FEMS microbes最新文献_第6页

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

Insights into the mechanism of mycelium transformation of Streptomyces toxytricini into pellet. 毒三角链霉菌菌丝转化成球的机制研究。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad017

Punit Kumar, Khushboo, Deepanshi Rajput, Kashyap K Dubey

{"title":"Insights into the mechanism of mycelium transformation of Streptomyces toxytricini into pellet.","authors":"Punit Kumar, Khushboo, Deepanshi Rajput, Kashyap K Dubey","doi":"10.1093/femsmc/xtad017","DOIUrl":"https://doi.org/10.1093/femsmc/xtad017","url":null,"abstract":"Formation of the mycelial pellet in submerged cultivation of Streptomycetes is unwanted in industrial fermentation processes as it imposes mass transfer limitations, changes in the rheology of a medium, and affects the production of secondary metabolites. Though detailed information is not available about the factors involved in regulating mycelial morphology, it is studied that culture conditions and the genetic information of strain play a crucial role. Moreover, the proteomic study has revealed the involvement of low molecular weight proteins such as; DivIVA, FilP, ParA, Scy, and SsgA proteins in apical growth and branching of hyphae, which results in the establishment of the mycelial network. The present study proposes the mechanism of pellet formation of Streptomyces toxytricini (NRRL B-5426) with the help of microscopic and proteomic analysis. The microscopic analysis revealed that growing hyphae contain a bud-like structure behind the apical tip, which follows a certain organized path of growth and branching, which was further converted into the pellet when shake flask to the shake flask inoculation was performed. Proteomic analysis revealed the production of low molecular weight proteins ranging between 20 and 95 kDa, which are involved in apical growth and hyphae branching and can possibly participate in the regulation of pellet morphology.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad017"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10524099","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

Legionella relative abundance in shower hose biofilms is associated with specific microbiome members. 军团菌在淋浴软管生物膜中的相对丰度与特定微生物组成员有关。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad016

Alessio Cavallaro, William J Rhoads, Émile Sylvestre, Thierry Marti, Jean-Claude Walser, Frederik Hammes

{"title":"Legionella relative abundance in shower hose biofilms is associated with specific microbiome members.","authors":"Alessio Cavallaro, William J Rhoads, Émile Sylvestre, Thierry Marti, Jean-Claude Walser, Frederik Hammes","doi":"10.1093/femsmc/xtad016","DOIUrl":"https://doi.org/10.1093/femsmc/xtad016","url":null,"abstract":"Legionella are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of Legionella with bacterial and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. Legionella spp. relative abundance in the biofilms ranged between 0-7.8%, of which only 0-0.46% was L. pneumophila. Our data suggest that some microbiome members were associated with high (e.g. Chthonomonas, Vrihiamoeba) or low (e.g. Aquabacterium, Vannella) Legionella relative abundance. The correlations of the different Legionella variants (30 Zero-Radius OTUs detected) showed distinct patterns, suggesting separate ecological niches occupied by different Legionella species. This study provides insights into the ecology of Legionella with respect to: (i) the colonization of a high number of real shower hoses biofilm samples; (ii) the ecological meaning of associations between Legionella and co-occurring bacterial/eukaryotic organisms; (iii) critical points and future directions of microbial-interaction-based-ecological-investigations.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad016"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10496943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10260569","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

Dynamic single cell analysis in a proximal-tubule-on-chip reveals heterogeneous epithelial colonization strategies of uropathogenic Escherichia coli under shear stress. 在近端微管芯片上的动态单细胞分析揭示了尿路致病性大肠杆菌在剪切压力下的异质上皮定植策略。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad007

Haris Antypas, Tianqi Zhang, Ferdinand X Choong, Keira Melican, Agneta Richter-Dahlfors

{"title":"Dynamic single cell analysis in a proximal-tubule-on-chip reveals heterogeneous epithelial colonization strategies of uropathogenic Escherichia coli under shear stress.","authors":"Haris Antypas, Tianqi Zhang, Ferdinand X Choong, Keira Melican, Agneta Richter-Dahlfors","doi":"10.1093/femsmc/xtad007","DOIUrl":"https://doi.org/10.1093/femsmc/xtad007","url":null,"abstract":"The urinary tract is a hydrodynamically challenging microenvironment and uropathogenic Escherichia coli (UPEC) must overcome several physiological challenges in order to adhere and establish a urinary tract infection. Our previous work in vivo revealed a synergy between different UPEC adhesion organelles, which facilitated effective colonization of the renal proximal tubule. To allow high-resolution real-time analysis of this colonization behavior, we established a biomimetic proximal-tubule-on-chip (PToC). The PToC allowed for single-cell resolution analysis of the first stages of bacterial interaction with host epithelial cells, under physiological flow. Time-lapse microscopy and single-cell trajectory analysis in the PToC revealed that while the majority of UPEC moved directly through the system, a minority population initiated heterogeneous adhesion, identified as either rolling or bound. Adhesion was predominantly transient and mediated by P pili at the earliest time-points. These bound bacteria initiated a founder population which rapidly divided, leading to 3D microcolonies. Within the first hours, the microcolonies did not express extracellular curli matrix, but rather were dependent on Type 1 fimbriae as the key element in the microcolony structure. Collectively, our results show the application of Organ-on-chip technology to address bacterial adhesion behaviors, demonstrating a well-orchestrated interplay and redundancy between adhesion organelles that enables UPEC to form microcolonies and persist under physiological shear stress.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad007"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9662433","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

Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage. 定量PCR与宏基因组学监测抗生素耐药基因:平衡高灵敏度和广泛覆盖。

FEMS microbes Pub Date : 2023-01-01 DOI: 10.1093/femsmc/xtad008

Catarina Ferreira, Saria Otani, Frank Møller Aarestrup, Célia M Manaia

{"title":"Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.","authors":"Catarina Ferreira, Saria Otani, Frank Møller Aarestrup, Célia M Manaia","doi":"10.1093/femsmc/xtad008","DOIUrl":"https://doi.org/10.1093/femsmc/xtad008","url":null,"abstract":"The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"4 ","pages":"xtad008"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/62/d3/xtad008.PMC10117749.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10036436","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: 3