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The microbiome can predict mucosal healing in small intestine in patients with Crohn’s disease



Mucosal healing is the main treatment goal for Crohn’s disease. In this situation, some patients have difficulty with endoscopic evaluation of the entire small intestine. Crohn’s disease is closely associated with the gut microbiota, but the relationship between the microbiome and disease activity in the small intestine remains unclear. We examined the association between the microbiome and endoscopic findings in the small intestine and determined whether the microbiome can predict mucosal healing.


The patients with Crohn’s disease who were scheduled for capsule or balloon-assisted endoscopy were included in this prospective study. Patients whose entire small intestine was evaluated were divided into two groups based on ulcerative findings. The microbiomes in the fecal samples were analyzed using 16S rRNA sequencing.


The 38 enrolled patients were divided into the ulcer group (24) and mucosal healing group (14). The ulcer group exhibited lower α diversity. Six genera, namely Faecalibacterium (P = 0.008), Lachnospira (P = 0.009), Paraprevotella (P = 0.01), Dialister (P = 0.012), Streptococcus (P = 0.025), and Clostridium (P = 0.028) were enriched in the mucosal healing group. A predictive score for mucosal healing was defined using these six genera. The area under the curve was 0.795 and the sensitivity and specificity for predicting mucosal healing were 0.643 and 0.917, respectively.


Fecal microbiome is corelated with disease activity in the entire small intestine in Crohn’s disease patients. The predictive score proposed by microbiota characteristics was a potential biomarker for mucosal healing in the small intestine.

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Crohn's disease




Capsule endoscopy


Balloon-assisted endoscopy


C-reactive protein


Fecal calprotectin


Positive predictive value


Negative predictive value


Under the curve


Receiver-operating characteristics


Linear discriminant analysis Effect Size


Principal Coordinate Analysis


Ulcerative colitis


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We received no financial support for this research. We thank Ms. Akina Ooishi at the Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine for technical assistance in DNA isolation and 16S rRNA gene sequencing.

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Correspondence to Masanao Nakamura.

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Hattori, S., Nakamura, M., Yamamura, T. et al. The microbiome can predict mucosal healing in small intestine in patients with Crohn’s disease. J Gastroenterol 55, 1138–1149 (2020).

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  • Crohn’s disease
  • Gut microbiota
  • Mucosal healing
  • Small intestine