Fecal microbiota transplantation refurbishes the crypt-associated microbiota in ulcerative colitis

Manasvini Markandey; Aditya Bajaj; Mahak Verma; Shubi Virmani; Mukesh Kumar Singh; Preksha Gaur; Prasenjit Das; C V Srikanth; Govind Makharia; Saurabh Kedia; Vineet Ahuja

doi:10.1016/j.isci.2023.106738

Fecal microbiota transplantation refurbishes the crypt-associated microbiota in ulcerative colitis

iScience. 2023 Apr 23;26(5):106738. doi: 10.1016/j.isci.2023.106738. eCollection 2023 May 19.

Affiliations

¹ Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India.
² Regional Centre for Biotechnology, 3rd Milestone Gurugram-Faridabad Expressway, Faridabad 121001, India.
³ Department of Pathology, All India Institute of Medical Sciences, New Delhi, India.

Abstract

A crypt autochthonous microbial population called crypt-associated microbiota (CAM) is localized intimately with gut regenerative and immune machinery. The present report utilizes laser capture microdissection coupled with 16S amplicon sequencing to characterize the CAM in patients with ulcerative colitis (UC) before and after fecal microbiota transplantation with anti-inflammatory diet (FMT-AID). Compositional differences in CAM and its interactions with mucosa-associated microbiota (MAM) were compared between the non-IBD controls and in patients with UC pre- and post-FMT (n = 26). Distinct from the MAM, CAM is dominated by aerobic members of Actinobacteria and Proteobacteria and exhibits resilience of diversity. CAM underwent UC-associated dysbiosis and demonstrated restoration post-FMT-AID. These FMT-restored CAM taxa correlated negatively with disease activity in patients with UC. The positive effects of FMT-AID extended further in refurbishing CAM-MAM interactions, which were obliterated in UC. These results encourage investigation into host-microbiome interactions established by CAM, to understand their role in disease pathophysiology.

Keywords: Gastroenterology; Microbiome.