The Gut Microbiota and their Metabolites: Potential Implications for the Host Epigenome

Adv Exp Med Biol. 2016;902:33-44. doi: 10.1007/978-3-319-31248-4_3.


The gut microbiota represents a metabolically active biomass of up to 2 kg in adult humans. Microbiota-derived molecules significantly contribute to the host metabolism. Large amounts of bacterial metabolites are taken up by the host and are subsequently utilized by the human body. For instance, short chain fatty acids produced by the gut microbiota are a major energy source of humans.It is widely accepted that microbiota-derived metabolites are used as fuel for beta-oxidation (short chain fatty acids) and participate in many metabolic processes (vitamins, such as folic acid). Apart from these direct metabolic effects, it also becomes more and more evident that these metabolites can interact with the mammalian epigenetic machinery. By interacting with histones and DNA they may be able to manipulate the host's chromatin state and functionality and hence its physiology and health.In this chapter, we summarize the current knowledge on possible interactions of different bacterial metabolites with the mammalian epigenetic machinery, mostly based on in vitro data. We discuss the putative impact on chromatin marks, for example histone modifications and DNA methylation. Subsequently, we speculate about possible beneficial and adverse consequences for the epigenome, the physiology and health of the host, as well as plausible future applications of this knowledge for in vivo translation to support personal health.

Keywords: (early life) nutrition; (early life) programming; Bacterial metabolites; Breast feeding; DNA methylation; Epigenetics; Histone modification.

Publication types

  • Review

MeSH terms

  • Chromatin / chemistry
  • Chromatin / metabolism
  • DNA / genetics
  • DNA / metabolism
  • DNA Methylation
  • Epigenesis, Genetic*
  • Fatty Acids, Volatile / biosynthesis*
  • Folic Acid / biosynthesis*
  • Gastrointestinal Microbiome / genetics*
  • Gastrointestinal Tract / microbiology
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Metabolome / genetics*
  • Obesity / genetics
  • Obesity / microbiology
  • Symbiosis / genetics*


  • Chromatin
  • Fatty Acids, Volatile
  • Histones
  • DNA
  • Folic Acid