{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:17:41Z","timestamp":1785403061499,"version":"3.56.0"},"reference-count":40,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["OTOOLE22G0"],"award-info":[{"award-number":["OTOOLE22G0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-ES033988"],"award-info":[{"award-number":["R01-ES033988"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30-DK117469"],"award-info":[{"award-number":["P30-DK117469"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Cystic fibrosis (CF) alters gut physiology, yet its impact on microbial communities across colonic regions (ascending, transverse, descending colon) and microhabitats (lumen, mucosa) remains incompletely understood. Here, we applied culturomics to characterize gut microbiota in a small cohort of 32 individuals (22 non-CF, 10 CF). Persons with CF (pwCF) exhibited significantly higher viable bacterial loads than non-CF individuals, particularly in mucosal samples. Anaerobes predominated overall, with relative enrichment of aerobes in the mucosa of pwCF. Alpha diversity was reduced in mucosal samples and aerobic cultures for pwCF, whereas beta diversity was influenced by all the tested variables except the colonic region. Phylum-level analyses revealed enrichment of Proteobacteria and depletion of Actinobacteria, Bacteroidota, and Firmicutes in samples from pwCF, consistent with stool analysis. Random forest models identified selected oral-associated microbes as key predictive taxa and accurately classified polyp status within this cohort. Whole-genome sequencing of\n                      <jats:italic toggle=\"yes\">Bacteroides fragilis<\/jats:italic>\n                      (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 21) and\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 15) isolates, representing a subset of 109 gut bacterial genomes sequenced from this cohort, revealed minimal genomic variation across colonic regions and sample types, indicating intra-individual strain stability. The understandings from this pilot culturome study, after future validation, may help in developing targeted microbial therapeutic approaches to address the gut dysbiosis of CF.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>This pilot study of a small cohort represents the first culturome analysis of the cystic fibrosis colon. Our preliminary findings demonstrate that cystic fibrosis (CF)-associated gut dysbiosis is spatially specific, with mucosal bacterial communities showing pronounced alterations while luminal communities show comparatively subtle phylum-specific shifts. This spatial specificity suggests the mucosal microenvironment as a potential therapeutic target and indicates that interventions focused solely on luminal bacteria may be insufficient. The promising predictive accuracy of culturome-based machine learning models in this small cohort suggests these viable bacterial signatures could serve as biomarkers for CF management pending larger validation studies. Additionally, our initial observations of CFTR modulator effects on gut microbial communities provide insight for future studies optimizing combination therapies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03126-25","type":"journal-article","created":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T14:05:22Z","timestamp":1772201122000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["The regional landscape of the human colon culturome in health and cystic fibrosis"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2942-6315","authenticated-orcid":false,"given":"Sarvesh V.","family":"Surve","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca A.","family":"Valls","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaitlyn E.","family":"Barrack","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorraine L.","family":"Gwilt","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00d1dhh09","id-type":"ROR","asserted-by":"publisher"}],"name":"Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center","place":["Lebanon, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy B.","family":"Gardner","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00d1dhh09","id-type":"ROR","asserted-by":"publisher"}],"name":"Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center","place":["Lebanon, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2861-4392","authenticated-orcid":true,"given":"George A.","family":"O'Toole","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.2570460"},{"key":"e_1_3_4_3_2","unstructured":"Cystic Fibrosis Foundation. 2023. Patient registry annual data report"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10620-022-07812-1"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1080\/17476348.2023.2228194"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00167-25"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a009753"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep22493"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.05933-11"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cit715"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00274-19"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0714-x"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-017-0968-8"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03420-24"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jpeds.2015.02.049"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.medmic.2022.100057"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00311-21"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03144-23"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3552"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0041-0"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217"},{"key":"e_1_3_4_23_2","article-title":"Genome sequences of 109 gut bacteria isolated from colonoscopy samples of individuals with and without cystic fibrosis","author":"Surve SV","unstructured":"Surve SV, Valls RA, O\u2019Toole GA. Genome sequences of 109 gut bacteria isolated from colonoscopy samples of individuals with and without cystic fibrosis. Microbiol Resour Announc in press.","journal-title":"Microbiol Resour Announc"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00834-3"},{"key":"e_1_3_4_25_2","unstructured":"NHLBI NIH. Calculate your BMI. Available from: https:\/\/www.nhlbi.nih.gov\/calculate-your-bmi. Retrieved 26 Sep 2025."},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1002\/jpn3.12350"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","unstructured":"Valls R Barrack KE O\u2019Toole G Bliska JB Surve S. 2025. Sex and regional effects of Bacteroides in the gut. bioRxiv. doi:10.1101\/2025.08.27.672693","DOI":"10.1101\/2025.08.27.672693"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02574-12"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1312524110"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00286-23"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01451-25"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2022.12.017"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-10328-3"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-021-02305-z"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1908639"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2024.05.002"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2025.05.006"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmjgast-2019-000297"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-024-01680-3"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01384-21"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-40182-9"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03126-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03126-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T13:10:37Z","timestamp":1775567437000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.03126-25"}},"subtitle":[],"editor":[{"given":"Wei-Hua","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,7]]},"references-count":40,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4,7]]}},"alternative-id":["10.1128\/spectrum.03126-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.03126-25","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.09.29.679198","asserted-by":"object"}]},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,7]]},"assertion":[{"value":"2025-10-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-21","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-27","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03126-25"}}