{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T16:05:35Z","timestamp":1791561935835,"version":"4.3.4"},"reference-count":31,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science and Technology Council","award":["MOST 109-2410-H-179-001-MY2"],"award-info":[{"award-number":["MOST 109-2410-H-179-001-MY2"]}]},{"award":["MOST 109-2410-H-179-001-MY2"],"award-info":[{"award-number":["MOST 109-2410-H-179-001-MY2"]}],"id":[{"id":"https:\/\/ror.org\/02kv4zf79","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nutrients"],"abstract":"<jats:p>Background\/Objectives: In this exploratory longitudinal study, we examined dietary intake and gut microbiota across preparation, competition, and transition phases in competitive long-distance runners and explored microbial patterns associated with phase-specific dietary intake. Methods: Seven competitive long-distance runners were assessed across three training phases. At each phase, dietary intake and body composition were assessed, and fecal samples were collected. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Phase-related taxonomic differences were evaluated using repeated-measures approaches with multiple-testing correction, and differential abundance analysis was performed using DESeq2 with participant identity included as a blocking factor. Additionally, exploratory k-means clustering based on energy, carbohydrate, and protein intake was used to characterize dietary intake patterns. Results: Energy, protein, and fat intake differed significantly across training phases, whereas carbohydrate intake did not reach statistical significance. Exploratory alpha- and beta-diversity analyses yielded no statistically detectable differences across phases. At the phylum level, Synergistetes showed an overall phase effect after FDR correction, although no pairwise comparison remained significant after Bonferroni adjustment. In the DESeq2 analysis, Haemophilus was more abundant during the transition than preparation phase, Enterococcus was more abundant during preparation than transition, and Cronobacter was more abundant during preparation than competition (all adjusted p &lt; 0.05). Exploratory dietary clustering identified additional cluster-associated microbial differences, but cluster membership substantially overlapped with the training phase. Conclusions: Dietary intake varied across the competitive training cycle. Community-level diversity results were presented for exploratory purposes only in this small cohort. A limited number of taxa showed phase-related differences after multiple-testing correction. Because dietary intake and training phase changed concurrently, the cluster-associated microbial findings should be interpreted as exploratory patterns within the combined nutritional and training context rather than as independent dietary effects.<\/jats:p>","DOI":"10.3390\/nu18183036","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T08:03:17Z","timestamp":1789632197000},"page":"3036","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Gut Microbiota and Dietary Intake Across Training Phases in Competitive Long-Distance Runners: An Exploratory Longitudinal Study"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-7407-3173","authenticated-orcid":false,"given":"Chun-Yu","family":"Kuo","sequence":"first","affiliation":[{"name":"Graduate Institute of Sports Science, National Taiwan Sport University, Taoyuan City 33301, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4638-5412","authenticated-orcid":false,"given":"Wan-Chun","family":"Chiu","sequence":"additional","affiliation":[{"name":"School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei City 11031, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Ting-Yin","family":"Chou","sequence":"additional","affiliation":[{"name":"Department of Sports Training Science-Athletics, National Taiwan Sport University, Taoyuan City 33301, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5086-5094","authenticated-orcid":false,"given":"Yi-Ju","family":"Hsu","sequence":"additional","affiliation":[{"name":"Graduate Institute of Sports Science, National Taiwan Sport University, Taoyuan City 33301, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1126\/science.1058709","article-title":"Commensal host-bacterial relationships in the gut","volume":"292","author":"Hooper","year":"2001","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"eabp9960","DOI":"10.1126\/science.abp9960","article-title":"The microbiome and gut homeostasis","volume":"377","author":"Lee","year":"2022","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Liu, X., Xu, M., Wang, H., and Zhu, L. (2025). Role and Mechanism of Short-Chain Fatty Acids in Skeletal Muscle Homeostasis and Exercise Performance. Nutrients, 17.","DOI":"10.3390\/nu17091463"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.jshs.2022.09.002","article-title":"Unlocking a novel determinant of athletic performance: The role of the gut microbiota, short-chain fatty acids, and \u201cbiotics\u201d in exercise","volume":"12","author":"Sales","year":"2023","journal-title":"J. Sport Health Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Clauss, M., G\u00e9rard, P., Mosca, A., and Leclerc, M. (2021). Interplay Between Exercise and Gut Microbiome in the Context of Human Health and Performance. Front. Nutr., 8.","DOI":"10.3389\/fnut.2021.637010"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"fuaf037","DOI":"10.1093\/femsre\/fuaf037","article-title":"Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience","volume":"49","author":"Mohr","year":"2025","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.jshs.2016.05.001","article-title":"Endurance exercise and gut microbiota: A review","volume":"6","author":"Mach","year":"2017","journal-title":"J. Sport Health Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1038\/s41591-019-0485-4","article-title":"Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism","volume":"25","author":"Scheiman","year":"2019","journal-title":"Nat. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1017\/S0029665114001463","article-title":"Links between diet, gut microbiota composition and gut metabolism","volume":"74","author":"Flint","year":"2015","journal-title":"Proc. Nutr. Soc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.1038\/s42255-024-01108-6","article-title":"Feeding gut microbes to nourish the brain: Unravelling the diet-microbiota-gut-brain axis","volume":"6","author":"Schneider","year":"2024","journal-title":"Nat. Metab."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1123\/ijsnem.2018-0305","article-title":"A Framework for Periodized Nutrition for Athletics","volume":"29","author":"Stellingwerff","year":"2019","journal-title":"Int. J. Sport Nutr. Exerc. Metab."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1007\/s40279-017-0694-2","article-title":"Periodized Nutrition for Athletes","volume":"47","author":"Jeukendrup","year":"2017","journal-title":"Sports Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1123\/ijsnem.2019-0004","article-title":"Contemporary Nutrition Strategies to Optimize Performance in Distance Runners and Race Walkers","volume":"29","author":"Burke","year":"2019","journal-title":"Int. J. Sport Nutr. Exerc. Metab."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Cao, W., He, Y., Fu, R., Chen, Y., Yu, J., and He, Z. (2025). A Review of Carbohydrate Supplementation Approaches and Strategies for Optimizing Performance in Elite Long-Distance Endurance. Nutrients, 17.","DOI":"10.3390\/nu17050918"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Patel, B.K., Patel, K.H., Lee, C.N., and Moochhala, S. (2024). Intestinal Microbiota Interventions to Enhance Athletic Performance-A Review. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms251810076"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e0012922","DOI":"10.1128\/msystems.00129-22","article-title":"Gut Microbial Stability is Associated with Greater Endurance Performance in Athletes Undertaking Dietary Periodization","volume":"7","author":"Furber","year":"2022","journal-title":"mSystems"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Kuo, C.Y., Lo, Y.C., Chen, W.L., and Hsu, Y.J. (2025). Phase-Specific Alterations in Gut Microbiota and Their Associations with Energy Intake and Nutritional Clustering in Competitive Weightlifters. Nutrients, 17.","DOI":"10.3390\/nu17203199"},{"key":"ref_18","unstructured":"Taiwan Food and Drug Administration (2025, October 14). Taiwanese Food Composition and Nutrient Database, Available online: https:\/\/consumer.fda.gov.tw\/Food\/TFND.aspx?nodeID=178."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"S17","DOI":"10.1080\/02640414.2011.585473","article-title":"Carbohydrates for training and competition","volume":"29","author":"Burke","year":"2011","journal-title":"J. Sports Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.jand.2015.12.006","article-title":"Position of the Academy of Nutrition and Dietetics, Dietitians of Canada, and the American College of Sports Medicine: Nutrition and Athletic Performance","volume":"116","author":"Thomas","year":"2016","journal-title":"J. Acad. Nutr. Diet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s12970-017-0189-4","article-title":"International Society of Sports Nutrition Position Stand: Protein and exercise","volume":"14","author":"Kerksick","year":"2017","journal-title":"J. Int. Soc. Sports Nutr."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5279","DOI":"10.1093\/nar\/21.22.5279","article-title":"Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride","volume":"21","author":"Zhu","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Friedman, J., and Alm, E.J. (2012). Inferring correlation networks from genomic survey data. PLoS Comput. Biol., 8.","DOI":"10.1371\/journal.pcbi.1002687"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1080\/17461391.2021.1933199","article-title":"The influence of exercise training volume alterations on the gut microbiome in highly-trained middle-distance runners","volume":"22","author":"Craven","year":"2022","journal-title":"Eur. J. Sport Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s12970-019-0290-y","article-title":"The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: An observational study","volume":"16","author":"Jang","year":"2019","journal-title":"J. Int. Soc. Sports Nutr."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Krawczyk, B., Wityk, P., Ga\u0142\u0119cka, M., and Michalik, M. (2021). The Many Faces of Enterococcus spp.-Commensal, Probiotic and Opportunistic Pathogen. Microorganisms, 9.","DOI":"10.3390\/microorganisms9091900"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"711","DOI":"10.4161\/19490976.2014.983774","article-title":"Cronobacter sakazakii: Stress survival and virulence potential in an opportunistic foodborne pathogen","volume":"5","author":"Feeney","year":"2014","journal-title":"Gut Microbes"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s40798-022-00453-8","article-title":"Effect of High-intensity Training and Probiotics on Gut Microbiota Diversity in Competitive Swimmers: Randomized Controlled Trial","volume":"8","author":"Bielik","year":"2022","journal-title":"Sports Med. Open"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/s40168-017-0320-4","article-title":"Community characteristics of the gut microbiomes of competitive cyclists","volume":"5","author":"Petersen","year":"2017","journal-title":"Microbiome"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"5","DOI":"10.20517\/mrr.2022.16","article-title":"Next-generation sequencing of the athletic gut microbiota: A systematic review","volume":"2","author":"Sabater","year":"2023","journal-title":"Microbiome Res. 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