Faecal Microbiota transplantation affects liver DNA methylation in Non-alcoholic fatty liver disease: a multi-omics approach

Daniela Stols-Gonçalves; Anne Linde Mak; Mette S Madsen; Eduard W J van der Vossen; Eveline Bruinstroop; Peter Henneman; Femke Mol; Torsten P M Scheithauer; Loek Smits; Julia Witjes; Abraham Stijn Meijnikman; Joanne Verheij; Max Nieuwdorp; Adriaan G Holleboom; Evgeni Levin

doi:10.1080/19490976.2023.2223330

Faecal Microbiota transplantation affects liver DNA methylation in Non-alcoholic fatty liver disease: a multi-omics approach

Gut Microbes. 2023 Dec 31;15(1):2223330. doi: 10.1080/19490976.2023.2223330.

Authors

Daniela Stols-Gonçalves¹, Anne Linde Mak^{1

2}, Mette S Madsen^{3

4}, Eduard W J van der Vossen¹, Eveline Bruinstroop^{2

5}, Peter Henneman^{2

6}, Femke Mol¹, Torsten P M Scheithauer^{1

2

7}, Loek Smits¹, Julia Witjes^{1

2}, Abraham Stijn Meijnikman^{1

2}, Joanne Verheij^{2

8}, Max Nieuwdorp^{1

2}, Adriaan G Holleboom^{1

2}, Evgeni Levin^{1

2

9}

Affiliations

¹ Department of Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands.
² Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
³ Gubra, Hørsholm, Denmark.
⁴ Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
⁵ Department of Endocrinology, Amsterdam University Medical Centre, Amsterdam, The Netherlands.
⁶ Department of Human Genetics, Amsterdam University Medical Centre, Amsterdam, The Netherlands.
⁷ Department of Internal Medicine, Amsterdam University Medical Centre (UMC), Vrije Universiteit (VU) University Medical Centre, Amsterdam, Netherlands.
⁸ Department of Pathology, Amsterdam University Medical Centre, Amsterdam, The Netherlands.
⁹ Horaizon BV, Delft, The Netherlands.

Abstract

Individuals with nonalcoholic fatty liver disease (NAFLD) have an altered gut microbiota composition. Moreover, hepatic DNA methylation may be altered in the state of NAFLD. Using a fecal microbiota transplantation (FMT) intervention, we aimed to investigate whether a change in gut microbiota composition relates to altered liver DNA methylation in NAFLD. Moreover, we assessed whether plasma metabolite profiles altered by FMT relate to changes in liver DNA methylation. Twenty-one individuals with NAFLD underwent three 8-weekly vegan allogenic donor (n = 10) or autologous (n = 11) FMTs. We obtained hepatic DNA methylation profiles from paired liver biopsies of study participants before and after FMTs. We applied a multi-omics machine learning approach to identify changes in the gut microbiome, peripheral blood metabolome and liver DNA methylome, and analyzed cross-omics correlations. Vegan allogenic donor FMT compared to autologous FMT induced distinct differential changes in I) gut microbiota profiles, including increased abundance of Eubacterium siraeum and potential probiotic Blautia wexlerae; II) plasma metabolites, including altered levels of phenylacetylcarnitine (PAC) and phenylacetylglutamine (PAG) both from gut-derived phenylacetic acid, and of several choline-derived long-chain acylcholines; and III) hepatic DNA methylation profiles, most importantly in Threonyl-TRNA Synthetase 1 (TARS) and Zinc finger protein 57 (ZFP57). Multi-omics analysis showed that Gemmiger formicillis and Firmicutes bacterium_CAG_170 positively correlated with both PAC and PAG. E siraeum negatively correlated with DNA methylation of cg16885113 in ZFP57. Alterations in gut microbiota composition by FMT caused widespread changes in plasma metabolites (e.g. PAC, PAG, and choline-derived metabolites) and liver DNA methylation profiles in individuals with NAFLD. These results indicate that FMTs might induce metaorganismal pathway changes, from the gut bacteria to the liver.

Keywords: DNA methylation; faecal microbiota transplantation (FMT); multi-omics analysis; non-alcoholic fatty liver disease (NAFLD).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Choline
DNA Methylation
Fecal Microbiota Transplantation
Gastrointestinal Microbiome*
Humans
Multiomics
Non-alcoholic Fatty Liver Disease* / therapy

Substances

Choline

Grants and funding

E. vd V. is supported by a CVON INCONTROL-2 grant. M.N. is supported by a personal ZONMW VICI grant 2020 (09150182010020). M.S.M. is supported by a grant from Innovation Fund Denmark [7038-00008B]. A.G.H. is supported by the Amsterdam UMC Fellowship grant, the Amsterdam UMC Innovation grant, two grants from the Dutch Gastroenterology Foundation MLDS and two grants from Holland~Health TKI‐PPP.