Epigenetics and the Microbiome: Two Special Players in the Diet – Health Interaction


Welcome to lesson 5 of our module “The Power of Nutrition”: Epigenetics and the Microbiome: Two Special Players in the Diet – Health Interaction.

In this lesson, we focus on two special mechanisms that appear to be mediators between our diet and health: the gut microbiome and epigenetics. We’re going to find out what they are, how they influence health and how our diet influences them.

What will I learn in this lesson?

  • How epigenetic changes induced by our diet can lead to obesity and further development of disease.
  • Some examples of how diet influences epigenetic changes including DNA methylation and the development of cancer.
  • An introduction to how important the gut microbiome is to our overall health.
  • The different factors that affect the gut microbiome, including diet.

Before moving on to the next lesson, we recommend that you watch the video and pass the quiz.

Note: In each video lesson, the key facts and learnings will be sent to your module cheat sheet, which will become available for PAN members after completing the final test.



Moore, LD et al. “DNA Methylation and Its Basic Function.” Neuropsychopharmacology 38, no. 1 (January 2013): 23–38. https://doi.org/10.1038/npp.2012.112.

Bibikova, M et al. “High Density DNA Methylation Array with Single CpG Site Resolution.” Genomics 98, no. 4 (October 2011): 288–95. https://doi.org/10.1016/j.ygeno.2011.07.007.

Lactase gene
Leseva, MN et al. “Differences in DNA Methylation and Functional Expression in Lactase Persistent and Non-Persistent Individuals.” Scientific Reports 8, no. 1 (December 2018): 5649. https://doi.org/10.1038/s41598-018-23957-4.

Information on expression in enterocytes
“Enterocytes - an Overview | ScienceDirect Topics.” Accessed May 31, 2021. https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/enterocytes.

NCD - epigenetics interaction
Ramos-Lopez, O et al. “Guide for Current Nutrigenetic, Nutrigenomic, and Nutriepigenetic Approaches for Precision Nutrition Involving the Prevention and Management of Chronic Diseases Associated with Obesity.” Journal of Nutrigenetics and Nutrigenomics 10, no. 1–2 (2017): 43–62. https://doi.org/10.1159/000477729.

Ma, J et al. “Whole Blood DNA Methylation Signatures of Diet Are Associated With Cardiovascular Disease Risk Factors and All-Cause Mortality.” Circulation: Genomic and Precision Medicine 13, no. 4 (August 2020): CIRCGEN.119.002766, e002766. https://doi.org/10.1161/CIRCGEN.119.002766.

DNA methylation in cancer
“The Role of Methylation in Gene Expression | Learn Science at Scitable.” Accessed May 31, 2021. https://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070/.

Obesity and epigenetics
Wahl, S et al. “Epigenome-Wide Association Study of Body Mass Index, and the Adverse Outcomes of Adiposity.” Nature 541, no. 7635 (January 2017): 81–86. https://doi.org/10.1038/nature20784.

Diet and epigenetics
Hibler, E et al. “Impact of a Diet and Activity Health Promotion Intervention on Regional Patterns of DNA Methylation.” Clinical Epigenetics 11, no. 1 (December 2019): 133. https://doi.org/10.1186/s13148-019-0707-0.

Gut Microbiome
Number of microbes
Sender, R et al. “Revised Estimates for the Number of Human and Bacteria Cells in the Body.” PLOS Biology 14, no. 8 (August 19, 2016): e1002533. https://doi.org/10.1371/journal.pbio.1002533.

Definition, connection to diseases
Altveş, S et al. “Interaction of the Microbiota with the Human Body in Health and Diseases.” Bioscience of Microbiota, Food and Health 39, no. 2 (2020): 23–32. https://doi.org/10.12938/bmfh.19-023.

Diversity rhythm in T2D prediction
Reitmeier, S et al. “Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.” Cell Host & Microbe 28, no. 2 (August 2020): 258-272.e6. https://doi.org/10.1016/j.chom.2020.06.004.

Short-chain fatty acids
Shuwen, H et al. “Protective Effect of the ‘Food-Microorganism-SCFAs’ Axis on Colorectal Cancer: From Basic Research to Practical Application.” Journal of Cancer Research and Clinical Oncology 145, no. 9 (September 4, 2019): 2169–97. https://doi.org/10.1007/s00432-019-02997-x.

Influencers of gut microbiota
Figure 1B: Clarke, G et al. “Gut Reactions: Breaking Down Xenobiotic–Microbiome Interactions.” Edited by Charles P. France. Pharmacological Reviews 71, no. 2 (April 2019): 198–224. https://doi.org/10.1124/pr.118.015768.

Modified Figure 1 of: Schroeder, Bjoern O, and Fredrik Bäckhed. “Signals from the Gut Microbiota to Distant Organs in Physiology and Disease.” Nature Medicine 22, no. 10 (October 2016): 1079–89. https://doi.org/10.1038/nm.4185.

Epigenetics - microbiome interaction
Gerhauser, C. “Impact of Dietary Gut Microbial Metabolites on the Epigenome.” Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1748 (June 5, 2018): 20170359. https://doi.org/10.1098/rstb.2017.0359.

Additional Attribution

Background music in video: https://www.bensound.com/royalty-free-music

CpG islands diagram:
Figure 6. DNA methylation. (A) CpG methylation mechanism is mediated by DNA methyltransferases and consists in the addition of a methyl group to the carbon in the 5th position of cytosines that precedes guanine nucleotides. (B) CpG islands are DNA sequences rich in CpG sites (>50% CpG sites within a 200bp sequence). Methylation of CpG islands inside a promoter region may control gene expression.
CC BY 3.0 DOI: 10.5772/intechopen.70201

Lesson Content