Journal article
Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease
GL D'Adamo, M Chonwerawong, LJ Gearing, VR Marcelino, JA Gould, EL Rutten, SM Solari, PWR Khoo, TJ Wilson, T Thomason, EL Gulliver, PJ Hertzog, EM Giles, SC Forster
Cell Reports Medicine | CELL PRESS | Published : 2023
Abstract
Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, funct..
View full abstractRelated Projects (2)
Grants
Awarded by Kenneth Rainin Foundation
Funding Acknowledgements
This work was supported by the Australian National Health and Medical Research Council grants 1159239 (S.C.F.), 1181105 (S.C.F., E.M.G.), and 1186371 (S.C.F., P.J.H.); the Australian Research Council DP190101504 (S.C.F.) and DE220100965 (V.R.M.); the Walter Cottman Endowment Fund (E.M.G., S.C.F.); the Gastroenterological Society of Australia (E.M.G., S.C.F.); and the Kenneth Rainin Foundation (E.M.G., S.C.F.). S.C.F. is supported by a CSL Centenary Fellowship. The authors would also like to acknowledge the clinical staff in endoscopy at Monash Children's Hospital, the patients and parents that kindly consented to contribute to the study, the Monash eResearch Team, the Ramaciotti Centre for Cryo-Electron Microscopy (Monash University), the CSIRO UROP Program, Prof. Kim-Anh Le Cao, and the support of the Victorian State Government Operational Infrastructure Scheme. Funding for the open-access charge was provided by Monash University.