FEMS microbes最新文献_第5页

Whole genomes of deep-sea sponge-associated bacteria exhibit high novel natural product potential. 深海海绵相关细菌的全基因组显示出很高的新型天然产物潜力。

FEMS microbes Pub Date : 2023-02-22 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad005

Poppy J Hesketh-Best, Grant G January, Matthew J Koch, Philip J Warburton, Kerry L Howell, Mathew Upton

{"title":"Whole genomes of deep-sea sponge-associated bacteria exhibit high novel natural product potential.","authors":"Poppy J Hesketh-Best, Grant G January, Matthew J Koch, Philip J Warburton, Kerry L Howell, Mathew Upton","doi":"10.1093/femsmc/xtad005","DOIUrl":"10.1093/femsmc/xtad005","url":null,"abstract":"Global antimicrobial resistance is a health crisis that can change the face of modern medicine. Exploring diverse natural habitats for bacterially-derived novel antimicrobial compounds has historically been a successful strategy. The deep-sea presents an exciting opportunity for the cultivation of taxonomically novel organisms and exploring potentially chemically novel spaces. In this study, the draft genomes of 12 bacteria previously isolated from the deep-sea sponges Phenomena carpenteri and Hertwigia sp. are investigated for the diversity of specialized secondary metabolites. In addition, early data support the production of antibacterial inhibitory substances produced from a number of these strains, including activity against clinically relevant pathogens Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Draft whole-genomes are presented of 12 deep-sea isolates, which include four potentially novel strains: Psychrobacter sp. PP-21, Streptomyces sp. DK15, Dietzia sp. PP-33, and Micrococcus sp. M4NT. Across the 12 draft genomes, 138 biosynthetic gene clusters were detected, of which over half displayed less than 50% similarity to known BGCs, suggesting that these genomes present an exciting opportunity to elucidate novel secondary metabolites. Exploring bacterial isolates belonging to the phylum Actinomycetota, Pseudomonadota, and Bacillota from understudied deep-sea sponges provided opportunities to search for new chemical diversity of interest to those working in antibiotic discovery.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad005"},"PeriodicalIF":0.0,"publicationDate":"2023-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a8/1d/xtad005.PMC10117722.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10081532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Editorial: Thematic issue on bacterial-viral co-infections. 社论：细菌病毒共同感染专题。

FEMS microbes Pub Date : 2023-01-19 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtac031

Sam Manna, Daniel M Weinberger, Catherine Satzke

引用次数: 0

Direct wastewater extraction as a simple and effective method for SARS-CoV-2 surveillance and COVID-19 community-level monitoring. 直接废水提取是SARS-CoV-2监测和新冠肺炎社区级监测的一种简单有效的方法。

FEMS microbes Pub Date : 2023-01-12 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad004

Megan E J Lott, William A Norfolk, Cody A Dailey, Amelia M Foley, Carolina Melendez-Declet, Megan J Robertson, Stephen L Rathbun, Erin K Lipp

{"title":"Direct wastewater extraction as a simple and effective method for SARS-CoV-2 surveillance and COVID-19 community-level monitoring.","authors":"Megan E J Lott, William A Norfolk, Cody A Dailey, Amelia M Foley, Carolina Melendez-Declet, Megan J Robertson, Stephen L Rathbun, Erin K Lipp","doi":"10.1093/femsmc/xtad004","DOIUrl":"10.1093/femsmc/xtad004","url":null,"abstract":"Wastewater surveillance has proven to be an effective tool to monitor the transmission and emergence of infectious agents at a community scale. Workflows for wastewater surveillance generally rely on concentration steps to increase the probability of detection of low-abundance targets, but preconcentration can substantially increase the time and cost of analyses while also introducing additional loss of target during processing. To address some of these issues, we conducted a longitudinal study implementing a simplified workflow for SARS-CoV-2 detection from wastewater, using a direct column-based extraction approach. Composite influent wastewater samples were collected weekly for 1 year between June 2020 and June 2021 in Athens-Clarke County, Georgia, USA. Bypassing any concentration step, low volumes (280 µl) of influent wastewater were extracted using a commercial kit, and immediately analyzed by RT-qPCR for the SARS-CoV-2 N1 and N2 gene targets. SARS-CoV-2 viral RNA was detected in 76% (193/254) of influent samples, and the recovery of the surrogate bovine coronavirus was 42% (IQR: 28%, 59%). N1 and N2 assay positivity, viral concentration, and flow-adjusted daily viral load correlated significantly with per-capita case reports of COVID-19 at the county-level (ρ = 0.69-0.82). To compensate for the method's high limit of detection (approximately 106-107 copies l-1 in wastewater), we extracted multiple small-volume replicates of each wastewater sample. With this approach, we detected as few as five cases of COVID-19 per 100 000 individuals. These results indicate that a direct-extraction-based workflow for SARS-CoV-2 wastewater surveillance can provide informative and actionable results.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad004"},"PeriodicalIF":0.0,"publicationDate":"2023-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10036434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Show us the data: global COVID-19 wastewater monitoring efforts, equity, and gaps. 向我们展示数据:全球COVID-19废水监测工作、公平性和差距。

FEMS microbes Pub Date : 2023-01-12 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad003

Colleen C Naughton, Fernando A Roman, Ana Grace F Alvarado, Arianna Q Tariqi, Matthew A Deeming, Krystin F Kadonsky, Kyle Bibby, Aaron Bivins, Gertjan Medema, Warish Ahmed, Panagis Katsivelis, Vajra Allan, Ryan Sinclair, Joan B Rose

{"title":"Show us the data: global COVID-19 wastewater monitoring efforts, equity, and gaps.","authors":"Colleen C Naughton, Fernando A Roman, Ana Grace F Alvarado, Arianna Q Tariqi, Matthew A Deeming, Krystin F Kadonsky, Kyle Bibby, Aaron Bivins, Gertjan Medema, Warish Ahmed, Panagis Katsivelis, Vajra Allan, Ryan Sinclair, Joan B Rose","doi":"10.1093/femsmc/xtad003","DOIUrl":"10.1093/femsmc/xtad003","url":null,"abstract":"A year since the declaration of the global coronavirus disease 2019 (COVID-19) pandemic, there were over 110 million cases and 2.5 million deaths. Learning from methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater-based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater. Unlike COVID-19 case and mortality data, there was not a global dashboard to track wastewater monitoring of SARS-CoV-2 RNA worldwide. This study provides a 1-year review of the \"COVIDPoops19\" global dashboard of universities, sites, and countries monitoring SARS-CoV-2 RNA in wastewater. Methods to assemble the dashboard combined standard literature review, Google Form submissions, and daily, social media keyword searches. Over 200 universities, 1400 sites, and 55 countries with 59 dashboards monitored wastewater for SARS-CoV-2 RNA. However, monitoring was primarily in high-income countries (65%) with less access to this valuable tool in low- and middle-income countries (35%). Data were not widely shared publicly or accessible to researchers to further inform public health actions, perform meta-analysis, better coordinate, and determine equitable distribution of monitoring sites. For WBE to be used to its full potential during COVID-19 and beyond, show us the data.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad003"},"PeriodicalIF":0.0,"publicationDate":"2023-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10036431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 110

Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties. 两个橄榄树品种年度发育周期中的地上和地下微生物组。

FEMS microbes Pub Date : 2023-01-06 eCollection Date: 2023-01-01 DOI: 10.1093/femsmc/xtad001

Myrsini Kakagianni, Myrto Tsiknia, Maria Feka, Sotirios Vasileiadis, Kleopatra Leontidou, Nektarios Kavroulakis, Katerina Karamanoli, Dimitrios G Karpouzas, Constantinos Ehaliotis, Kalliope K Papadopoulou

{"title":"Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties.","authors":"Myrsini Kakagianni, Myrto Tsiknia, Maria Feka, Sotirios Vasileiadis, Kleopatra Leontidou, Nektarios Kavroulakis, Katerina Karamanoli, Dimitrios G Karpouzas, Constantinos Ehaliotis, Kalliope K Papadopoulou","doi":"10.1093/femsmc/xtad001","DOIUrl":"10.1093/femsmc/xtad001","url":null,"abstract":"The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties 'Koroneiki' and 'Chondrolia Chalkidikis' grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad001"},"PeriodicalIF":0.0,"publicationDate":"2023-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a8/67/xtad001.PMC10117799.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10036435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

An antimicrobial thiopeptide producing novel actinomycetes Streptomyces terrae sp. nov., isolated from subsurface soil of arable land. 从耕地地下土壤中分离出一种产生新型放线菌地链霉菌的抗菌硫肽。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad014

Stanzin Choksket, Mahaldeep Kaur, Anil Kumar Pinnaka, Suresh Korpole

{"title":"An antimicrobial thiopeptide producing novel actinomycetes Streptomyces terrae sp. nov., isolated from subsurface soil of arable land.","authors":"Stanzin Choksket, Mahaldeep Kaur, Anil Kumar Pinnaka, Suresh Korpole","doi":"10.1093/femsmc/xtad014","DOIUrl":"https://doi.org/10.1093/femsmc/xtad014","url":null,"abstract":"An antimicrobial producing Gram-positive, aerobic, nonmotile, and filamentous actinobacterial strain SKN60T was isolated from soil The isolate exhibited 99.3% and 99.0% identity with Streptomyces laurentii ATCC 31255T and S. roseicoloratus TRM 44457T, respectively, in 16S rRNA gene sequence analysis. However, the genome sequence displayed maximum ANI (88.45%) and AAI (85.61%) with S. roseicoloratus TRM 44457T. Similarly, the dDDH showed 33.7% identity with S. roseicoloratus TRM 44457T. It formed a cluster with S. roseicoloratus TRM 44457T and S. laurentii ATCC 31255T in phylogenomic tree. Cell wall analysis revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine as major polar lipids and diaminopimelic acid as diagnostic diamino acid. Major fatty acids were iso-C15:0, anteiso-C15:0, and iso-C16:0. The G+C content was found to be 72.3 mol%. Genome sequence analysis using antiSMASH database showed occurrence of a thiopeptide biosynthesis gene cluster with 94% similarity to berninamycin from S. bernensis UC5144. The mass of 1146 Da is identical with berninamycin. But subtle differences observed in leader peptide sequence of thiopeptide and berninamycin. Notably, S. bernensis is not validly reported and thus SKN60T is the only strain containing berninamycin BGC as no other phylogenetic relative had it. Additionally, strain SKN60T differed in phenotypic and genetic characteristics with all phylogenetic relatives of the genus Streptomyces. Therefore, it is proposed as a novel species with the name Streptomyces terrae sp. nov. strain SKN60T (=MTCC 13163T; = JCM 35768T).","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad014"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10495126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Acinetobacter baumannii website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace. 鲍曼不动杆菌网站(Ab-web):一个多学科的知识中心、交流平台和工作空间。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad009

Nabil Karah, Valeria Mateo-Estrada, Santiago Castillo-Ramírez, Paul G Higgins, Benjamin Havenga, Wesaal Khan, Sara Domingues, Gabriela Jorge Da Silva, Laurent Poirel, Patrice Nordmann, Cecilia Ambrosi, Chaoying Ma, Siobhán McClean, María Paula Quiroga, Verónica E Alvarez, Daniela Centron, Raffaele Zarrilli, Johanna J Kenyon, Thomas A Russo, Benjamin A Evans, Andres Opazo-Capurro, Rayane Rafei, Monzer Hamze, Ziad Daoud, Irfan Ahmad, Philip N Rather, Ruth M Hall, Gottfried Wilharm, Bernt Eric Uhlin

{"title":"The Acinetobacter baumannii website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace.","authors":"Nabil Karah, Valeria Mateo-Estrada, Santiago Castillo-Ramírez, Paul G Higgins, Benjamin Havenga, Wesaal Khan, Sara Domingues, Gabriela Jorge Da Silva, Laurent Poirel, Patrice Nordmann, Cecilia Ambrosi, Chaoying Ma, Siobhán McClean, María Paula Quiroga, Verónica E Alvarez, Daniela Centron, Raffaele Zarrilli, Johanna J Kenyon, Thomas A Russo, Benjamin A Evans, Andres Opazo-Capurro, Rayane Rafei, Monzer Hamze, Ziad Daoud, Irfan Ahmad, Philip N Rather, Ruth M Hall, Gottfried Wilharm, Bernt Eric Uhlin","doi":"10.1093/femsmc/xtad009","DOIUrl":"https://doi.org/10.1093/femsmc/xtad009","url":null,"abstract":"Acinetobacter baumannii is a Gram-negative bacterium increasingly implicated in hospital-acquired infections and outbreaks. Effective prevention and control of such infections are commonly challenged by the frequent emergence of multidrug-resistant strains. Here we introduce Ab-web (https://www.acinetobacterbaumannii.no), the first online platform for sharing expertise on A. baumannii. Ab-web is a species-centric knowledge hub, initially with 10 articles organized into two main sections, 'Overview' and 'Topics', and three themes, 'epidemiology', 'antibiotic resistance', and 'virulence'. The 'workspace' section provides a spot for colleagues to collaborate, build, and manage joint projects. Ab-web is a community-driven initiative amenable to constructive feedback and new ideas.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad009"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10132847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10131695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Organic and inorganic nutrients modulate taxonomic diversity and trophic strategies of small eukaryotes in oligotrophic oceans. 有机和无机营养物调节寡营养海洋中小型真核生物的分类多样性和营养策略。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtac029

Naomi Villiot, Amy E Maas, Alex J Poulton, Leocadio Blanco-Bercial

{"title":"Organic and inorganic nutrients modulate taxonomic diversity and trophic strategies of small eukaryotes in oligotrophic oceans.","authors":"Naomi Villiot, Amy E Maas, Alex J Poulton, Leocadio Blanco-Bercial","doi":"10.1093/femsmc/xtac029","DOIUrl":"https://doi.org/10.1093/femsmc/xtac029","url":null,"abstract":"As the oligotrophic gyres expand due to global warming, exacerbating resource limitation impacts on primary producers, predicting changes to microbial assemblages and productivity requires knowledge of the community response to nutrient availability. This study examines how organic and inorganic nutrients influence the taxonomic and trophic composition (18S metabarcoding) of small eukaryotic plankton communities (< 200 µm) within the euphotic zone of the oligotrophic Sargasso Sea. The study was conducted by means of field sampling of natural microbial communities and laboratory incubation of these communities under different nutrient regimes. Dissimilarity in community composition increased along a depth gradient, with a homogeneous protist community within the mixed layer and distinct microbial assemblages at different depths below the deep chlorophyll maximum. A nutrient enrichment assay revealed the potential of natural microbial communities to rapidly shift in composition in response to nutrient addition. Results highlighted the importance of inorganic phosphorus availability, largely understudied compared to nitrogen, in constraining microbial diversity. Dissolved organic matter addition led to a loss of diversity, benefiting a limited number of phagotrophic and mixotrophic taxa. Nutrient history of the community sets the physiological responsiveness of the eukaryotic community to changing nutrient regimes and needs to be considered in future studies.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtac029"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Disparity in pseudohyphal morphogenic switching response to the quorum sensing molecule 2-phenylethanol in commercial brewing strains of Saccharomyces cerevisiae. 酿酒酵母商业酿酒菌株假菌丝形态发生切换对群体感应分子2-苯乙醇响应的差异。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad002

Scott J Britton, Lisa J Rogers, Jane S White, Hedwig Neven, Dawn L Maskell

{"title":"Disparity in pseudohyphal morphogenic switching response to the quorum sensing molecule 2-phenylethanol in commercial brewing strains of Saccharomyces cerevisiae.","authors":"Scott J Britton, Lisa J Rogers, Jane S White, Hedwig Neven, Dawn L Maskell","doi":"10.1093/femsmc/xtad002","DOIUrl":"https://doi.org/10.1093/femsmc/xtad002","url":null,"abstract":"Saccharomyces cerevisiae can undergo filamentous growth in response to specific environmental stressors, particularly nitrogen-limitation, whereby cells undergo pseudohyphal differentiation, a process where cells transition from a singular ellipsoidal appearance to multicellular filamentous chains from the incomplete scission of the mother-daughter cells. Previously, it was demonstrated that filamentous growth in S. cerevisiae is co-regulated by multiple signaling networks, including the glucose-sensing RAS/cAMP-PKA and SNF pathways, the nutrient-sensing TOR pathway, the filamentous growth MAPK pathway, and the Rim101 pathway, and can be induced by quorum-sensing aromatic alcohols, such as 2-phenylethanol. However, the prevalent research on the yeast-pseudohyphal transition and its induction by aromatic alcohols in S. cerevisiae has been primarily limited to the strain Σ1278b. Due to the prospective influence of quorum sensing on commercial fermentation, the native variation of yeast-to-filamentous phenotypic transition and its induction by 2-phenylethanol in commercial brewing strains was investigated. Image analysis software was exploited to enumerate the magnitude of whole colony filamentation in 16 commercial strains cultured on nitrogen-limiting SLAD medium; some supplemented with exogenous 2-phenylethanol. The results demonstrate that phenotypic switching is a generalized, highly varied response occurring only in select brewing strains. Nevertheless, strains exhibiting switching behavior altered their filamentation response to exogenous concentrations of 2-phenylethanol.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad002"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10036433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates. 利用转录组数据研究铜绿假单胞菌临床分离株c-di-GMP信号网络的挑战。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad012

Melisa Gür, Jelena Erdmann, Anke Will, Ziwei Liang, Jens Bo Andersen, Tim Tolker-Nielsen, Susanne Häussler

{"title":"Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates.","authors":"Melisa Gür, Jelena Erdmann, Anke Will, Ziwei Liang, Jens Bo Andersen, Tim Tolker-Nielsen, Susanne Häussler","doi":"10.1093/femsmc/xtad012","DOIUrl":"https://doi.org/10.1093/femsmc/xtad012","url":null,"abstract":"In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding DGCs. This approach might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, while we demonstrate that the selection of subgroups of clinical isolates with high versus low expression of sigma factor encoding genes served the identification of their downstream regulons, we were unable to confirm the predicted DGC regulons, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon prolonged cultivation of clinical P. aeruginosa isolates.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad012"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9981114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0