Transient suppression of bacterial populations associated with gut health is critical in success of exclusive enteral nutrition for children with Crohn's disease

Runde, J. et al. (2023) Transient suppression of bacterial populations associated with gut health is critical in success of exclusive enteral nutrition for children with Crohn's disease. Journal of Crohn's and Colitis, 17(7), pp. 1103-1113. (doi: 10.1093/ecco-jcc/jjad031) (PMID:36934439)

Abstract

Background and Aims: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn’s disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking. Methods: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct ‘phenotypes’ or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis. Results: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy. Conclusions: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.

• Item Type: Articles
• Keywords: Microbial therapeutics, gut microbiome, genome-resolved metagenomics.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Gerasimidis, Professor Konstantinos
• Authors: Runde, J., Veseli, I., Fogarty, E. C., Watson, A. R., Clayssen, Q., Yosef, M., Shaiber, A., Verma, R., Quince, C., Gerasimidis, K., Rubin, D. T., and Eren, A. M.
• College/School: College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
• Journal Name: Journal of Crohn's and Colitis
• Publisher: Oxford University Press
• ISSN: 1873-9946
• ISSN (Online): 1876-4479
• Published Online: 19 March 2023
• Copyright Holders: Copyright © 2023 The Authors
• First Published: First published in Journal of Crohn's and Colitis 17(7):1103–1113
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher
• Data DOI: 10.6084/m9.figshare.15108726.v1