{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:28:56Z","timestamp":1792639736896,"version":"4.5.0"},"update-to":[{"DOI":"10.12688\/f1000research.125074.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T00:00:00Z","timestamp":1669766400000}}],"reference-count":82,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T00:00:00Z","timestamp":1669766400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["SRC022"],"award-info":[{"award-number":["SRC022"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010757","name":"National Centre for the Replacement Refinement and Reduction of Animals in Research","doi-asserted-by":"publisher","award":["NC\/S001700\/1"],"award-info":[{"award-number":["NC\/S001700\/1"]}],"id":[{"id":"10.13039\/501100010757","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000292","name":"Cystic Fibrosis Trust","doi-asserted-by":"publisher","award":["SRC022"],"award-info":[{"award-number":["SRC022"]}],"id":[{"id":"10.13039\/501100000292","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    The respiratory tract is a compartmentalised and heterogenous environment. The nasopharynx and sinuses of the upper airways have distinct properties from the lungs and these differences may shape bacterial adaptation and evolution. Upper airway niches act as early colonisation sites for respiratory bacterial pathogens, including those, such as\n                    <ns4:italic>Pseudomonas aeruginosa<\/ns4:italic>\n                    , that can go on to establish chronic infection of the lungs in people with cystic fibrosis (CF). Despite the importance of upper airway environments in facilitating early adaptation to host environments, currently available\n                    <ns4:italic>in vitro<\/ns4:italic>\n                    models for study of respiratory infection in CF focus exclusively on the lungs. Furthermore, animal models, widely used to bridge the gap between\n                    <ns4:italic>in vitro<\/ns4:italic>\n                    systems and the clinical scenario, do not allow the upper and lower airways to be studied in isolation. We have developed a suite of culture media reproducing key features of the upper and lower airways, for the study of bacterial adaptation and evolution in different respiratory environments. For both upper and lower airway-mimicking media, we have developed formulations that reflect airway conditions in health and those that reflect the altered environment of the CF respiratory tract. Here, we describe the development and validation of these media and their use for study of genetic and phenotypic adaptations in\n                    <ns4:italic>P. aeruginosa<\/ns4:italic>\n                    during growth under upper or lower airway conditions in health and in CF.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.125074.2","type":"journal-article","created":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T05:55:13Z","timestamp":1669787713000},"page":"1007","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":26,"title":["Development of liquid culture media mimicking the conditions of sinuses and lungs in cystic fibrosis and health"],"prefix":"10.12688","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8867-2925","authenticated-orcid":false,"given":"Dilem","family":"Ruhluel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2741-6172","authenticated-orcid":false,"given":"Siobhan","family":"O'Brien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne L","family":"Fothergill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7911-8153","authenticated-orcid":false,"given":"Daniel R","family":"Neill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2022,11,30]]},"reference":[{"key":"ref3","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1186\/s12890-016-0339-5","article-title":"Cystic fibrosis lung environment and Pseudomonas aeruginosa infection.","volume":"16","author":"A Bhagirath","year":"2016 Dec 5","journal-title":"BMC Pulm. 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[Dataset].","author":"D Ruhluel","year":"2022"}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,2]],"date-time":"2022-12-02T04:41:52Z","timestamp":1669956112000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,30]]},"references-count":82,"URL":"https:\/\/doi.org\/10.12688\/f1000research.125074.2","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.141209.r156986","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.141209.r156986","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,30]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.141209.r156986, Ville-Petri Friman, Department of Biology, University of York, York, UK, 02 Dec 2022, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2#referee-response-156986","order":0,"name":"referee-response-156986","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.137340.r152082, Sheyda Azimi, Jelly Vanderwoude, School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia State University, Atlanta, GA, USA, 25 Oct 2022, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/11-1007\/v1#referee-response-152082","order":1,"name":"referee-response-152082","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>DILEM RUHLUEL<\/b>; \n<i>Posted: 18 Nov 2022<\/i>; Thank you for the positive comments regarding the manuscript and for your helpful suggestions for improvements and discussion points. We have addressed each point raised, below and have submitted an updated manuscript version in which the changes have been made.  \n<i>The authors determined these novel media's viability over 30 days by measuring PAO1 biofilm formation at 0, 10, 20, and 30 days. While it is nice to show that the media sustain similar levels of biofilm growth regardless of whether the media is freshly prepared, this might not be the best indicator of media stability over long periods. Instead, it would have been nice to see the authors conduct LCMS analyses to determine the stability of each of the chemical components at 0 and 30 days and detect if any possible degradation had occurred. Also, it is important to determine whether the growth of&nbsp;P. aeruginosa&nbsp;in the stored media displays any altered metabolism, physiology, or spatial organization.<\/i>  We agree both that LCMS would offer a more complete determination of chemical stability and that investigation of bacterial metabolism, physiology and spatial organisation would be desirable. We have added a sentence to the discussion, highlighting the need for further studies into media stability. These studies are underway in our lab.  \n<i>Additionally, instead of hand-picking a short list of four genes, it would have greatly strengthened the supporting case for these novel media by RNA-seq analysis. For example, comparing the entire transcriptional profile of&nbsp;P. aeruginosa&nbsp;grown in new media (fresh and stored at 4&deg; C) to the transcriptional profile of cells grown in SCFM2 and&nbsp;in vivo&nbsp;samples would confirm the similarity of these preclinical models to the infection and healthy environments.  I also understand that these experiments can be addressed in the future and are out of the scope of this study, which aimed to introduce these novel media for upper and lower respiratory tracts; however, I recommend that authors address this in the discussion section. I recommend authors include these studies and discuss the key benefits of using the novel HSM, CFSM, HLM, and CFLM media over the other versions available.<\/i>  We completely agree and these studies have already begun. The large RNAseq dataset will require careful analysis. We feel that the space and word count needed to describe those data fully would make the current manuscript overly lengthy. As the reviewers suggest, we have instead mentioned the need for these investigations in the discussion.  \n<i>In the section titled \u201cAirway mimicking media is stable for at least 30 days at 4&deg; C,\u201d the wording of the first sentence leads to some confusion. At first glance, it appears to imply that PAO1 was cultured for 30 days, although the authors meant to say that PAO1 was cultured in media that had been stored for 30 days. The authors may want to re-write this sentence to avoid confusion.<\/i>  Sorry for this confusion, we have now reworded the sentence.  \n<i>In Tables 3, 8, and 12, please use a consistent format for the concentration units \u03bcg\/L or \u03bcg\/l.<\/i>  We have now used \u03bcg\/l throughout.  \n<i>In Figure 5, the legend below the chart is redundant, as it shows the same data as the labels on the X-axis. I would recommend removing this legend to simplify the readers' view.<\/i>  This figure has been reworked and the legend removed.  \n<i>In Figure 6, standard deviation bars and significance labels would help the reader understand which relationships are significant without having to reference the text.<\/i>  Standard deviation bars and significance labels have now been added to these graphs and we have described ANOVA summary statistics in the main text.  \n<i>There are studies on the evolution of&nbsp;P. aeruginosa&nbsp;in TSB, SCFM, and SCFM2 by Schick A, Kassen R (2018)1<\/i>\n<i>, Azimi&nbsp;et al.,&nbsp;20202<\/i>\n<i>, and Flynn&nbsp;et al.,&nbsp;20163<\/i>\n<i>, showing the emergence of various morphotypes in the populations that authors may want to include.<\/i>  Thank you for highlighting this. Reference to these studies has been added to our discussion.  \n<i>The emergence of the observed morphotypes and phenotypes in this study is similar to what is observed as a result of evolving&nbsp;P. aeruginosa&nbsp;in other preclinical infection models are not unique to novel developed media. I suggest that authors include&nbsp;previous studies, discussing how future studies of genetic and phenotypic adaptation to the developed media are required. Thus, future analysis can confirm the unique adaptive traits observed in this study, similar to upper and lower CF respiratory infections.<\/i>  Thank you for this suggestion. We have added the three references mentioned in the previous comment, alongside some discussion of the need to deconvolute those phenotypes that are adaptive for different respiratory environments from those that are merely adaptive to different modes of growth.  \n<i>In Table 14, I believe the title is somewhat of a misnomer. The table shows when each morphotype appears and whether it is maintained in the populations. I would consider re-titling this table to reflect the prevalence of each morphotype over the evolution period.<\/i>  We have re-titled this table. Unfortunately, these data were captured as presence\/absence for each morphotype, at each time point. We don\u2019t, therefore, have information on relative or absolute morphotype abundance over time.","URL":"https:\/\/f1000research.com\/articles\/11-1007\/v2#referee-comment-9031","order":2,"name":"referee-comment-9031","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work is supported by an NC3Rs PhD studentship grant (NC\/S001700\/1), awarded to DN and JF. JF and DN acknowledge grant support for the Strategic Research Centre (SRC) \u201cAn evidence-based preclinical framework for the development of antimicrobial therapeutics in cystic fibrosis\u201d (PIPE-CF; Project No. SRC 022) from the UK Cystic Fibrosis Trust and CF Foundation (US).","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}