Increased Relative Abundance of Lactobacilli Species in the Gut Microbiota of Patients with Crohn’s Disease and Ulcerative Colitis

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Abstract
Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are associated with gut microbiota alterations. While lactobacilli are traditionally considered beneficial probiotics, recent studies report their increased abundance in IBD, suggesting a more complex role. This study aimed to assess the species diversity and representation of lactobacilli in CD and UC patients compared to healthy volunteers. Fecal samples from 40 CD patients, 40 UC patients, and 42 healthy controls were analyzed using 16S rRNA sequencing, shotgun metagenomic sequencing, and qPCR. Both sequencing methods revealed significantly higher Lactobacillaceae family relative proportions in IBD patients versus healthy controls. qPCR confirmed the overall relative enrichment of lactobacilli, while species-level differences were identified by both 16S rRNA and shotgun metagenomic sequencing. Over 28% of IBD patients harbored six or more lactobacilli species versus only 2% of controls. Species-level analysis identified Ligilactobacillus salivarius, Lactobacillus gasseri, and Limosilactobacillus mucosae as having significantly higher relative abundances in IBD patients. The increased occurrence of specific species with known virulence potential challenges the traditional view of lactobacilli as universally beneficial, indicating that certain lactobacilli may be associated with dysbiosis in IBD.
Funding Information
  • Kazan Federal University (FZSM-2026-0005)