Diet or Genetics – what shapes our gut microbiome?

Among the different factors identified in modulating the composition and function of our gut microbiota, diet and host genetics are two of the most studied factors, with evidence suggesting that host genetics outweighs diet in shaping our gut communities. 

Interestingly, host phylogenetic background and its impact on the gut microbiota is not only believed to dominate in humans but also in primates. Although the groups diverged molecularly millions of years ago, understanding the forces that shape the primate gut microbiota could be key in finding new therapeutic perspectives to tackle chronic diseases in humans. The recent publication from Gomez et al.1, a scientist dedicated to the study of primates and their gut microbiome, suggests a discordance in the proposed effect of host genetic control over the microbial communities in the gut.

Image_Primates Article

In their study, the researchers characterised faecal samples (n= 448) from 9 different primate species (located in Central America, Mexico and Africa) and 4 human groups (including traditional agriculturalists, hunter-gatherers, and Central African Republic and Western researchers).

As observed earlier, the data indicated differences in the microbiota depending on lifestyle and the geographical distribution2-3 . However, an expanded comparative model applied across such ecologically and phylogenetically diverse sample population indicated a striking similarity between phylogenetically distant groups. Specially in the case of African Old World monkeys (i.e. African cercopithecines) and humans from non-industrial populations (i.e. hunter gatherers and traditional agriculturalists).

The observed microbiota convergence is also interesting from the perspective that in the case of the human groups, cooking was expected to contribute to the microbial differences. Yet, as mentioned by the researchers, it is the complexity of the nutritional profiles (variety of diet and nutritional components) from these groups that may facilitate such resemblance. 

The Western researchers, who from three to six months had a shift in both diet and lifestyle during their field work in the Central African Republic, showed a substantial change in their microbiota with a tendency to compositionally assemble like the populations from the traditional groups. 

These results demonstrating the plasticity of the human gut microbiota are a step towards unveiling possible strategies to reset the human microbial networks characteristic from industrialised populations. It has been hypothesised that a mismatch regarding our genome-diet, that is in short shifting from a rural to an industrialised diet, is the possible cause for the arising of chronic diseases in the Western world including cancer and diabetes. All triggered by the fact that our body is not originally adapted to the altered nutrient profiles including high glycaemic loads and processed fats.

The patterns observed need to be corroborated from more exhaustive studies including bigger sample sizes and a better assessment of diet composition and feeding behavioural data.



1Gomez et al. (2019) Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints. mSphere  4(4).

2De Filippo et al. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107(33): p. 14691-6.

3Yatsunenko  et al. (2012) Human gut microbiome viewed across age and geography. Nature 486(7402): p. 222-7.




Evolution table