Protein-Calorie Malnutrition Is Associated with Altered Colonic Mucosal Microbiota in Inflammatory Bowel Disease

Background/Objectives: Protein-calorie malnutrition (PCM) is common among patients with inflammatory bowel disease (IBD). However, the relationship between PCM and the gut microbiota in patients with IBD remains unclear. This study aimed to investigate the association between PCM and the colonic mucosal microbiota in patients with IBD. Methods: Colonic mucosal samples were obtained from 24 IBD patients with PCM and 24 IBD type-matched patients without PCM. PCM was defined as a body mass index (BMI) < 18.5 kg/m2 and/or weight loss of ≥10% within the preceding 6 months. The full-length bacterial 16S ribosomal RNA gene (V1–V9) was sequenced using the PacBio Sequel IIe. Alpha and beta diversity and species-level differential abundance were analyzed, adjusting for age, sex, BMI, and disease type. Results: Among 48 patients (36 Crohn’s disease and 12 ulcerative colitis), diversity indices (Chao1, p = 0.474; Shannon, p = 0.931) and overall composition (Bray–Curtis, p = 0.719) did not differ by PCM status, although microbial composition was associated with age (p = 0.011) and biopsy-site inflammation (p = 0.001). PCM was associated with 12 differentially abundant taxa, including enrichment of Intestinibacter bartlettii and depletion of Bifidobacterium longum, Sphingomonas leidyi, and Clostridium innocuum, along with changes in several previously unclassified species. Conclusions: IBD patients with PCM exhibited shifts in the colonic mucosal microbiota including reduction in Bifidobacterium longum, a well-known probiotic. Further investigations into the role of the microbiota in PCM in IBD patients and the potential beneficial effects of probiotics are warranted.