The human gut microbiota of modern societies differs substantially from the ancestral microbiota, nowdays represented by traditional populations living in developing world, such as rural Burkina Faso populations.
Rapid modernization, dietary changes and medical practices (such as antibiotic usage), is causing progressive alteration of the gut microbiota (including acquisition of antibiotic-resistant species), and these events may contribute to inflammation and autoimmunity and developing of non-communicable diseases (NCCDs).
Western diets (rich in fat, animal protein and simple sugars) has progressively reduced the abundance of gut bacteria that are common in traditional rural populations, especially fiber-degraders species, so reducing production of anti-inflammatory metabolites (such as short-chain fatty acids), and shifting the microbiota in favour of microbes able to degrade mucus and contributing to “leaky-gut”.
The human gut microbiota have rapidly adapted to environmental pressures and our current diet. On the contrast, our human genome, evolving relatively slowly, is not well adapted to these microorganisms and their associated functions. The incompatibility between the microbiota and the human genome may result in chronic inflammation and autoimmunity, typically of NCCDs.