Journal article

Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing

JJ Teh, EM Berendsen, EC Hoedt, S Kang, J Zhang, F Zhang, Q Liu, AL Hamilton, A Wilson-O'Brien, J Ching, JJY Sung, J Yu, SC Ng, MA Kamm, M Morrison

ISME JOURNAL | SPRINGERNATURE | Published : 2021

Abstract

The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn's disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative ..

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Grants

Funding Acknowledgements

The work presented in this manuscript was supported by The Leona M. and Harry B. Helmsley Charitable Trust via the Australasian Gastrointestinal Research Foundation, as part of the Eastern IBD Gut Microbiota (ENIGMA) project. The samples analysed were obtained from the POCER study (ClinicalTrials.gov identifier NCT00989560) led by MAK, and was supported by the Gutsy Group, Gandel Philanthropy, Angior Foundation and Crohns Colitis Australia. The research by JJT, EMB, SK, ECH and MM was carried out at the Translational Research Institute, Woolloongabba, QLD 4102, Australia. The Translational Research Institute is supported by a grant from the Australian Government.