ranjan Sen","doi":"10.1093/femsle/fnae111","DOIUrl":"10.1093/femsle/fnae111","url":null,"abstract":"<p><p>Bacterial transcription terminator, Rho is an RNA (Ribonucleic Acid)-dependent ATPase that terminates transcription. Several structures of pretermination complexes of the Rho-transcription elongation complex (EC) revealed a static picture of components of the EC that come close to the nascent RNA-bound Rho, where many of the residues of EC reside ≤10 Å from the Rho residues. However, the in vitro-formed Rho-EC complexes do not reveal the in vivo Rho-EC dynamic interaction patterns during the termination process. Here we report synthetic defect analyses of various combinations of the mutations in RNAP β, β' and ω-subunits, NusA, NusG, and Rho proteins to delineate the functional network of this process. Several mutations in the β-flap and β'-Zn-finger and -Clamp helices domains of RNAP are synthetically defective in the presence of Rho mutants indicating functional involvement of these domains. Mutations in the NusA RNA-binding domains were synthetically defective with the Rho mutants suggesting its involvement. Our genetic analyses also revealed functional antagonisms between the ω-subunit of RNAP and the NusG-CTD (c-terminal domain) during termination. We concluded that the regions surrounding the RNA exit channel, the RNA-binding domains of NusA, the RNAP ω-subunit, and NusG-CTD constitute a functional network with Rho just before the onset of in vivo Rho-dependent termination.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mycorrhizal inoculation success depends on soil health and crop productivity.","authors":"Ido Rog, Marcel G A van der Heijden, Franz Bender, Raphaël Boussageon, Antonin Lambach, Klaus Schlaeppi, Natacha Bodenhausen, Stefanie Lutz","doi":"10.1093/femsle/fnaf031","DOIUrl":"10.1093/femsle/fnaf031","url":null,"abstract":"<p><p>As the human population grows, so does the demand for higher agricultural yields. As a result, agricultural intensification practices are increasing while soil health is often declining. Integrating the benefits of microorganisms into agricultural management systems can reduce the need for external resource inputs. One particular group of plant symbionts that can help plants to acquire additional nutrients and promote plant growth are arbuscular mycorrhizal fungi (AMF). The application of AMF in agricultural practice has been hampered by the variability in the success of mycorrhizal inoculation and the lack of consistency in different fields. Here, we tested whether it is possible to predict mycorrhizal inoculation success based on soil health and productivity. We hypothesized higher inoculation success on fields with poor soil health because in such fields, mycorrhiza can improve nutrient uptake and biotic resistance to pathogens. We calculated a soil health index by aggregating six biotic and abiotic variables from 54 maize fields and tested its correlation with the mycorrhizal growth response (MGR). The MGR was linked to soil health and significantly higher in less healthy soils and less productive fields. This implies that soil inoculation with AMF has most potential in fields with poor soil health and low productivity. Based on these findings, we propose a soil health framework that highlights the potential benefits of AMF field inoculation.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143614088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Growth inhibition by ppc deletion is rescued by isocitrate dehydrogenase mutations in Escherichia coli.","authors":"Yoshihiro Toya, Tatsumi Imada, Mai Ishibashi, Yuichi Kawamoto, Kinuka Isshiki, Atsushi Shibai, Chikara Furusawa, Hiroshi Shimizu","doi":"10.1093/femsle/fnaf013","DOIUrl":"10.1093/femsle/fnaf013","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochemical characterization of diaminopimelate decarboxylase from the hyperthermophile Thermotoga maritima.","authors":"Tetsuya Miyamoto, Akari Yazawa, Rio Mishima, Kumiko Sakai-Kato","doi":"10.1093/femsle/fnaf024","DOIUrl":"10.1093/femsle/fnaf024","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}