5 June 2024

Understanding the interactions between gut microbiome and host epigenetics


Recent research highlights a complex and dynamic relationship between the gut microbiome and host epigenetics, suggesting a bidirectional "epigenome-microbiome axis" that could revolutionise our understanding of health and disease.

Genome and Microbes

“We know that the gut microbiota is important for our health and immune system. However, much less is known about how an animal host is controlling or regulating its microbiota. We wanted to investigate new ways in which the host shapes its microbiota.” postdoc Michael Le Pepke explains.

A bidirectional relationship

The review led by postdoc Michael Le Pepke from Center for Evolutionary Hologenomics reveals that the gut microbiome acts as an epigenetic effector, influencing the host's gene expression through for example DNA and histone modifications. Intriguingly, the host can also modify its gut microbiome through epigenetic changes that affect the expression of immune genes, gut barrier function, or the activity of non-coding RNAs.

“This literature study has uncovered multiple bidirectional interactions between the host epigenome and the gut microbiota, which outlines an “epigenome-microbiome axis”. Importantly, this shows that the host can affect its microbiota through various epigenetic mechanisms and changes in gene expression.” says Michael.

Innovative treatments

The new findings suggest that the host’s ability to shape its microbiome through epigenetic mechanisms could lead to innovative treatments for gastrointestinal diseases or gut dysbiosis caused by epigenetic dysregulation.

“We are currently developing new tools to engineer specific parts of the epigenome. This may allow us to change microbiomes and improve beneficial microbial traits without any genetic modifications.” Michael adds.

Advancements in epigenetic engineering tools now allow researchers to investigate the causality within the epigenome-microbiome axis, offering new approaches to engineer microbial traits. By targeting host epigenetic mechanisms that regulate the microbiome, the researchers envision new therapeutic strategies that harness the body's natural systems to promote health.

Lessons to be learned from the wild

“Both the host epigenome and its microbiota can respond rapidly to environmental changes and such responses may be inherited across generations. If this “holo-epigenome” is a relevant biological unit in the wild, this can change our understanding of rapid adaptive evolution of host-microbe relationships.” Michael ends.

The research not only underscores the profound interconnectedness of the gut microbiome and host epigenetics but also opens up exciting possibilities for applications in health and food sciences. 

Read the review Science Direct here.


Postdoc Michael Le Pepke