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Fecal swabs and saliva samples were collected from the participants. 16S ribosomal RNA gene sequencing was performed on the samples. Compared with the HC group, reduced bacterial richness and diversity were detected in the feces of patients with SLE, and increased bacterial diversity in their saliva. Both feces and saliva samples explained the cohort variation. The feces were characterized by enrichment of <jats:italic>Lactobacillus<\/jats:italic>, and depletion of an unclassified bacterium in the Ruminococcaceae family and <jats:italic>Bifidobacterium<\/jats:italic>. Lack of <jats:italic>Bifidobacterium<\/jats:italic> was observed in patients with arthritis. <jats:italic>Akkermansia<\/jats:italic> and <jats:italic>Ruminococcus<\/jats:italic> negatively correlated with the serum levels of C3. In saliva, <jats:italic>Veillonella<\/jats:italic>, <jats:italic>Streptococcus<\/jats:italic>, and <jats:italic>Prevotella<\/jats:italic> were dominant, and <jats:italic>Bacteroides<\/jats:italic> was negatively associated with disease activity. These findings can assist us to comprehensively understand the bacterial profiles of different body niches in SLE patients.<\/jats:p>","DOI":"10.3389\/fimmu.2021.626217","type":"journal-article","created":{"date-parts":[[2021,7,1]],"date-time":"2021-07-01T17:08:15Z","timestamp":1625159295000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":47,"title":["Distinct Microbiomes of Gut and Saliva in Patients With Systemic Lupus Erythematous and Clinical 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