{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T17:14:43Z","timestamp":1774286083426,"version":"3.50.1"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T00:00:00Z","timestamp":1771027200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T00:00:00Z","timestamp":1774224000000},"content-version":"vor","delay-in-days":37,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42377106"],"award-info":[{"award-number":["42377106"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Res Notes"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>Dietary fiber is a key modulator of the gut microbiome, yet its specific role following antibiotic exposure remains under-characterized in large populations. Previous studies suggest high-fiber diets promote recovery, but often rely on small cohorts. We aimed to re-evaluate these microbial signatures and their association with current microbiome states in a large, diverse adult population.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We analyzed 16\u00a0S rRNA gene sequencing data from the American Gut Project (AGP). Participants with recent antibiotic exposure were stratified by high-fiber (HF;\n                      <jats:italic>N<\/jats:italic>\n                      \u2009=\u2009971) or low-fiber (LF;\n                      <jats:italic>N<\/jats:italic>\n                      \u2009=\u2009955) intake. We assessed alpha and beta diversity and identified differentially abundant genera using LEfSe. Key biomarkers were validated using ANCOM-BC and multivariable linear regression adjusting for age, sex, and BMI.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Contrary to previous models, high-fiber intake was not associated with a uniform enrichment of commensal Clostridia. Instead,\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      and\n                      <jats:italic>Lachnospira<\/jats:italic>\n                      were identified as genus-level biomarkers significantly enriched in the HF group, while\n                      <jats:italic>Bacteroides<\/jats:italic>\n                      and\n                      <jats:italic>Parabacteroides<\/jats:italic>\n                      were enriched in the LF group. These associations were confirmed to be robust by multivariable linear regression (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.001). High-fiber intake was not associated with significantly higher alpha diversity within the one-month post-antibiotic timeframe.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Post-antibiotic microbiome signatures associated with fiber intake are distinct and specific. We identified\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      and\n                      <jats:italic>Lachnospira<\/jats:italic>\n                      as robust targets for dietary interventions, challenging simplistic models of recovery and highlighting the need for precision nutrition strategies to enhance gut resilience.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13104-026-07708-7","type":"journal-article","created":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T07:35:14Z","timestamp":1771054514000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Re-evaluating gut microbiome signatures of post-antibiotic dietary fiber intake in a large adult cohort"],"prefix":"10.1186","volume":"19","author":[{"given":"Yuwei","family":"Tang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xi","family":"Fu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,2,14]]},"reference":[{"issue":"6","key":"7708_CR1","doi-asserted-by":"publisher","first-page":"e517","DOI":"10.1016\/S2666-5247(24)00020-X","volume":"5","author":"Y Sun","year":"2024","unstructured":"Sun Y, Fu X. Comprehensive examination of travel-related antimicrobial resistance and the gut Microbiome. Lancet Microbe. 2024;5(6):e517.","journal-title":"Lancet Microbe"},{"issue":"4","key":"7708_CR2","doi-asserted-by":"publisher","first-page":"ofx171","DOI":"10.1093\/ofid\/ofx171","volume":"4","author":"AY Guh","year":"2017","unstructured":"Guh AY, Adkins SH, Li Q, Bulens SN, Farley MM, Smith Z, Holzbauer SM, Whitten T, Phipps EC, Hancock EB, et al. Risk factors for Community-Associated clostridium difficile infection in adults: A Case-Control study. Open Forum Infect Dis. 2017;4(4):ofx171.","journal-title":"Open Forum Infect Dis"},{"issue":"12 Suppl 2","key":"7708_CR3","doi-asserted-by":"publisher","first-page":"S194","DOI":"10.1093\/infdis\/jiaa408","volume":"223","author":"CM Pike","year":"2021","unstructured":"Pike CM, Theriot CM. Mechanisms of colonization resistance against clostridioides difficile. J Infect Dis. 2021;223(12 Suppl 2):S194\u2013200.","journal-title":"J Infect Dis"},{"issue":"3","key":"7708_CR4","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.chom.2020.12.012","volume":"29","author":"C Tanes","year":"2021","unstructured":"Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Roy Paladhi U, Chau L, Panfen E, Fischbach MA, Braun J, et al. Role of dietary fiber in the recovery of the human gut Microbiome and its metabolome. Cell Host Microbe. 2021;29(3):394\u2013e407395.","journal-title":"Cell Host Microbe"},{"key":"7708_CR5","doi-asserted-by":"crossref","unstructured":"Hewlett KK, PeBenito A, Hecht AL, Tiffany C, Tanes C, Glover RC, Fawad JA, Friedman ES, Reynolds JC, Bittinger K et al. Dietary fiber modulates the window of susceptibility to Clostridioides difficile infection. Gastroenterology 2025.","DOI":"10.1053\/j.gastro.2025.04.027"},{"key":"7708_CR6","doi-asserted-by":"publisher","unstructured":"McDonald D, Hyde E, Debelius Justine W, Morton James T, Gonzalez A, Ackermann G, Aksenov Alexander A, Behsaz B, Brennan C, Chen Y et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 2018, 3(3):https:\/\/doi.org\/10.1128\/msystems.00031","DOI":"10.1128\/msystems.00031"},{"issue":"8","key":"7708_CR7","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible Microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852\u20137.","journal-title":"Nat Biotechnol"},{"issue":"7","key":"7708_CR8","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from illumina amplicon data. Nat Methods. 2016;13(7):581\u20133.","journal-title":"Nat Methods"},{"issue":"7","key":"7708_CR9","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","volume":"72","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069\u201372.","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"7708_CR10","doi-asserted-by":"publisher","first-page":"3514","DOI":"10.1038\/s41467-020-17041-7","volume":"11","author":"H Lin","year":"2020","unstructured":"Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020;11(1):3514.","journal-title":"Nat Commun"},{"issue":"Suppl 1Suppl 1","key":"7708_CR11","doi-asserted-by":"publisher","first-page":"4554","DOI":"10.1073\/pnas.1000087107","volume":"108","author":"L Dethlefsen","year":"2011","unstructured":"Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108(Suppl 1Suppl 1):4554\u201361.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"7708_CR12","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/nri3535","volume":"13","author":"CG Buffie","year":"2013","unstructured":"Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol. 2013;13(11):790\u2013801.","journal-title":"Nat Rev Immunol"},{"issue":"3","key":"7708_CR13","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/s12263-010-0206-6","volume":"6","author":"K Pokusaeva","year":"2011","unstructured":"Pokusaeva K, Fitzgerald GF, van Sinderen D. Carbohydrate metabolism in bifidobacteria. Genes Nutr. 2011;6(3):285\u2013306.","journal-title":"Genes Nutr"},{"key":"7708_CR14","first-page":"925","volume":"7","author":"A O\u2019Callaghan","year":"2016","unstructured":"O\u2019Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol. 2016;7:925.","journal-title":"Front Microbiol"},{"issue":"2","key":"7708_CR15","doi-asserted-by":"publisher","first-page":"e00889","DOI":"10.1128\/mBio.00889-14","volume":"5","author":"M Vital","year":"2014","unstructured":"Vital M, Howe AC, Tiedje JM, Moran MA. Revealing the bacterial butyrate synthesis pathways by analyzing (Meta)genomic data. mBio. 2014;5(2):e00889\u201300814.","journal-title":"mBio"},{"key":"7708_CR16","doi-asserted-by":"publisher","first-page":"1186892","DOI":"10.3389\/fimmu.2023.1186892","volume":"14","author":"XF Liu","year":"2023","unstructured":"Liu XF, Shao JH, Liao YT, Wang LN, Jia Y, Dong PJ, Liu ZZ, He DD, Li C, Zhang X. Regulation of short-chain fatty acids in the immune system. Front Immunol. 2023;14:1186892.","journal-title":"Front Immunol"},{"issue":"4","key":"7708_CR17","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/s41429-023-00595-1","volume":"76","author":"AA Kadry","year":"2023","unstructured":"Kadry AA, El-Antrawy MA, El-Ganiny AM. Impact of short chain fatty acids (SCFAs) on antimicrobial activity of new \u03b2-lactam\/\u03b2-lactamase inhibitor combinations and on virulence of Escherichia coli isolates. J Antibiot (Tokyo). 2023;76(4):225\u201335.","journal-title":"J Antibiot (Tokyo)"},{"issue":"8","key":"7708_CR18","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1038\/s41577-024-01014-8","volume":"24","author":"ER Mann","year":"2024","unstructured":"Mann ER, Lam YK, Uhlig HH. Short-chain fatty acids: linking diet, the Microbiome and immunity. Nat Rev Immunol. 2024;24(8):577\u201395.","journal-title":"Nat Rev Immunol"},{"issue":"5","key":"7708_CR19","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1016\/j.cell.2016.10.043","volume":"167","author":"MS Desai","year":"2016","unstructured":"Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, et al. A dietary Fiber-Deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016;167(5):1339\u2013e13531321.","journal-title":"Cell"},{"issue":"20","key":"7708_CR20","doi-asserted-by":"publisher","first-page":"3705","DOI":"10.1016\/j.cell.2022.09.007","volume":"185","author":"E Hayase","year":"2022","unstructured":"Hayase E, Hayase T, Jamal MA, Miyama T, Chang CC, Ortega MR, Ahmed SS, Karmouch JL, Sanchez CA, Brown AN, et al. Mucus-degrading bacteroides link carbapenems to aggravated graft-versus-host disease. Cell. 2022;185(20):3705\u2013e37193714.","journal-title":"Cell"},{"issue":"7","key":"7708_CR21","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1016\/j.tim.2014.04.003","volume":"22","author":"D Paredes-Sabja","year":"2014","unstructured":"Paredes-Sabja D, Shen A, Sorg JA. Clostridium difficile spore biology: sporulation, germination, and spore structural proteins. Trends Microbiol. 2014;22(7):406\u201316.","journal-title":"Trends Microbiol"},{"key":"7708_CR22","doi-asserted-by":"crossref","unstructured":"Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ. Gut microbiota and colonization resistance against bacterial enteric infection. Microbiol Mol Biology Reviews: MMBR 2019, 83(3).","DOI":"10.1128\/MMBR.00007-19"},{"key":"7708_CR23","doi-asserted-by":"crossref","unstructured":"Mart\u00edn R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Berm\u00fadez-Humar\u00e1n LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023, 47(4).","DOI":"10.1093\/femsre\/fuad039"},{"key":"7708_CR24","doi-asserted-by":"publisher","first-page":"200315","DOI":"10.1016\/j.hnm.2025.200315","volume":"40","author":"X Sun","year":"2025","unstructured":"Sun X, Zhang Z, Hu J. Isolation, probiotic characterization and whole-genome sequencing of gut Faecalibacterium Prausnitzii. Hum Nutr Metabolism. 2025;40:200315.","journal-title":"Hum Nutr Metabolism"},{"key":"7708_CR25","doi-asserted-by":"publisher","first-page":"113868","DOI":"10.1016\/j.bcp.2020.113868","volume":"175","author":"R Lin","year":"2020","unstructured":"Lin R, Sun Y, Mu P, Zheng T, Mu H, Deng F, Deng Y, Wen J. Lactobacillus rhamnosus GG supplementation modulates the gut microbiota to promote butyrate production, protecting against Deoxynivalenol exposure in nude mice. Biochem Pharmacol. 2020;175:113868.","journal-title":"Biochem Pharmacol"},{"key":"7708_CR26","doi-asserted-by":"publisher","first-page":"102841","DOI":"10.1016\/j.tmaid.2025.102841","volume":"65","author":"E Abbasi","year":"2025","unstructured":"Abbasi E. The impact of climate change on travel-related vector-borne diseases: A case study on dengue virus transmission. Travel Med Infect Dis. 2025;65:102841.","journal-title":"Travel Med Infect Dis"}],"container-title":["BMC Research Notes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13104-026-07708-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13104-026-07708-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13104-026-07708-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T16:44:30Z","timestamp":1774284270000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13104-026-07708-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,14]]},"references-count":26,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["7708"],"URL":"https:\/\/doi.org\/10.1186\/s13104-026-07708-7","relation":{},"ISSN":["1756-0500"],"issn-type":[{"value":"1756-0500","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,14]]},"assertion":[{"value":"21 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 February 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 February 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study utilized publicly available, de-identified data from the American Gut Project (AGP). The original AGP study was approved by the University of California, San Diego Institutional Review Board, and all participants provided written informed consent.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"124"}}