Microbiology-Sgm最新文献

{"title":"Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations.","authors":"Minako Izutsu, Devin M Lake, Zachary W D Matson, Jack P Dodson, Richard E Lenski","doi":"10.1099/mic.0.001494","DOIUrl":"10.1099/mic.0.001494","url":null,"abstract":"<p><p>Population bottlenecks can impact the rate of adaptation in evolving populations. On the one hand, each bottleneck reduces the genetic variation that fuels adaptation. On the other hand, each founder that survives a bottleneck can undergo more generations and leave more descendants in a resource-limited environment, which allows surviving beneficial mutations to spread more quickly. A theoretical model predicted that the rate of fitness gains should be maximized using ~8-fold dilutions. Here we investigate the impact of repeated bottlenecks on the dynamics of adaptation using numerical simulations and experimental populations of <i>Escherichia coli</i>. Our simulations confirm the model's prediction when populations evolve in a regime where beneficial mutations are rare and waiting times between successful mutations are long. However, more extreme dilutions maximize fitness gains in simulations when beneficial mutations are common and clonal interference prevents most of them from fixing. To examine these predictions, we propagated 48 <i>E. coli</i> populations with 2-, 8-, 100-, and 1000-fold dilutions for 150 days. Adaptation began earlier and fitness gains were greater with 100- and 1000-fold dilutions than with 8-fold dilutions, consistent with the simulations when beneficial mutations are common. However, the selection pressures in the 2-fold treatment were qualitatively different from the other treatments, violating a critical assumption of the model and simulations. Thus, varying the dilution factor during periodic bottlenecks can have multiple effects on the dynamics of adaptation caused by differential losses of diversity, different numbers of generations, and altered selection.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 9","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11410044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299612","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":"Microbe Profile: <i>Pseudonocardia</i>: antibiotics for every niche.","authors":"Bonnie Whatmough, Neil A Holmes, Barrie Wilkinson, Matthew I Hutchings, Jonathan Parra, Katherine R Duncan","doi":"10.1099/mic.0.001501","DOIUrl":"10.1099/mic.0.001501","url":null,"abstract":"<p><p><i>Pseudonocardia</i> species comprise a genus of filamentous, sporulating bacteria belonging to the phylum Actinomycetota, formerly Actinobacteria. They are found in marine and freshwater sediments and soils and associated with marine animals, insects, and plants. To date, they have mostly been studied because of their mutually beneficial symbiosis with fungus-growing ants in the tribe <i>Attini</i>. They have also attracted interest due to their biosynthetic capabilities, including the production of variably glycosylated polyenes and other novel antifungal compounds, and for their capacity to grow on a variety of hydrocarbons. The majority of clinically used antibiotics are derived from the specialised metabolites of filamentous actinomycete bacteria and most of these come from the genus <i>Streptomyces</i>. However, in the quest for novel chemistry there is increasing interest in studying other filamentous actinomycete genera, including <i>Pseudonocardia</i>. Here we outline the biological properties, genome size and structure and key features of the genus <i>Pseudonocardia</i>, namely their specialised metabolites and ecological roles.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 9","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11412249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299613","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":"Use of Rgg quorum-sensing machinery to create an innovative recombinant protein expression system in <i>Streptococcus thermophilus</i>.","authors":"Rozenn Gardan, Edith Honvo-Houeto, Christine Mézange, Nathanael Jean Maillot, Aurélie Balvay, Sylvie Rabot, Luis G Bermúdez-Humarán, Philippe Langella, Véronique Monnet, Vincent Juillard","doi":"10.1099/mic.0.001487","DOIUrl":"10.1099/mic.0.001487","url":null,"abstract":"<p><p><i>Streptococcus thermophilus</i> holds promise as a chassis for producing and secreting heterologous proteins. Used for thousands of years to ferment milk, this species has generally recognized as safe (GRAS) status in the USA and qualified presumption of safety (QPS) status in Europe. In addition, it can be easily genetically modified thanks to its natural competence, and it secretes very few endogenous proteins, which means less downstream processing is needed to purify target proteins, reducing costs. Extracellular degradation of heterologous proteins can be eliminated by introducing mutations that inactivate the genes encoding the bacterium's three major surface proteases. Here, we constructed an inducible expression system that utilizes a peptide pheromone (SHP₁₃₅₈) and a transcriptional regulator (Rgg₁₃₅₈) involved in quorum-sensing regulation. We explored the functionality of a complete version of the system, in which the inducer is produced by the bacterium itself, by synthesizing a luciferase reporter protein. This complete version was assessed with bacteria grown in a chemically defined medium but also <i>in vivo,</i> in the faeces of germ-free mice. We also tested an incomplete version, in which the inducer had to be added to the culture medium, by synthesizing luciferase and a secreted form of elafin, a human protein with therapeutic properties. Our results show that, in our system, protein production can be modulated by employing different concentrations of the SHP₁₃₅₈ inducer or other SHPs with closed amino acid sequences. We also constructed a genetic background in which all system leakiness was eliminated. In conclusion, with this new inducible expression system, we have added to the set of tools currently used to produce secreted proteins in <i>S. thermophilus</i>, whose myriad applications include the delivery of therapeutic peptides or proteins.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 9","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11414475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299614","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":"A new model of endotracheal tube biofilm identifies combinations of matrix-degrading enzymes and antimicrobials able to eradicate biofilms of pathogens that cause ventilator-associated pneumonia.","authors":"Dean Walsh, Chris Parmenter, Saskia E Bakker, Trevor Lithgow, Ana Traven, Freya Harrison","doi":"10.1099/mic.0.001480","DOIUrl":"10.1099/mic.0.001480","url":null,"abstract":"<p><p>Ventilator-associated pneumonia is defined as pneumonia that develops in a patient who has been on mechanical ventilation for more than 48 hours through an endotracheal tube. It is caused by biofilm formation on the indwelling tube, which introduces pathogenic microbes such as <i>Pseudomonas aeruginosa</i>, <i>Klebsiella pneumoniae</i> and <i>Candida albicans</i> into the patient's lower airways. Currently, there is a lack of accurate <i>in vitro</i> models of ventilator-associated pneumonia development. This greatly limits our understanding of how the in-host environment alters pathogen physiology and the efficacy of ventilator-associated pneumonia prevention or treatment strategies. Here, we showcase a reproducible model that simulates the biofilm formation of these pathogens in a host-mimicking environment and demonstrate that the biofilm matrix produced differs from that observed in standard laboratory growth medium. In our model, pathogens are grown on endotracheal tube segments in the presence of a novel synthetic ventilated airway mucus medium that simulates the in-host environment. Matrix-degrading enzymes and cryo-scanning electron microscopy were employed to characterize the system in terms of biofilm matrix composition and structure, as compared to standard laboratory growth medium. As seen in patients, the biofilms of ventilator-associated pneumonia pathogens in our model either required very high concentrations of antimicrobials for eradication or could not be eradicated. However, combining matrix-degrading enzymes with antimicrobials greatly improved the biofilm eradication of all pathogens. Our <i>in vitro</i> endotracheal tube model informs on fundamental microbiology in the ventilator-associated pneumonia context and has broad applicability as a screening platform for antibiofilm measures including the use of matrix-degrading enzymes as antimicrobial adjuvants.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861390","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: Characterisation of anhydro-sialic acid transporters from mucosa-associated bacteria.","authors":"Yunhan Wu, Andrew Bell, Gavin H Thomas, David N Bolam, Frank Sargent, Nathalie Juge, Tracy Palmer, Emmanuele Severi","doi":"10.1099/mic.0.001476","DOIUrl":"10.1099/mic.0.001476","url":null,"abstract":"","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876475","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":"A rapid on-site loop-mediated isothermal amplification technology as an early warning system for the detection of Shiga toxin-producing <i>Escherichia coli</i> in water.","authors":"Zina Alfahl, Sean Biggins, Owen Higgins, Alexandra Chueiri, Terry J Smith, Dearbháile Morris, Jean O'Dwyer, Paul D Hynds, Liam P Burke, Louise O'Connor","doi":"10.1099/mic.0.001485","DOIUrl":"10.1099/mic.0.001485","url":null,"abstract":"<p><p>Shiga toxin-producing <i>Escherichia coli</i> (STEC) is an important waterborne pathogen capable of causing serious gastrointestinal infections with potentially fatal complications, including haemolytic-uremic syndrome. All STEC serogroups harbour genes that encode at least one Shiga toxin (<i>stx1</i> and/or <i>stx2</i>), which constitute the primary virulence factors of STEC. Loop-mediated isothermal amplification (LAMP) enables rapid real-time pathogen detection with a high degree of specificity and sensitivity. The aim of this study was to develop and validate an on-site portable diagnostics workstation employing LAMP technology to permit rapid real-time STEC detection in environmental water samples. Water samples (<i>n</i>=28) were collected from groundwater wells (<i>n</i>=13), rivers (<i>n</i>=12), a turlough (<i>n</i>=2) and an agricultural drain (<i>n</i>=1) from the Corrib catchment in Galway. Water samples (100 ml) were passed through a 0.22 µm filter, and buffer was added to elute captured cells. Following filtration, eluates were tested directly using LAMP assays targeting <i>stx1</i>, <i>stx2</i> and <i>E. coli phoA</i> genes. The portable diagnostics workstation was used in field studies to demonstrate the on-site testing capabilities of the instrument. Real-time PCR assays targeting <i>stx1</i> and <i>stx2</i> genes were used to confirm the results. The limit of detection for <i>stx1</i>, <i>stx2</i> and <i>phoA</i> LAMP assays were 2, 2 and 6 copies, respectively. Overall, <i>stx1</i>, <i>stx2</i> and <i>phoA</i> genes were detected by LAMP in 15/28 (53.6 %), 9/28 (32.2 %) and 24/28 (85.7 %) samples, respectively. For confirmation, the LAMP results for <i>stx1</i> and <i>stx2</i> correlated perfectly (100 %) with those obtained using PCR. The portable diagnostics workstation exhibited high sensitivity throughout the on-site operation, and the average time from sample collection to final result was 40 min. We describe a simple, transferable and efficient diagnostic technology for on-site molecular analysis of various water sources. This method allows on-site testing of drinking water, enabling evidence-based decision-making by public health and water management authorities.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898750","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":"'Wild Type'.","authors":"Isabel Askenasy, Jemima E V Swain, Pok-Man Ho, Rahan Rudland Nazeer, Amelie Welch, Éva Bernadett Bényei, Leonardo Mancini, Sivan Nir, Pinyu Liao, Martin Welch","doi":"10.1099/mic.0.001495","DOIUrl":"10.1099/mic.0.001495","url":null,"abstract":"<p><p>In this opinion piece, we consider the meaning of the term 'wild type' in the context of microbiology. This is especially pertinent in the post-genomic era, where we have a greater awareness of species diversity than ever before. Genomic heterogeneity, <i>in vitro</i> evolution/selection pressures, definition of 'the wild', the size and importance of the pan-genome, gene-gene interactions (epistasis), and the nature of the 'wild-type gene' are all discussed. We conclude that wild type is an outdated and even misleading phrase that should be gradually phased out.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114052","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":"Mobility and growth in confined spaces are important mechanisms for the establishment of <i>Bacillus subtilis</i> in the rhizosphere.","authors":"Ilonka C Engelhardt, Nicola Holden, Tim J Daniell, Lionel X Dupuy","doi":"10.1099/mic.0.001477","DOIUrl":"10.1099/mic.0.001477","url":null,"abstract":"<p><p>The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of <i>Bacillus subtilis</i> and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12-24 h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700-1000 µm from the tip. Bacteria accumulated predominantly in confined pore spaces within 200 µm from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11574552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898751","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":"Identification of gene targets that potentiate the action of rifampicin on <i>Mycobacterium bovis</i> BCG.","authors":"Pooja Chand, Tom A Mendum, Rachel E Butler, Suzanne M Hingley-Wilson, Graham R Stewart","doi":"10.1099/mic.0.001488","DOIUrl":"10.1099/mic.0.001488","url":null,"abstract":"<p><p>Tuberculosis (TB) caused by bacteria of the <i>Mycobacterium tuberculosis</i> complex remains one of the most important infectious diseases of mankind. Rifampicin is a first line drug used in multi-drug treatment of TB, however, the necessary duration of treatment with these drugs is long and development of resistance is an increasing impediment to treatment programmes. As a result, there is a requirement for research and development of new TB drugs, which can form the basis of new drug combinations, either due to their own anti-mycobacterial activity or by augmenting the activity of existing drugs such as rifampicin. This study describes a TnSeq analysis to identify mutants with enhanced sensitivity to sub-minimum inhibitory concentrations (MIC) of rifampicin. The rifampicin-sensitive mutants were disrupted in genes of a variety of functions and the majority fitted into three thematic groups: firstly, genes that were involved in DNA/RNA metabolism, secondly, genes involved in sensing and regulating mycobacterial cellular systems, and thirdly, genes involved in the synthesis and maintenance of the cell wall. Selection at two concentrations of rifampicin (1/250 and 1/62 MIC) demonstrated a dose response for mutants with statistically significant sensitivity to rifampicin. The dataset reveals mechanisms of how mycobacteria are innately tolerant to and initiate an adaptive response to rifampicin; providing putative targets for the development of adjunctive therapies that potentiate the action of rifampicin.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989376","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":"Synergy between Group 2 capsules and lipopolysaccharide underpins serum resistance in extra-intestinal pathogenic <i>Escherichia coli</i>.","authors":"Naoise McGarry, Domhnall Roe, Stephen G J Smith","doi":"10.1099/mic.0.001493","DOIUrl":"10.1099/mic.0.001493","url":null,"abstract":"<p><p><i>Escherichia coli (E. coli</i>) is a major cause of urinary tract infections, bacteraemia, and sepsis. CFT073 is a prototypic, urosepsis isolate of sequence type (ST) 73. This laboratory, among others, has shown that strain CFT073 is resistant to serum, with capsule and other extracellular polysaccharides imparting resistance. The interplay of such polysaccharides remains under-explored. This study has shown that CFT073 mutants deficient in lipopolysaccharide (LPS) O-antigen and capsule display exquisite serum sensitivity. Additionally, O-antigen and LPS outer core mutants displayed significantly decreased surface K2 capsule, coupled with increased unbound K2 capsule being detected in the supernatant. The R1 core and O6 antigen are involved in the tethering of K2 capsule to the CFT073 cell surface, highlighting the importance of the R1 core in serum resistance. The dependence of capsule on LPS was shown to be post-transcriptional and related to changes in cell surface hydrophobicity. Furthermore, immunofluorescence microscopy suggested that the surface pattern of capsule is altered in such LPS core mutants, which display a punctate capsule pattern. Finally, targeting LPS biosynthesis using sub-inhibitory concentrations of a WaaG inhibitor resulted in increased serum sensitivity and decreased capsule in CFT073. Interestingly, the dependency of capsule on LPS has been observed previously in other <i>Enterobacteria</i>, indicating that the synergy between these polysaccharides is not just strain, serotype or species-specific but may be conserved across several pathogenic Gram-negative species. Therefore, using WaaG inhibitor derivatives to target LPS is a promising therapeutic strategy to reduce morbidity and mortality by reducing or eliminating surface capsule.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 8","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11342863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037539","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}