{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T23:35:03Z","timestamp":1792798503820,"version":"4.5.0"},"reference-count":41,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,8,23]],"date-time":"2025-08-23T00:00:00Z","timestamp":1755907200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"B-CTS-100-UGR20, I+D+i Programa operative FEDER Andaluc\u00eda 2014\u20132020"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Medical Sciences"],"abstract":"<jats:p>Introduction: Gut dysbiosis has been associated with the development of autoimmune diseases, including systemic lupus erythematosus (SLE). Although previous studies suggest microbial alterations in SLE, evidence at the species level and its clinical relevance remain limited. This study aimed to characterise the gut microbiota at species level in SLE patients and evaluate its association with clinical features. Materials and methods: A total of 57 SLE patients and 57 matched controls were included. Faecal samples were collected using the OMNIgene-GUT kit, and microbial DNA was extracted with the Maxwell RSC PureFood GMO kit. Metagenomic sequencing was performed using the Illumina MiSeq platform, and the data was analysed with QIIME2. Microbial diversity and relative abundance were assessed using the phyloseq package, and differentially abundant taxa were identified using DESeq2. Clinical subgroups among SLE patients were identified via k-means clustering. Results: SLE patients exhibited significantly different beta diversity compared to controls (p = 0.001), with increased abundance of Pseudomonadota (3.81% vs. 6.80%, p &lt; 0.05) and decreased Bacteroidota (53.42% vs. 38.04%, p &lt; 0.05). Only 10 bacterial species were consistently present across all SLE samples, including Akkermansia muciniphila, Bacteroides dorei, and Lactobacillus gasseri. Hypertensive patients and those treated with corticosteroids presented a marked depletion of key microbial taxa. Conversely, Belimumab-treated patients displayed a distinct microbiota enriched in species such as Alistipes shahii and Prevotella corporis. Conclusions: This study confirms significant gut microbiota alterations in SLE and pinpoints microbial profiles associated with clinical subgroups. These findings suggest gut dysbiosis may contribute to SLE pathogenesis and indicate biomarkers for disease stratification.<\/jats:p>","DOI":"10.3390\/medsci13030151","type":"journal-article","created":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T00:09:32Z","timestamp":1756080572000},"page":"151","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Association of Gut Dysbiosis with Disease Phenotype and Treatment in Systemic Lupus Erythematosus"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1088-0032","authenticated-orcid":false,"given":"Irene","family":"Medina-Mart\u00ednez","sequence":"first","affiliation":[{"name":"University of Granada, 18016 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7479-1835","authenticated-orcid":false,"given":"Roc\u00edo","family":"Gil-Guti\u00e9rrez","sequence":"additional","affiliation":[{"name":"Department of Nursing, Faculty of Health Sciences, University of Granada, 18071 Granada, Spain"},{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Garc\u00eda-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"},{"name":"Microbiology Service, San Cecilio University Hospital, 18016 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7578-2682","authenticated-orcid":false,"given":"Francisco Javier","family":"de la Hera-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"},{"name":"Systemic Autoimmune Diseases Unit, San Cecilio University Hospital, 18016 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuria","family":"Navarrete-Navarrete","sequence":"additional","affiliation":[{"name":"Systemic Autoimmune Diseases Unit, Virgen de las Nieves University Hospital, 18014 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1789-4226","authenticated-orcid":false,"given":"M\u00f3nica","family":"Zamora-Pasadas","sequence":"additional","affiliation":[{"name":"Systemic Autoimmune Diseases Unit, Virgen de las Nieves University Hospital, 18014 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norberto","family":"Ortego-Centeno","sequence":"additional","affiliation":[{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"},{"name":"Department of Medicine, Faculty of Medicine, University of Granada, 18071 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Luis","family":"Callejas-Rubio","sequence":"additional","affiliation":[{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"},{"name":"Systemic Autoimmune Diseases Unit, San Cecilio University Hospital, 18016 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7611-781X","authenticated-orcid":false,"given":"Federico","family":"Garc\u00eda-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"},{"name":"Department of Clinical Microbiology, San Cecilio University Hospital, 18016 Granada, Spain"},{"name":"Biomedical Research Network Center, Infectious Diseases (CIBER-INFEC), 18100 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6876-3782","authenticated-orcid":false,"given":"Julio","family":"G\u00e1lvez-Peralta","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain"},{"name":"Biomedical Research Network Center, Liver and Digestive Diseases (CIBER-EHD), 18016 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1927-0628","authenticated-orcid":false,"given":"Alba","family":"Rodr\u00edguez-Nogales","sequence":"additional","affiliation":[{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"},{"name":"Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9165-4349","authenticated-orcid":false,"given":"Mar\u00eda","family":"Correa-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Department of Nursing, Faculty of Health Sciences, University of Granada, 18071 Granada, Spain"},{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blanca","family":"Rueda-Medina","sequence":"additional","affiliation":[{"name":"Department of Nursing, Faculty of Health Sciences, University of Granada, 18071 Granada, Spain"},{"name":"Institute for Biosanitary Research of Granada (ibs.Granada), 18012 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Wang, X., Yuan, W., Yang, C., Wang, Z., 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