Effects of short chain fatty acid producing bacteria on epigenetic regulation of FFAR3 in type 2 diabetes and obesity

Gene. 2014 Mar 1;537(1):85-92. doi: 10.1016/j.gene.2013.11.081. Epub 2013 Dec 8.


The human gut microbiota and microbial influences on lipid and glucose metabolism, satiety, and chronic low-grade inflammation are known to be involved in metabolic syndrome. Fermentation end products, especially short chain fatty acids, are believed to engage the epigenetic regulation of inflammatory reactions via FFARs (free fatty acid receptor) and other short chain fatty acid receptors. We studied a potential interaction of the microbiota with epigenetic regulation in obese and type 2 diabetes patients compared to a lean control group over a four month intervention period. Intervention comprised a GLP-1 agonist (glucagon-like peptide 1) for type 2 diabetics and nutritional counseling for both intervention groups. Microbiota was analyzed for abundance, butyryl-CoA:acetate CoA-transferase gene and for diversity by polymerase chain reaction and 454 high-throughput sequencing. Epigenetic methylation of the promoter region of FFAR3 and LINE1 (long interspersed nuclear element 1) was analyzed using bisulfite conversion and pyrosequencing. The diversity of the microbiota as well as the abundance of Faecalibacterium prausnitzii were significantly lower in obese and type 2 diabetic patients compared to lean individuals. Results from Clostridium cluster IV and Clostridium cluster XIVa showed a decreasing trend in type 2 diabetics in comparison to the butyryl-CoA:acetate CoA-transferase gene and according to melt curve analysis. During intervention no significant changes were observed in either intervention group. The analysis of five CpGs in the promoter region of FFAR3 showed a significant lower methylation in obese and type 2 diabetics with an increase in obese patients over the intervention period. These results disclosed a significant correlation between a higher body mass index and lower methylation of FFAR3. LINE-1, a marker of global methylation, indicated no significant differences between the three groups or the time points, although methylation of type 2 diabetics tended to increase over time. Our results provide evidence that a different composition of gut microbiota in obesity and type 2 diabetes affect the epigenetic regulation of genes. Interactions between the microbiota and epigenetic regulation may involve not only short chain fatty acids binding to FFARs. Therefore dietary interventions influencing microbial composition may be considered as an option in the engagement against metabolic syndrome.

Keywords: Austrian Nutrition Society; BMI; Butyryl-CoA:acetate CoA-transferase gene; CpG; DGGE; FFAR; FFAR3; FFQ; Faecalibacterium prausnitzii; G-protein coupled receptor; GLP-1; GLP-1 agonist; GPR; HDAC; HbA(1c); IFN-γ; IL; Interleukin; KEGG; Kyoto Encyclopedia of Genes and Genomes; LCFA; LINE-1; LPS; NF-κB; OEGE; PCA; PPAR-γ; PYY; SCFA; T; b.i.d.; body mass index; cytosine-guanine dinucleotide; denaturing gradient gel electrophoresis; drug overdose; food frequency questionnaire; free fatty acid receptor; glucagon like peptide-1; glycol hemoglobin; histone deacetylase; interferon-γ; lat. bis in die (two times per day); lipopolysaccharide; long chain fatty acid; long interspersed nuclear element 1; nuclear factor κB; o.d.; peptide YY; peroxisome proliferator-activated receptor-γ; principal component analysis; short chain fatty acid; time point.

MeSH terms

  • Adult
  • Aged
  • Biodiversity
  • Body Mass Index
  • Case-Control Studies
  • Coenzyme A-Transferases / genetics
  • DNA Methylation
  • Diabetes Mellitus, Type 2 / drug therapy
  • Diabetes Mellitus, Type 2 / genetics*
  • Diabetes Mellitus, Type 2 / microbiology
  • Epigenesis, Genetic*
  • Fatty Acids, Volatile / metabolism*
  • Feces / microbiology
  • Feeding Behavior
  • Female
  • Gastrointestinal Tract / microbiology*
  • Glucagon-Like Peptide 1 / agonists
  • Glucagon-Like Peptide 1 / analogs & derivatives
  • Glucagon-Like Peptide 1 / therapeutic use
  • Gram-Positive Bacteria / physiology
  • Gram-Positive Endospore-Forming Bacteria / genetics
  • Humans
  • Liraglutide
  • Long Interspersed Nucleotide Elements
  • Male
  • Microbiota / physiology
  • Middle Aged
  • Obesity / genetics*
  • Obesity / microbiology
  • Promoter Regions, Genetic
  • Receptors, G-Protein-Coupled / genetics*


  • FFAR3 protein, human
  • Fatty Acids, Volatile
  • Receptors, G-Protein-Coupled
  • Liraglutide
  • Glucagon-Like Peptide 1
  • Coenzyme A-Transferases
  • butyryl-CoA acetoacetate CoA transferase