{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T06:18:13Z","timestamp":1787811493691,"version":"build-2784847793"},"reference-count":66,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Colonization factors (CFs) are important microbial traits associated with persistence and host adaptation in the gut, yet their large-scale organization in cervid gut microbiomes remains unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A total of 3,311 non-redundant high-quality metagenome-assembled genomes (MAGs), derived from 688 cervid gut metagenomic samples across 15 publicly available projects and one in-house dataset, were analyzed. CF-associated genes were identified by comparison against the GHA CF database, and CF repertoires were characterized at genome, host-species, and gastrointestinal-segment levels.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>A total of 138,729 CF-associated genes spanning 71 CF families were identified. MAGs from Cervinae contained richer CF repertoires than those from Caprinae, and CF47 (Peptidase_C69), CF24_29 (QueH), and CF18 (Glycos_transf_2) were among the most prevalent families. CF repertoires were strongly structured by taxonomy, showed a moderate association with bacterial phylogenetic distance, and formed two recurrent genome-level configurations with distinct KEGG functional profiles. Integration of sample metadata further revealed differentiation of CF repertoires across host species and gastrointestinal segments, representing the major ecological dimensions examined in this study. Segment-associated CF variation was accompanied by redistribution of broader functional profiles, including enrichment of carbohydrate and lipid metabolism in the jejunum, membrane transport in the ileum, xenobiotics biodegradation in the cecum, and environmental adaptation in the rumen.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>These findings provide a genome-resolved view of CF repertoire organization in cervid gut microbiomes and demonstrate that colonization-associated functions are structured across microbial lineages and ecological contexts. This study highlights the importance of considering microbial taxonomy and host-associated environments when interpreting the distribution of CF repertoires in mammalian gut ecosystems.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1929306","type":"journal-article","created":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T05:34:15Z","timestamp":1787808855000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-resolved analysis of colonization factor repertoires reveals ecological stratification in cervid gut microbiomes"],"prefix":"10.3389","volume":"17","author":[{"given":"Hao","family":"Ni","sequence":"first","affiliation":[{"name":"College of Life Sciences, Changchun Sci-Tech University, Changchun","place":["Jilin, China"]},{"name":"College of Food and Pharmaceutical Engineering, Wuzhou University","place":["Wuzhou, China"]},{"name":"College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing","place":["Heilongjiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing-Long","family":"Gong","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Jilin Agricultural University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Ming","family":"Li","sequence":"additional","affiliation":[{"name":"College of Chinese Medicine Materials, Jilin Agricultural University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Jilin Agricultural University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue","family":"Leng","sequence":"additional","affiliation":[{"name":"College of Chinese Medicine Materials, Jilin Agricultural University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Hao","family":"Song","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Jilin Agricultural University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Changchun Sci-Tech University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhong-Yuan","family":"Li","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Drug Discovery and Optimization, Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, Key Laboratory of Medical Biotechnology and Translational Medicine, School of Pharmacy, Guilin Medical University","place":["Guilin, China"]},{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao","place":["Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Li","sequence":"additional","affiliation":[{"name":"College of Food and Pharmaceutical Engineering, Wuzhou University","place":["Wuzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Zhe","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Jilin Agricultural University, Changchun","place":["Jilin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1007\/s00018-018-2943-4","article-title":"An insight into gut microbiota and its functionalities.","volume":"76","author":"Adak","year":"2019","journal-title":"Cell. 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