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However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole\u2010metagenome shotgun sequencing on fecal samples from 30 patients with RA\u2010ILD, and 30 with RA\u2010non\u2010ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference\u2010based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA\u2010ILD and RA\u2010non\u2010ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as <jats:italic>Bifidobacterium longum<\/jats:italic>, <jats:italic>Dorea formicigenerans<\/jats:italic>, and <jats:italic>Collinsella aerofaciens<\/jats:italic> were enriched in both patient groups. <jats:italic>Ruminococcus gnavus<\/jats:italic> (RA\u2010ILD), <jats:italic>Gemmiger formicilis<\/jats:italic>, and <jats:italic>Ruminococcus bromii<\/jats:italic> (RA\u2010non\u2010ILD) were uniquely enriched. Conversely, <jats:italic>Faecalibacterium prausnitzii<\/jats:italic>, <jats:italic>Bacteroides<\/jats:italic> spp., and <jats:italic>Roseburia inulinivorans<\/jats:italic> showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including <jats:italic>Saccharomyces cerevisiae<\/jats:italic> and <jats:italic>Candida albicans<\/jats:italic>, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA\u2010ILD and RA\u2010non\u2010ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA\u2010ILD and RA\u2010non\u2010ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research.<\/jats:p>","DOI":"10.1002\/jmv.29781","type":"journal-article","created":{"date-parts":[[2024,7,4]],"date-time":"2024-07-04T07:25:35Z","timestamp":1720077935000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis\u2010associated interstitial lung disease"],"prefix":"10.1002","volume":"96","author":[{"given":"Yida","family":"Xing","sequence":"first","affiliation":[{"name":"Department of Rheumatology Second Affiliated Hospital of Dalian Medical University Dalian 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