Microbiology-Sgm最新文献

{"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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causing <i>Streptococcus anginosu</i>s.","authors":"Yu-Juan Lin, Chih-Ho Chen, Ian Yi-Feng Chang, Ruei-Lin Chiang, Hsing-Yi Wang, Cheng-Hsun Chiu, Yi-Ywan M Chen","doi":"10.1099/mic.0.001535","DOIUrl":"https://doi.org/10.1099/mic.0.001535","url":null,"abstract":"<p><p><i>Streptococcus anginosus</i> is a common isolate of the oral cavity and an opportunistic pathogen for systemic infections. Although the pyogenic infections caused by <i>S. anginosus</i> are similar to those caused by <i>Streptococcus pyogenes</i>, <i>S. anginosus</i> lacks most of the well-characterized virulence factors of <i>S. pyogenes</i>. To investigate the pathogenicity of <i>S. anginosus</i>, we analysed the genome of a newly identified <i>S. anginosus</i> strain, KH1, which was associated with toxic shock-like syndrome in an immunocompetent adolescent. The genome of KH1 contains nine genomic islands, two Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated systems and many phage-related proteins, indicating that the genome is influenced by prophages and horizontal gene transfer. Comparative genome analysis of 355 <i>S</i>. <i>anginosus</i> strains revealed a significant difference between the sizes of the pan genome and core genome, reflecting notable strain variations. We further analysed the transcriptomes of KH1 under conditions mimicking either the oral cavity or the bloodstream. We found that in an artificial saliva medium, the expression of a putative quorum quenching system and pyruvate oxidase for H₂O₂ production was upregulated, which could optimize the competitiveness of <i>S. anginosus</i> in the oral ecosystem. Conversely, in a modified serum medium, purine and glucan biosynthesis, competence and bacteriocin production were significantly upregulated, likely facilitating the survival of KH1 in the bloodstream. These findings indicate that <i>S. anginosus</i> can utilize diverse mechanisms to adapt to different environmental niches and establish infection, despite its lack of toxin production.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460449","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":"100+ years of phase variation: the premier bacterial bet-hedging phenomenon.","authors":"Christopher D Bayliss, Jack L Clark, Marjan W van der Woude","doi":"10.1099/mic.0.001537","DOIUrl":"10.1099/mic.0.001537","url":null,"abstract":"<p><p>Stochastic, reversible switches in the expression of <i>Salmonella</i> flagella variants were first described by Andrewes in 1922. Termed phase variation (PV), subsequent research found that this phenomenon was widespread among bacterial species and controlled expression of major determinants of bacterial-host interactions. Underlying mechanisms were not discovered until the 1970s/1980s but were found to encompass intrinsic aspects of DNA processes (i.e. DNA slippage and recombination) and DNA modifications (i.e. DNA methylation). Despite this long history, discoveries are ongoing with expansions of the phase-variable repertoire into new organisms and novel insights into the functions of known loci and switching mechanisms. Some of these discoveries are somewhat controversial as the term 'PV' is being applied without addressing key aspects of the phenomenon such as whether mutations or epigenetic changes are reversible and generated prior to selection. Another 'missing' aspect of PV research is the impact of these adaptive switches in real-world situations. This review provides a perspective on the historical timeline of the discovery of PV, the current state-of-the-art, controversial aspects of classifying phase-variable loci and possible 'missing' real-world effects of this phenomenon.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143517153","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":"Group B <i>Streptococcus</i> growth in human urine is associated with asymptomatic bacteriuria rather than urinary tract infection and is unaffected by iron sequestration.","authors":"Deepak S Ipe, Kelvin G K Goh, Devika Desai, Nouri Ben-Zakour, Matthew J Sullivan, Scott A Beatson, Glen C Ulett","doi":"10.1099/mic.0.001533","DOIUrl":"10.1099/mic.0.001533","url":null,"abstract":"<p><p>Group B <i>Streptococcus</i> (GBS) causes various infections in adults, including urinary tract infection (UTI) and asymptomatic bacteriuria (ABU). Some bacteria that cause ABU can utilize urine as a substrate for growth, which can promote asymptomatic colonization in the host. An analysis of diverse GBS isolates associated with ABU and UTI for growth in human urine has not been undertaken. Here, we examined a large collection of clinical urinary GBS isolates from individuals with acute UTI (<i>n</i>=62), and ABU with bacteriuria ≥10⁴ c.f.u. ml^-1 (<i>n</i>=206) or <10⁴ c.f.u. ml^-1 (<i>n</i>=90) for their ability to grow in human urine. Among all 358 GBS isolates analysed, 40 exhibited robust growth in urine in contrast to 25 that were unable to grow and non-culturable after incubation in urine. Growth phenotypes were disproportionately represented among the different groups of isolates, whereby robust growth was significantly more likely to be associated with high-grade ABU versus low-grade ABU or acute UTI (38/40 vs. 11/25; odds ratio 4.6, 95% CI, 1.5-14.8). Growth of bacteria in urine can depend on iron bioavailability, and we therefore performed growth assays using urine supplemented with 2,2-dipyridyl to chelate iron. In contrast to a control strain of ABU <i>Escherichia coli,</i> for which iron limitation significantly attenuated growth, iron sequestration had no significant attenuation effect on the growth of ABU GBS strain 834 in urine. Despite this finding, PCR confirmed the presence of several known growth-associated genes in GBS 834, including <i>fhuD</i> for iron uptake. We conclude that GBS adaptation for growth in human urine is more likely to be associated with high-grade ABU than acute UTI, and for GBS 834, this growth trait is not significantly constrained by conditions of iron sequestration.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459998","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: Characterizing a stable five-species microbial community for use in experimental evolution and ecology.","authors":"Meaghan Castledine, Joseph Pennycook, Arthur Newbury, Luke Lear, Zoltan Erdos, Rai Lewis, Suzanne Kay, Dirk Sanders, David Sünderhauf, Angus Buckling, Elze Hesse, Daniel Padfield","doi":"10.1099/mic.0.001528","DOIUrl":"https://doi.org/10.1099/mic.0.001528","url":null,"abstract":"","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143081630","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":"SOS - save our seaside! The microbiological risks to human health of raw sewage in our coastal waters.","authors":"Jonathan A G Cox","doi":"10.1099/mic.0.001529","DOIUrl":"10.1099/mic.0.001529","url":null,"abstract":"<p><p>Most of us enjoy a day at the beach, but we rarely consider that recreational use of our coastal waters could impact our health. This article explores the microbiological threats of sewage discharge to our fun in the sea and proposes a simple way to make sure it's only sand that you and your family bring home from a visit to the seaside.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366630","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":"The nisin O cluster: species dissemination, candidate leader peptide proteases and the role of regulatory systems.","authors":"Jacob Scadden, Rebecca Ansorge, Stefano Romano, Andrea Telatin, Dave J Baker, Rhiannon Evans, Cristina Gherghisan-Filip, Zhenrun J Zhang, Melinda J Mayer, Arjan Narbad","doi":"10.1099/mic.0.001531","DOIUrl":"10.1099/mic.0.001531","url":null,"abstract":"<p><p>Nisin O is an antimicrobial peptide encoded by the human gut bacterium <i>Blautia obeum</i> A2-162 which has antimicrobial activity against clinically relevant organisms. The nisin O biosynthetic gene cluster (BGC) varies from other nisin BGCs as it lacks a leader-peptide cleaving protease and contains two bacterial two-component response regulator-histidine kinase (RK) systems. The dissemination of the nisin O cluster, the final proteolytic biosynthesis step and the regulation of nisin O are currently unknown and are the foci of this study. We identified six nisin O-like BGCs across <i>Blautia</i>, <i>Dorea</i> and <i>Ruminococcus</i> species using comparative genomics. These BGCs show evidence of genetic transfer between genera, with genes involved in transposition discovered up- and downstream of the BGCs. All nisin O-like BGCs contained two RK systems but no protease. Mining the <i>B. obeum</i> A2-162 genome identified candidate proteases that were cloned and used in pre-nisin O leader peptide cleavage assays. None of the candidate proteases removed the leader; however, cleavage was achieved using trypsin. To maximize the expression of the <i>nsoA1-4</i> peptides, the interactions of the two RK systems with predicted promoters in the nisin O cluster were assessed using a PepI reporter assay. We observed that the P<i>nsoR2K2</i> promoter was constitutively expressed, with NsoR1K1 increasing its activity, and that there was increased <i>nsoA1-4</i> expression when the nisin A RK system and nisin A were present. Long-read cDNA sequencing confirmed <i>nso</i> gene transcription in the heterologous expression system and identified a novel, highly expressed gene. This study provides evidence that the nisin O BGC has been transferred between different gut-associated genera, with all clusters lacking a protease and containing two RK systems. We hypothesize that this BGC has lost its protease due to negative selection as a result of high trypsin concentrations in the gut. Further work is required to maximize nisin O expression for it to be used as a potential antimicrobial therapy.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392335","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":"Crosstalk between cyclic-di-guanosine monophosphate and the sensor kinase MtrB regulates MtrA-dependent genes, bacterial growth, biofilm formation and lysosomal trafficking of <i>Mycobacterium tuberculosis</i>.","authors":"Shreya Bagchi, Arun Kumar Sharma, Soumya Mal, Manikuntala Kundu, Joyoti Basu","doi":"10.1099/mic.0.001532","DOIUrl":"https://doi.org/10.1099/mic.0.001532","url":null,"abstract":"<p><p>Cyclic-di-guanosine monophosphate (c-di-GMP) plays an important role in bacterial signalling networks. C-di-GMP exerts a regulatory function through binding to diverse molecules that include transcription factors, riboswitches and sensor kinases (SKs), thereby regulating diverse processes. Here, we demonstrate the crosstalk between c-di-GMP and the SK MtrB of <i>Mycobacterium tuberculosis</i>. MtrB phosphorylates and regulates its cognate response regulator MtrA. C-di-GMP binds directly to the cytosolic domain of MtrB to inhibit its autophosphorylation. C-di-GMP levels in <i>M. tuberculosis</i> were manipulated by overexpressing a c-di-GMP synthesizing enzyme <i>ydeH</i> and a degrading enzyme <i>rv1357c</i>. We demonstrate that overexpression of <i>ydeH</i> lowers growth of the bacterium both <i>in vitro</i> and in <i>M. tuberculosis</i> grown in macrophages. This is in conformity with lowered expression of <i>mtrA</i> and selected genes of the <i>mtrA</i> regulon involved in cell wall turnover in the <i>ydeH</i>-overexpressing strain compared to the parent strain. We also demonstrate that overexpression of <i>ydeH</i> in <i>M. tuberculosis</i> hinders biofilm formation, whereas overexpression of <i>rv1357c</i> has the opposite effect. Neither of the two genes could rescue the biofilm defective phenotype of the MtrB knock out mutant (<i>ΔmtrB</i>), suggesting that c-di-GMP exerts its role on biofilm formation through MtrB. Finally, we show by fluorescence microscopy that the trafficking of <i>M. tuberculosis</i> overexpressing <i>ydeH</i> is significantly higher than that of the parent strain and that this is linked to reduced expression of the MtrB-dependent genes <i>esxG</i> and <i>esxH</i>, which play a role in subversion of lysosomal trafficking of <i>M. tuberculosis</i>. These results provide important new insight into the crosstalk between c-di-GMP and MtrB in <i>M. tuberculosis</i>.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371372","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":"Building an inclusive culture at scientific meetings: foundations for future progress.","authors":"Kevin Maringer, Edward Cunningham-Oakes, Ffion Lane, Kirsty L Jones, Bruno Francesco Rodrigues de Oliveira, Aisha Baba-Dikwa, Arindam Mitra, Blanca Perez-Sepulveda, Callie R Chappell, Guerrino Macori, I'ah Donovan-Banfield, Prerna Vohra, Rowan Casey, Roshan Nepal, C M Anjam Khan","doi":"10.1099/mic.0.001527","DOIUrl":"10.1099/mic.0.001527","url":null,"abstract":"<p><p>Scientific meetings and conferences are crucial in knowledge dissemination, fostering collaborations, professional development and inspiring innovative research. However, their traditional structure and organization have remained largely unchanged, perpetuating barriers that continue to exclude scientists from historically marginalized backgrounds. In response, the Microbiology Society has begun its journey to address these longstanding challenges, redesigning its meetings to create a more inclusive culture and a welcoming environment for all participants.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11803081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143257178","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":"Linking volatile metabolites from bacterial pathogens to exhaled breath condensate of people with cystic fibrosis.","authors":"P Hansani Karunarathne, Christopher Bridges, Lacy Remisoski, Madisen Crane, Claudia Soria Casanova, Samantha N Kinne, Alicia L Castillo Bahena, Marissa Gil, Lienwil Padillo, Gabriel Querido, Jenna Mielke, Marc McClelland, Doug Conrad, Robert A Quinn","doi":"10.1099/mic.0.001536","DOIUrl":"https://doi.org/10.1099/mic.0.001536","url":null,"abstract":"<p><p>Obtaining sputum samples from people with cystic fibrosis (pwCF) for microbiology has become challenging due to the positive clinical effects of the cystic fibrosis transmembrane conductance regulator modulator therapy, elexacaftor-tezacaftor-ivacaftor (ETI). Although ETI improves lung function and reduces sputum production, recent data shows that bacterial pathogens persist, making continued monitoring of infection important. As an alternative to sputum sampling, this study developed a non-invasive technique called 'Cough Breath' (CB) to identify volatile organic compounds (VOCs) in exhaled breath condensate (EBC) and link them to cystic fibrosis (CF) bacterial pathogens using purge and trap GC-MS. The CB culturing approach was able to isolate pathogens from expectorated particulates simultaneously with EBC collection; however, culturing positivity was low, with 6% of samples collected (<i>n</i>=47) positive for either <i>Pseudomonas aeruginosa</i> or <i>Staphylococcus aureus</i>. From EBC, we identified VOCs matching those uniquely produced by <i>P. aeruginosa</i> (7), <i>S. aureus</i> (12), <i>Achromobacter xylosoxidans</i> (8) and <i>Granulicatella adiacens</i> (2); however, the overall detection rate was also low. Expanding to VOCs produced across multiple pathogens identified 30 frequently detected in the EBC of pwCF, including 2,3-pentanedione, propyl pyruvate, oxalic acid diallyl ester, methyl isobutyl ketone, methyl nitrate, 2-propenal, acetonitrile, acetoin and 2,3-butanedione. Comparing isolate volatilomes and EBC samples from the same pwCF enhanced detection rates with key VOCs, such as 2,3-pentanedione (86%) and propyl pyruvate (83%), in <i>P. aeruginosa</i> isolates. Further investigation showed that VOC production differed across strains and at different growth phases, creating variability that may explain the overall low EBC detection rate. Although this study successfully cultured CF pathogens from cough particulates and matched their unique VOCs in EBC samples, our results indicate that microbial volatiles more generally indicative of infection, such as 2,3-pentanedione, may have the most utility in aiding diagnostics in pwCF on ETI who have reduced sputum production in the clinic.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"171 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460228","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}