{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T07:36:59Z","timestamp":1774251419601,"version":"3.50.1"},"reference-count":54,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T00:00:00Z","timestamp":1774224000000},"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. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable \u03b1-diversity, characterized by depletion of health-associated Firmicutes (e.g.,\n                      <jats:italic>Faecalibacterium<\/jats:italic>\n                      and\n                      <jats:italic>Roseburia<\/jats:italic>\n                      ) and enrichment of Proteobacteria (e.g.,\n                      <jats:italic>Klebsiella<\/jats:italic>\n                      ). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g.,\n                      <jats:italic>Fusarium<\/jats:italic>\n                      sp.\n                      <jats:italic>c181<\/jats:italic>\n                      ). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with\n                      <jats:italic>Faecalibacterium prausnitzii<\/jats:italic>\n                      and\n                      <jats:italic>Faecalibacterium<\/jats:italic>\n                      _SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1744020","type":"journal-article","created":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T06:43:00Z","timestamp":1774248180000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation"],"prefix":"10.3389","volume":"16","author":[{"given":"Wen","family":"Sun","sequence":"first","affiliation":[{"name":"Centre for Translational Medicine, Shenzhen Bao\u2019an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine","place":["Shenzhen, 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