Footnotes

• ACM and TYF are joint first authors.

• Twitter @ACMasi10, @DrChrisLamb, @CJStewart7

• Contributors AM and TYF conducted data analysis, interpretated results and drafted the initial manuscript. CAL, JMA, RAB, MKE, SR and JFP assisted with study design, provision of equipment, method optimisation, analysis and interpretation, and critically revising the article for important intellectual content. SJC and JC performed the RNA-sequencing and bioinformatics and assisted with analysis and interpretation, and drafting the article. NDE and JB assisted with study design, analysis and interpretation, and critically revising the article for important intellectual content. CS conceptualised the study, performed the experiments and assisted with data analysis/interpretation and drafting the manuscript. All authors approved the final manuscript.

• Funding CS received funding from the Wellcome Institutional Strategic Support Fund (ISSF) and Newcastle University Academic Track scheme.

• Disclaimer The funders had no role in the design and conduct of the study.

• Competing interests TYF, JMA, RAB, MKE, JFP, CJS have filled a patent for the enteroid anaerobic co-culture system. CJS has received honorarium from Danone Nutricia.

• Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.

• Provenance and peer review Not commissioned; internally peer reviewed.