Background Inflammatory bowel disease (IBD) has been associated with dysbiosis of the gut microbiota. The prevalence of overweight and obesity (OW/OB) in IBD patients is becoming significant, but the gut microbiota remains unexplored.

Methods Here, we conducted metagenomic shotgun sequencing on stool samples from 36 ulcerative colitis (UC) patients, 24 Crohn’s disease (CD) patients, and 31 healthy control (HC) individuals, including 12 control individuals and 15 patients with OW/OB.

Results Based on the taxonomic profiles of the gut microbiota, we found significant differences in the gut microbiota between patients with IBD and healthy individuals. BMI is an important factor influencing the differences in the microbiota between IBD patients.

Conclusions More importantly, we reported that Fusobacterium pseudoperiodonticum and Klebsiella variicola may potentially influence OW/OB individuals towards CD. Our analysis emphasizes the adverse effects of changes in the gut microbiota in OW/OB individuals, as well as the finding that the gut microbiota of OW/OB patients further promotes inflammation.