Microbiome and genetics: How our genes shape our gut bacteria

Heather Campbell
 min read

Microbiome and genetics are more closely linked than one would think.

Microbiome and genetics: How our genes shape our gut bacteriaAlso called the intestinal flora, microbiota comprises numerous micro-organisms that live in our intestines in symbiosis with our body.

Microbiome and genetics are intrinsically linked. Genes determine bacteria selection in the gut microbiota, impacting our energy metabolism, food preferences, and the strength of our gut barrier. Secretors are also genetic, which help select the right bacteria beneficial to our health.

The microbiota is composed of bacteria, viruses, and fungi that evolve in our digestive system.

Read on to understand how your genetic make up influences your health.

Microbiome and genetics: Introduction

Having a balanced intestinal microbiota allows for good health.

Indeed, it has several significant functions in our body: it allows the good digestion of food, acts as a barrier against diseases, and helps in the optimal functioning of our immune system.

Genetics have a more significant impact on our gut microbiota than the environment, as they influence the gut microbiota through various mechanisms, such as differences in the structure of the gut mucosa or in the immune system.

Microbiome and genetics of twins

Studies were conducted with pairs of twins to learn how our heredity impacts the composition of our intestinal microbiota.

Of these individuals, about half were monozygotic, so-called “identical twins,” resulting from the early division of a single fertilized egg and having identical genetic makeup.

The other pairs of twins were dizygotic or so-called “fraternal twins.” They were born from the simultaneous fertilization of two eggs by two different spermatozoa and therefore have different genetic heritages.

The results showed that the composition of the gut microbiota of monozygotic twins was much closer than that of dizygotic twins, and thus, shows the critical role of genetics  in selecting intestinal bacterial germs.

What genes are involved in germ selection in the gut microbiota?

Other studies have also determined the nature of the genes involved in the composition of the gut microbiota.

These genes were first:

  • Genes that allow the immune system to distinguish between what belongs to the organism and what is foreign to it
  • Genes related to food sensoriality (taste, smell)
  • Genes that control the body’s chemical reactions involved in digestion and the conversion of food into energy
  • Genes involved in the reinforcement of the intestinal mucosal barrier.

In other words, the factors that determine the genetic selection of the bacteria in the gut microbiota are our energy metabolism, our food preferences, and the strength of our gut barrier.

This selection is ultimately optimal for establishing symbiotic relationships of bacteria with our organism.

Blood groups, which are markers that allow immunity to distinguish self from non-self, are another genetic mode of selecting the gut microbiota.

Generally, blood types are based on red blood cells. But it is important to know that the same groups are also present in the intestinal mucus of 80% of individuals. They are called “secretors.”

These contribute to selecting bacteria beneficial to our health, such as lactobacillus.

In about 25% of non-secreting individuals, these lactobacilli are rare in the microbiota. This can lead to dysbiosis, which is responsible for severe colitis in premature newborns.

This will also increase the risk of inflammatory colitis in later life.

Childhood environment and genetics condition the results of our dietary efforts

Under the effect of dietary changes, studies have revealed that our genetic heritage is involved in microbiota variations.

For example, our genes will contribute to human inequalities in diet. Indeed, some people can gain weight at the slightest excess while others can afford to have lots of fun and keep a slim outline.

Besides genes, environmental events in early childhood related to nutrition can also permanently modify the nature of the intestinal microbiota and will also condition the response to dietary efforts that we may make later.

The gut microbiota is functionally adapted to each of us and seems to be very highly personalized.

Healthy people who live a healthy life will remain pretty stable over time.

However, specific environmental hazards to which life exposes us can break the perfect symbiosis initially determined. And unfortunately, this rupture will open the door to many diseases.

Related postWhat foods restore the intestinal flora? Simple & natural solutions


Even if all our body cells have an identical copy of our chromosomes and, thus, all our genes, they are not the same.

Indeed, to fulfill their functions, they will transform into different cells. They will transform into skin cells, retina cells, or the cells of our digestive tract.

All this without modifying the DNA, whose integrity must be respected in its transmission during cell divisions. This is epigenetics.

Epigenetics modifies the expression of genes in the body

Epigenetics includes all the mechanisms that regulate gene expression, which determines the life and transformation of cells.

These result from environmental modifications that will impact the cell function. They may regress or persist with the disappearance of the environmental agent.

Several mechanisms of epigenetic regulation have been identified, but others are still unknown:

  1. The first mechanism consists of attaching a chemical methyl group (methylation) to the gene or to the nearby DNA, which prevents its transcription.
  2. The second mechanism is the chemical transformation (methylation, acetylation) of specific proteins attached to the DNA, called “histones.” The latter chemically transforms to modify the spatial configuration of the DNA.

Regulation can also occur downstream of gene expression, allowing the synthesis of the substances they are responsible for coding. This is what tiny fragments of RNA (mircoRNAs) do.

The epigenome is the set of epigenetic modifications. Epigenetic changes in DNA are sometimes passed on to daughter cells during cell divisions and, more rarely, from one generation to the next in mammals.

Epigenetic mechanisms have a significant impact on our health

Epigenetic modifications play a critical role in cancer. There are genes whose overexpression promotes the emergence of cancerous diseases.

Examples include genes that drive cell multiplication or genes that reduce the removal of precancerous cells whose DNA has been partially damaged.

Epigenetics also plays an essential role in developing multifactorial diseases promoted by multiple genes, such as metabolic diseases or degenerative brain diseases.

Epigenetics could therefore be a therapeutic target in the future for many diseases.

The idea would be to correct the abnormal epigenetic modifications (which involve the appearance of these diseases) with epi-drugs without altering the rest of the epigenome.

The intestinal microbiota is involved in epigenetic mechanisms

Many substances are produced from our food by our intestinal microbiota, which can intervene in epigenetic mechanisms.

Among these we find polyphenols, short-chain fatty acids, polyamine, and specific vitamins like vitamin B8 or biotin.

These substances act through enzymes involved in the chemical transformation of histones or in DNA methylation.

The resulting epigenetic modifications of gut bacteria are also involved in regulating various physiological functions and in some behavioral changes.

Microbiome and genetics: Conclusion

Food and the external environment are not the only factors contributing to our intestinal microbiota’s proper functioning.

Indeed, genes also play an essential role in forming the microbiota.

If you have a healthy lifestyle and still suffer from intestinal pain, it may be worthwhile to check your genetics to find a solution.

Tip: Check our other article for tips on how to cleanse your colon every now and then and why it’s beneficial: How to cleanse your colon naturally? Food & activity tips

About Heather Campbell

As a nutritionist, my field of specialization is science-based nutritional advice but more importantly, it is my goal to share capturing and inspiring stories, examples and solutions which can help plus-size individuals overcome their specific difficulties. Read More