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Background and Objectives <p>Evaluating the gut microbial community in Crohn’s disease (CD) is best done before commencing therapy to avoid the effects of therapeutic intervention and provide a better understanding of microbial dysbiosis. We compared the microbial communities in both tissue and stool samples from treatment-naive CD patients with those in remission.</p> Methods <p>Adults with CD were prospectively recruited. Patients with Crohn’s disease activity index (CDAI) &gt; 150 and no prior therapy were included as treatment-naive active cases and those with CDAI ≤ 150 were considered to be in remission. Stool and rectal mucosal biopsy samples were collected, bacterial DNA was extracted, the V3-V4 region of the 16S rRNA gene was amplified and library preparation was done and sequenced on the Illumina MiSeq platform. The microbial community composition, diversity and predicted function were assessed using the QIIME2 pipeline and R packages. Microbial characteristics associated with disease status were determined.</p> Results <p>Thirty-four active CD cases (age 40.9 ± 11.2&#xa0;years, males 61.8%) and 33 in remission (age 39.5 ± 10.2&#xa0;years, 60.6% males) were recruited. Changes in bacterial diversity with disease status were more pronounced in stool than in tissue samples. On random forest analysis of the stool sample, genera such as <i>Romboutsia</i>, <i>Ruminococcus</i> and <i>Dorea</i> were associated with active CD, while <i>Bifidobacterium</i>, <i>Escherichia</i> and <i>Enterococcus</i> were associated with remission. In the mucosal sample, <i>Bacillus</i>, <i>Megasphaera</i> and other species were associated with active CD, while <i>Veillonella</i>, <i>Fusobacterium</i>, <i>Bifidobacterium</i> and other species were associated with remission. Several predicted metabolic pathways showed significant differences between the mucosal bacteria of active CD and those in remission. This difference was less pronounced between the two groups’ stool samples.</p> Conclusion <p>The microbial community structure and predicted function in treatment-naïve CD differ from those in remission. The predicted differences at the functional level are prominent in the mucosal microbiota, which are not replicated in the fecal community.</p> Graphical Abstract <p></p>

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Gut microbiota in treatment-naïve active Crohn’s disease compared to those in remission: Divergent trends in mucosal versus fecal bacterial community

  • 期刊论文

  • 发表日期：

    2026年6月23日

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  • Amit Kumar Dutta,
  • Dilip Abraham,
  • Blossom Benny,
  • Karthikeyan Govindan,
  • Anjilivelil Joseph Joseph

摘要

Background and Objectives

Evaluating the gut microbial community in Crohn’s disease (CD) is best done before commencing therapy to avoid the effects of therapeutic intervention and provide a better understanding of microbial dysbiosis. We compared the microbial communities in both tissue and stool samples from treatment-naive CD patients with those in remission.

Methods

Adults with CD were prospectively recruited. Patients with Crohn’s disease activity index (CDAI) > 150 and no prior therapy were included as treatment-naive active cases and those with CDAI ≤ 150 were considered to be in remission. Stool and rectal mucosal biopsy samples were collected, bacterial DNA was extracted, the V3-V4 region of the 16S rRNA gene was amplified and library preparation was done and sequenced on the Illumina MiSeq platform. The microbial community composition, diversity and predicted function were assessed using the QIIME2 pipeline and R packages. Microbial characteristics associated with disease status were determined.

Results

Thirty-four active CD cases (age 40.9 ± 11.2 years, males 61.8%) and 33 in remission (age 39.5 ± 10.2 years, 60.6% males) were recruited. Changes in bacterial diversity with disease status were more pronounced in stool than in tissue samples. On random forest analysis of the stool sample, genera such as Romboutsia, Ruminococcus and Dorea were associated with active CD, while Bifidobacterium, Escherichia and Enterococcus were associated with remission. In the mucosal sample, Bacillus, Megasphaera and other species were associated with active CD, while Veillonella, Fusobacterium, Bifidobacterium and other species were associated with remission. Several predicted metabolic pathways showed significant differences between the mucosal bacteria of active CD and those in remission. This difference was less pronounced between the two groups’ stool samples.

Conclusion

The microbial community structure and predicted function in treatment-naïve CD differ from those in remission. The predicted differences at the functional level are prominent in the mucosal microbiota, which are not replicated in the fecal community.

Graphical Abstract