Footnotes

• X @IsraelsenMads, @mariacalvarezs1, @Camilla_Dalby, @NikolajTorp_, @microbiomix

• MI and CA-S contributed equally.

• Correction notice This article has been corrected since it published Online First. The author contribution statement has been added.

• Collaborators MicrobLiver consortium: Peer Bork, Mathias Mann, Jelle Matthijnssens, Aleksander Krag, Torben Hansen; GALAXY consortium: Ema Anastasiadou, Manimozhian Arumugam, Peer Bork, Torben Hansen, Roland Henrar, Hans Israelsen, Morten Karsdal, Cristina Legido-Quigley, Hans Olav Melberg, Maja Thiele, Jonel Trebicka, Aleksander Krag.

• Contributors Conceptualisation and methodology: MI, CA-S, TH, AK and MA. Data collection: MI, BSM CDH, NCT, SJ, JKH and KPL. Data generation: JI, VR and BL. Formal analysis: MI, CA-S and MA. Investigation: MI, CA-S, AK and MA. Resources: AK, TH and MA. Writing—original draft. MI, CA-S and MA. Visualisation: MI, CA-S and MA. Supervision: AK and MA. All authors contributed to the manuscript with important intellectual content and approved the final version.

• Funding Challenge Grant 'MicrobLiver' grant number NNF15OC0016692 from the Novo Nordisk Foundation. Novo Nordisk Foundation Center for Basic Metabolic Research is an independent research centre, based at the University of Copenhagen, Denmark, and partially funded by an unconditional donation from the Novo Nordisk Foundation (www.cbmr.ku.dk) (grant number NNF18CC0034900). CA-S was supported by Novo Nordisk Foundation (grant NNF16CC0020896). LJJ was supported by Novo Nordisk Foundation (grant NNF14CC0001).

• Competing interests LJJ owns shares in Amgen and Novo Nordisk A/S and is a member of the Scientific Advisory Board of ZS Associates. MT has received speaker’s fee from Echosens, Siemens Healthcare, Norgine, Tillotts Pharma and advisory fee from GE Healthcare. MA has received speaking and/or consulting fees from Roche A/S, Lundbeck Pharma A/S and SNIPR Biome ApS. AK has served as speaker for Norgine, Siemens and Nordic Bioscience and participated in advisory boards for Norgine and Siemens, all outside the submitted work.

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

• Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.