Faecal Microbiota Transplantation refurbishes the crypt-associated microbiota in Ulcerative colitis
Background Human colonic crypts harbor a unique, autochthonous microbial community called “crypt-associated microbiota”(CAM)1. The study is among the first reports highlighting compositional shifts in CAM and mucosa-associated microbiota (MAM) in patients with ulcerative colitis(UC), before and after fecal microbiota transplantation along with an anti-inflammatory diet (FMT-AID).  Methods Colonic biopsies from controls and from patients with UC before and after FMT-AID were methacarn-fixed, paraffin-embedded, and sectioned, followed by crypt isolation using Laser capture microdissection (LCM). CAM was identified using 16S rRNA gene sequencing from isolated crypts followed by data processing using QIIME2 and R-packages. MAM was characterised using whole biopsies. Results Distinct from MAM, CAM was dominated by aerobic Actinobacteria(54%) and Proteobacteria(38%) with the resilience of core and diversity. CAM underwent UC-associated dysbiosis which was restored after FMT-AID. FMT-restored CAM taxa correlated negatively with disease-associated parameters-Fecal calprotectin (FCal), Simple Clinical Colitis Activity Index (SCCAI) and Ulcerative Colitis Endoscopic Index of Severity (UCEIS). The positive effects of FMT-AID extended further in refurbishing the CAM-MAM interaction networks, which were obliterated in UC.  Conclusion FMT-AID refurbishes the CAM and recuperates CAM-MAM association in patients with UC.