title: Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis.
abstract: The core human gut microbiota contributes to the developmental origin of diseases by modifying metabolic pathways. To evaluate the predominant microbiota as an epigenetic modifier, we classified 8 pregnant women into two groups based on their dominant microbiota, i.e., Bacteroidetes, Firmicutes, and Proteobacteria. Deep sequencing of DNA methylomes revealed a clear association between bacterial predominance and epigenetic profiles. The genes with differentially methylated promoters in the group in which Firmicutes was dominant were linked to risk of disease, predominantly to cardiovascular disease and specifically to lipid metabolism, obesity, and the inflammatory response. This is one of the first studies that highlights the association of the predominant bacterial phyla in the gut with methylation patterns. Further longitudinal and in-depth studies targeting individual microbial species or metabolites are recommended to give us a deeper insight into the molecular mechanism of such epigenetic modifications.
  
  
  OBJECTIVE
  Epigenetics encompasses genomic modifications that are due to environmental factors and do not affect the nucleotide sequence. The gut microbiota has an important role in human metabolism and could be a significant environmental factor affecting our epigenome. To investigate the association of gut microbiota with epigenetic changes, we assessed pregnant women and selected the participants based on their predominant gut microbiota for a study on their postpartum methylation profile. Intriguingly, we found that blood DNA methylation patterns were associated with gut microbiota profiles. The gut microbiota profiles, with either Firmicutes or Bacteroidetes as a dominant group, correlated with differential methylation status of gene promoters functionally associated with cardiovascular diseases. Furthermore, differential methylation of gene promoters linked to lipid metabolism and obesity was observed. For the first time, we report here a position of the predominant gut microbiota in epigenetic profiling, suggesting one potential mechanism in obesity with comorbidities, if proven in further in-depth studies.
authors.affiliation: Functional Food Forum, University of Turku, Turku, Finland kumhim@utu.fi.
authors.forename: Himanshu
authors.initials: H
authors.lastname: Kumar
authors.affiliation: Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors.forename: Riikka
authors.initials: R
authors.lastname: Lund
authors.affiliation: Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors.forename: Asta
authors.initials: A
authors.lastname: Laiho
authors.forename: Krista
authors.initials: K
authors.lastname: Lundelin
authors.affiliation: Department of Microbiology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
authors.forename: Ruth E
authors.initials: RE
authors.lastname: Ley
authors.affiliation: Department of Pediatrics, Turku University Hospital, Turku, Finland.
authors.forename: Erika
authors.initials: E
authors.lastname: Isolauri
authors.affiliation: Functional Food Forum, University of Turku, Turku, Finland.
authors.forename: Seppo
authors.initials: S
authors.lastname: Salminen
mesh_terms: D041963:Bacteroidetes / Q000254:growth & development*; D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D041981:Gastrointestinal Tract / Q000382:microbiology / Q000502:physiology*; D006094:Gram-Positive Bacteria / Q000254:growth & development*; D006801:Humans; D064307:Microbiota; D010865:Pilot Projects; D011247:Pregnancy; D011401:Promoter Regions, Genetic; D020560:Proteobacteria / Q000254:growth & development*
chemical_list: D004247:DNA