Microbiology-Sgm最新文献

{"title":"Microbe Profile: <i>Streptomyces venezuelae -</i> a model species to study morphology and differentiation in filamentous bacteria.","authors":"Max L Jordan, Susan Schlimpert","doi":"10.1099/mic.0.001541","DOIUrl":"10.1099/mic.0.001541","url":null,"abstract":"<p><p><i>Streptomyces</i> bacteria are renowned for their multicellular lifestyle and production of bioactive molecules (natural products) with important applications in medicine, agriculture and industry. Studies of several <i>Streptomyces</i> species have provided a foundational understanding of their biology and metabolism. However, investigating the spatiotemporal processes governing the morphogenesis and development of these remarkable bacteria has been technically challenging due to their complex life cycle. The adoption of <i>Streptomyces venezuelae</i> as a new experimental model species has overcome these limitations and opened the door to fully explore the regulation and cell biology of <i>Streptomyces</i> development. A key advantage of <i>S. venezuelae</i> is its ability to complete its entire life cycle in liquid culture, facilitating the effective use of genome-wide analysis techniques and advanced cell biology approaches. This has provided significant new insights into the regulatory networks and molecular mechanisms underlying <i>Streptomyces</i> growth, division, developmental transitions and genome organization.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626547","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":"Glucose alters the evolutionary response to gentamicin in uropathogenic <i>Escherichia coli</i>.","authors":"Shalini Choudhary, Jacob A Smith, Alan McNally, Rebecca J Hall","doi":"10.1099/mic.0.001548","DOIUrl":"https://doi.org/10.1099/mic.0.001548","url":null,"abstract":"<p><p>Urinary tract infections (UTI) are a major health and economic concern. Uropathogenic <i>Escherichia coli</i> (UPEC) are the leading cause of UTI, and antibiotic-resistant UPEC are increasingly common. The microenvironment of the urinary tract is metabolically distinct, and there is growing interest in understanding the extent to which metabolism may influence UPEC infection and response to antibiotics, and how this varies between individuals. Diabetes, characterized in part by glycosuria, is a known risk factor for UTI and is associated with more severe infections. The role that glucose plays in driving UPEC evolution remains unclear. Through experimental evolution with a single UPEC isolate, we identified mutations in the RNA polymerase sigma factor <i>rpoS</i> associated with long-term glucose exposure. We found that the presence of the antibiotic gentamicin resulted in mutations in genes including <i>trkH</i>, which encodes a potassium ion uptake system previously linked to aminoglycoside resistance, and in the autotransporter <i>hyxB</i>. Strikingly, these mutations were not present in populations exposed to a combination of both glucose and gentamicin. This suggests that glucose may influence the survival of mutants in gentamicin, providing new avenues for understanding the evolution and treatment of UPEC-mediated UTI in high-risk individuals.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736241","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":"Phosphorelay changes and plasticity underlie the life history evolution of <i>Bacillus subtilis</i> sporulation and germination in serial batch culture.","authors":"Kathleen A Sagarin, Elizabeth Ouanemalay, Hilda Asante-Nyame, Vera Hong, Chloe De Palo, Frederick M Cohan","doi":"10.1099/mic.0.001540","DOIUrl":"10.1099/mic.0.001540","url":null,"abstract":"<p><p>Bacterial endospores facilitate survival in extreme and unpredictably fluctuating environments. However, under abundant nutrient conditions, the production of endospores is quickly reduced or lost. We hypothesized that endospore-forming bacteria exposed to frequent cycling of nutrient availability would evolve reduced sporulation efficiency. We employed replicated batch culture for 11 transfers to test the effects of rapid nutrient cycles on the evolution of the life history traits of sporulation, germination and growth in <i>Bacillus subtilis</i>. We periodically measured total cell and endospore densities during the period between transfers. Replicates evolved in parallel behaviourally and genetically. By the fourth transfer, we saw a reduction in endospore production, which continued to decline throughout the experiment. Our results support a decreased likelihood of sporulation being driven by frequent nutrient renewal. The proportion of endospores germinating after transfer increased significantly by the end of the experiment through the effects of plasticity alone. Every evolved replicate culture displayed colony dimorphism: the dominant morphology being translucent with reduced sporulation ability and the rarer being opaque with accelerated sporulation and highly efficient germination. Colony dimorphism was reflected in the genomes, with all isolates with reduced sporulation having mutations in elements of the sporulation phosphorelay, particularly <i>kinA</i>. Some opaque colonies had no mutations, indicating that those adaptive changes occurred through plasticity. These results suggest that our selection conditions of nutrient cycling resulted in the parallel evolution of communities of ecologically diverse strains, where most reduced sporulation while a smaller proportion accelerated it.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11914059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651677","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":"Development and validation of a novel suspended particulate matter sampling device for analysis of particle-bound microbial communities.","authors":"Fuad J Shatara, Kiyoko Yokota, Justin Peschman, Azul J Kothari, Jacob Schoville, Liyuan Hou, R Preston Withington Iv, Cole F Beale, Maria Pelusi, Kyle M Boldon, Jennifer Withington, R P Withington Iii, Hannah Nicklay, Michael R Twiss, Charles J Paradis, Erica L-W Majumder","doi":"10.1099/mic.0.001538","DOIUrl":"10.1099/mic.0.001538","url":null,"abstract":"<p><p>Biotic and abiotic materials attachment to suspended particulate matter in aquatic systems can increase their toxicity and health impacts and has led to an increased need for consistent sampling across various compartments. Sedimentation traps and continuous flow centrifuges are the traditional tools for sampling suspended particulate matter, while manta trawls have been widely used for surface water sampling of suspended or floating microplastics. Limitations, however, exist in the cost of sampling and infrastructure needed to deploy such devices. Here we report on the construction and usage of a novel suspended particulate matter sampling device, the microParticle Obtaining Trap (mPOT). Quality control testing of the mPOT showed suspended particle recovery rates of >90% for particles 100 µm and larger, while field sampling of groundwater, lake and river water shows consistent, size-fractionated recovery of particulate matter. The mPOT is well suited to sample systems not easily accessible by boat or for particles not commonly recovered by common suspended particulate matter sampling and for collection of particles smaller than 300 µm in size.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568597","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":"Phylogenetic groups and extraintestinal virulence genes of inflow <i>Escherichia coli</i> entering a municipal drinking water treatment facility (St. Paul, MN, USA).","authors":"James R Johnson, Brian D Johnston, Paul Thuras","doi":"10.1099/mic.0.001542","DOIUrl":"https://doi.org/10.1099/mic.0.001542","url":null,"abstract":"<p><p>Extraintestinal pathogenic <i>Escherichia coli</i> (ExPEC), a leading cause of urinary tract infections, sepsis and neonatal meningitis, circulates between diverse hosts and the environment. Consequently, identifying ExPEC reservoirs and transmission pathways has potentially great public health importance. Here, we used PCR-based methods to characterize 104 <i>E. coli</i> isolates from inflow water to the St. Paul, MN (USA), municipal drinking water treatment plant. Isolates were analysed for major phylogenetic groups and multiple extraintestinal virulence genes. Additionally, from the 65 (of 104) water samples that yielded multiple <i>E. coli</i> colonies, we screened <i>E. coli</i> population DNA for virulence genes. Thirty-three percent of isolates represented virulence-associated groups B2 and D, and 8% (95% CI: 3%, 15%) qualified molecularly as ExPEC. The ExPEC isolates, all from group B2 or D, had a median virulence gene score of 11.0 and collectively contained all but four of the 28 studied extraintestinal virulence genes. Population DNA screening increased the proportion of samples positive for individual virulence genes and, presumptively, for ExPEC [14% (95% CI: 10%, 30%) vs. 8%, <i>P</i>=0.03]. These findings identify a previously underappreciated potential mechanism for community-wide dissemination of ExPEC and underscore the importance of consistent disinfection of municipal drinking water.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732737","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":"Preserving and utilizing microbial diversity for innovation and sustainability.","authors":"Nelson Lima","doi":"10.1099/mic.0.001544","DOIUrl":"10.1099/mic.0.001544","url":null,"abstract":"<p><p>Microbial culture collections have been fundamental to microbiology since their inception in the late nineteenth century. Initiated by Professor Král, the collections preserve and distribute microbial strains, enabling scientific advancements. Over time, they evolved into microbiological resource centres, integrating taxonomic expertise and adhering to international legal frameworks and quality management systems. Legal frameworks, including the Nagoya Protocol and biosecurity regulations, ensure ethical access and use of microbial resources. Regional networks, such as Microbial Resource Research Infrastructure - European Research Infrastructure Consortium at the European level, or, in the future, the Global Biological Resources Centres Network, coordinate efforts, fostering innovation and collaboration. Today, microbial culture collections support biotechnology, personalized medicine, agriculture and environmental sustainability. They also play a crucial role in public education, addressing misconceptions about microbes. As research progresses, these collections will continue to contribute to scientific discovery, bioeconomic growth and solutions to global challenges such as climate change, food security and ecosystem health.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659475","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":"Transient expression of fluorescent proteins and Cas nucleases in <i>Phytophthora agathidicida</i> via PEG-mediated protoplast transformation.","authors":"Max Hayhurst, Jochem N A Vink, Maxence Remerand, Monica L Gerth","doi":"10.1099/mic.0.001547","DOIUrl":"10.1099/mic.0.001547","url":null,"abstract":"<p><p><i>Phytophthora</i> species are eukaryotic plant pathogens that cause root rot and dieback diseases in thousands of plant species worldwide. Despite their significant economic and ecological impacts, fundamental molecular tools such as DNA transformation methods are not yet established for many <i>Phytophthora</i> species. In this study, we have established a PEG/calcium chloride (CaCl₂)-mediated protoplast transformation method for <i>Phytophthora agathidicida</i>, the causal agent of kauri dieback disease. Adapting a protocol from <i>Phytophthora sojae</i>, we systematically optimized the protoplast digesting enzymes, recovery media composition and pH. Our findings reveal that chitinases are essential for <i>P. agathidicida</i> protoplast formation, and the optimum pH of the recovery medium is 5. The media type did not significantly impact protoplast regeneration. Using this protocol, we generated transformants using three plasmids (i.e. pTdTomatoN, pYF2-PsNLS-Cas9-GFP and pYF2-PsNLS-Cas12a-GFP), which expressed fluorescent proteins and/or Cas nucleases. The transformants were unstable unless maintained under antibiotic selective pressure; however, under selection, fluorescence was maintained across multiple generations and life cycle stages, including the production of fluorescent zoospores from transformed mycelia. Notably, we observed the expression of GFP-tagged Cas nucleases, which is promising for future CRISPR-Cas genome editing applications. This study demonstrates that <i>P. agathidicida</i> is amenable to PEG/CaCl₂-mediated protoplast transformation. Although the resulting transformants require antibiotic selective pressure to remain stable, this transient expression system can be valuable for applications such as cell tracking, chemotaxis studies and CRISPR-Cas genome editing. The protocol also provides a foundation for further optimization of transformation methods. It serves as a valuable tool for exploring the molecular biology of <i>P. agathidicida</i> and potentially other closely related <i>Phytophthora</i> species.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736243","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":"Corrigendum: An assessment of the airborne longevity of group A Streptococcus.","authors":"Henry P Oswin, Evie Blake, Allen E Haddrell, Adam Finn, Shiranee Sriskandan, Jonathan P Reid, Alice Halliday, Anu Goenka","doi":"10.1099/mic.0.001549","DOIUrl":"10.1099/mic.0.001549","url":null,"abstract":"","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11926885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664962","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":"Genetic and phenotypic analysis of the virulence plasmid of a non-Shigatoxigenic enteroaggregative <i>Escherichia coli</i> O104:H4 outbreak strain.","authors":"Rachel Whelan, Martyna Cyganek, Charlotte L Oxley, Benjamin Dickins, Jonathan C Thomas, Gareth McVicker","doi":"10.1099/mic.0.001550","DOIUrl":"10.1099/mic.0.001550","url":null,"abstract":"<p><p>Enteroaggregative <i>Escherichia coli</i> O104:H4 is best known for causing a worldwide outbreak in 2011 due to the acquisition of a Shiga-like toxin alongside traditional enteroaggregative virulence traits; however, whilst the 2011 outbreak strain has been well studied, the virulence plasmid of O104:H4 has been subjected to far less experimental analysis. In this paper, we analyse the genetic and phenotypic contribution of the pAA virulence plasmid to a non-Shigatoxigenic O104:H4 strain (1070/13) that was nonetheless implicated in a substantial UK outbreak in 2013. We find that pAA₁₀₇₀ is 99.95% identical across 88% of the plasmid sequence to pTY2 from the 2011 outbreak strain and has a copy number of ~2-3 plasmid molecules per chromosome. We demonstrate that pAA₁₀₇₀ carries a functional CcdAB plasmid addiction system that only marginally impacts its stability under the conditions tested. None of the other toxin-antitoxin systems encoded by the plasmid appear to be functional, though we note a surprisingly high stability of the plasmid <i>in vitro</i> regardless. We demonstrate the expected contribution of pAA₁₀₇₀ to intestinal cell adhesion but find that it does not contribute to biofilm formation. When assessing the impact of pAA₁₀₇₀ on motility, we discovered a region of the O104:H4 chromosome that can be excised, abolishing motility via truncation of the <i>fliR</i> gene. Ultimately, this work demonstrates the importance of mobile genetic elements to enteroaggregative <i>E. coli</i> as a pathovar in its own right and highlights the complexity but necessity of experimentally characterizing genuine outbreak strains rather than laboratory strains in order to understand virulence phenotypes.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732653","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":"Menadione reduces the expression of virulence- and colonization-associated genes in <i>Helicobacter pylori</i>.","authors":"Stephen Thompson, Omoyemi Rebecca Ojo, Lesley Hoyles, Jody Winter","doi":"10.1099/mic.0.001539","DOIUrl":"https://doi.org/10.1099/mic.0.001539","url":null,"abstract":"<p><p>Novel treatment options are needed for the gastric pathogen <i>Helicobacter pylori</i> due to its increasing antibiotic resistance. The vitamin K analogue menadione has been extensively studied due to interest in its anti-bacterial and anti-cancer properties. Here, we investigated the effects of menadione on <i>H. pylori</i> growth, viability, antibiotic resistance, motility and gene expression using clinical isolates. The MIC of menadione was 313 µM for 11/13 isolates and 156 µM for 2/13 isolates. The minimum bactericidal concentrations were 1.25-2.5 mM, indicating that concentrations in the micromolar range were bacteriostatic rather than bactericidal. We were not able to experimentally evolve resistance to menadione <i>in vitro</i>. Sub-MIC menadione (16 µM for 24 h) did not significantly inhibit bacterial growth but significantly (<i>P</i><0.05) changed the expression of 1291/1615 (79.9%) genes encoded by strain 322A. The expression of the virulence factor genes <i>cagA</i> and <i>vacA</i> was downregulated in the presence of sub-MIC menadione, while genes involved in stress responses were upregulated. Sub-MIC menadione significantly (<i>P</i><0.0001) inhibited the motility of <i>H. pylori</i>, consistent with the predicted effects of the observed significant (<i>P</i><0.05) downregulation of <i>cheY</i>, upregulation of <i>rpoN</i> and changes in the expression of flagellar assembly pathway genes seen in the transcriptomic analysis. Through in-depth interrogation of transcriptomic data, we concluded that sub-MIC menadione elicits a general stress response in <i>H. pylori</i> with survival in the stationary phase likely mediated by the upregulation of <i>surE</i> and <i>rpoN</i>. Sub-MIC menadione caused some modest increases in <i>H. pylori</i> susceptibility to antibiotics, but the effect was variable with strain and antibiotic type and did not reach statistical significance. Menadione (78 µM) was minimally cytotoxic to human gastric adenocarcinoma (AGS) cells after 4 h but caused a significant loss of cell viability after 24 h. Given its inhibitory effects on bacterial growth, motility and expression of virulence- and colonization-associated genes, menadione at low micromolar concentrations may have potential utility as a virulence-attenuating agent against <i>H. pylori</i>.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617379","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}