[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-443977-105":59,"doc-detail-443977-en":130},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":123,"head_meta":125,"extra_data":127,"updated_unix":129},105,"en","genome-wide-evolutionary-selection-pressures-acting-on-pseudomonas-aeruginosa-residing-in-different-environments","Genome-wide evolutionary selection pressures acting on Pseudomonas aeruginosa residing in different environments","","Pseudomonas aeruginosa is an opportunistic pathogen in cystic fibrosis (CF) airways and the broader environment. This study interrogates the International Pseudomonas Consortium Database (IPCD) to test whether CF-associated isolates show distinct evolutionary selection from environmental isolates by analyzing dN/dS for each open reading frame (ORF). While most ORFs show negative selection, 373 are non-negative and 206 differ between CF-derived and environmental isolates. Selected ORFs show metabolic-branchpoint enzyme enrichment, domain- and surface-specific niche pressures, and psl cluster gene loss linked to mucA loss-of-function mutations with compensatory alginate production.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/genome-wide-evolutionary-selection-pressures-acting-on-pseudomonas-aeruginosa-residing-in-different-environments/443977/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/genome-wide-evolutionary-selection-pressures-acting-on-pseudomonas-aeruginosa-residing-in-different-environments/443977.png","ImageObject",300,407,{"name":92,"@type":93},"Sarah ","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-01","2026-09-29",true,{"@type":102,"interactionType":103,"userInteractionCount":81},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What datasets and method were used to compare evolutionary selection between CF and environmental isolates?","Question",{"text":112,"@type":113},"The study analyzes International Pseudomonas Consortium Database (IPCD) isolates and calculates dN/dS for each open reading frame (ORF) to quantify evolutionary selection in CF-associated versus environmental lineages.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How do the majority of ORFs behave in terms of selection?",{"text":117,"@type":113},"Most ORFs display a pronounced signature of negative selection, indicating strong conservation.",{"name":119,"@type":110,"acceptedAnswer":120},"What genetic and functional links were found for selection in CF airways?",{"text":121,"@type":113},"Functional enrichment highlights enzymes at metabolic branchpoints, niche-specific selection appears in protein domains and surfaces, and psl biosynthetic gene cluster loss correlates with loss-of-function mutations in mucA, with elevated alginate production proposed as compensation.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},443977,1790779751,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":81,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},962085320529,"https://ap-avatar.wpscdn.com/davatar_9964176cb1d06d4a9deccf72a44ae3dc","Genome-wide evolutionary selection pressures acting on Pseudomonas aeruginosa residing in different environments  \nPok-Man Ho  , Rahan Rudland Nazeer, Martin Welch  *  \nDepartment of Biochemistry, University of Cambridge, Tennis Court Road,Cambridge, CB2 1QW, United Kingdom  \n∗ To whom correspondence should be [addressed. Email:](addressed. Email: mw240@cam.ac.uk)[ mw240@cam.ac.uk](addressed. Email: mw240@cam.ac.uk)  \nAbstract  \nPseudomonas aeruginosa is an opportunistic pathogen, commonly associated with the airways of people with cystic fibrosis (CF) and in the wider environment too. In this work, we interrogate the International Pseudomonas Consortium Database (IPCD) to ask the question of whether CF-associated isolates display different patterns of evolutionary selection compared with environmental isolates. We do this by analysing dN/dS for each open reading frame (ORF) in the CF-associated and environmental IPCD isolates. Most ORFs displayed a pronounced signature of negative selection (i.e. the ORFs were strongly conserved) . However, 373 ORFs displayed non-negative selection, and of these, 206 manifested differential signatures of selection in the CF-derived and environmental isolates. Functional analysis of the ORFs under selection pressure in the CF airways revealed a statistically significant enrichment of enzymes catalysing reactions at metabolic branchpoints. More fine-grained analyses revealed niche-specific selection pressures in individual domains and protein surfaces. Finally, we show that gene loss in the psl biosynthetic gene cluster correlates with the presence of loss-of-function mutations in the mucoidy regulator, mucA. We speculate that elevated alginate production due to these mucA mutations compensates for the loss of Psl production in these isolates.  \nGraphical abstract  \nIntroduction  \nPseudomonas aeruginosa is an opportunistic human pathogen renowned for its ability to adapt to new environments. A good example of this is when environmental strains invade and colonize the airways of people with cystic fibrosis (pwCF) [1, 2] . It is not yet clear why pwCF exhibit such a predilection for infection by P. aeruginosa, and there are probably several contributory factors to this. Nevertheless, collectively, a number of studies over the last decade or so have revealed a number  \nof open reading frames (ORFs) encoded by P. aeruginosa that appear to encode functions important for CF airway infection. Commonly encountered loss-of-function mutations in isolates from pwCF has revealed a set of ‘pathoadaptive’ genes that are potentially dispensable for colonization [2–4] . However, this approach tells us little about which genes might be essential for colonization. In 2015, Turner et al. began to directly address this using an experimental system that combined Tnseq and Monte Carlo simulations to identify genes that are  \nReceived: August 11, 2025. Revised: November 13, 2025. Accepted: November 24, 2025 © The Author(s) 2025. Published by Oxford University Press.  \nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License ([https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/)), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.  \n2 Ho et al.  \nessential, conditionally essential and non-essential for growth in different culture media, including artificial sputum medium and expectorated CF sputum (albeit, only from a single patient) [5] . More recently, Weimann et al. (2024) employed Bayesian simulations of the pan-genome to identify differential patterns of genomic adaptation in CF and non-CF associated P. aeruginosa, enabling the authors to propose a list of genes exhibiting high mutational burdens [2]. However, no previous reports have explicitly investigated whether isolates of P. aeruginosa from pwCF and isolates from the environment exhibit differential ","cbCait7JegkkH7Ck","https://ap.wps.com/l/cbCait7JegkkH7Ck","pdf",1862691,13,"English","# Abstract\n# Introduction\n## dN/dS as a measure of selection pressure\n## Limitations of prior simulation-based approaches","[{\"question\":\"What datasets and method were used to compare evolutionary selection between CF and environmental isolates?\",\"answer\":\"The study analyzes International Pseudomonas Consortium Database (IPCD) isolates and calculates dN/dS for each open reading frame (ORF) to quantify evolutionary selection in CF-associated versus environmental lineages.\"},{\"question\":\"How do the majority of ORFs behave in terms of selection?\",\"answer\":\"Most ORFs display a pronounced signature of negative selection, indicating strong conservation.\"},{\"question\":\"What genetic and functional links were found for selection in CF airways?\",\"answer\":\"Functional enrichment highlights enzymes at metabolic branchpoints, niche-specific selection appears in protein domains and surfaces, and psl biosynthetic gene cluster loss correlates with loss-of-function mutations in mucA, with elevated alginate production proposed as compensation.\"}]","Genome-wide evolutionary selection pressures acting on Pseudomonas aeruginosa residing in different environments | PDF",1790706276,33]