Transitional mycobiomes-rural urban transition leads to reduction of diversity and loss of fungal species in the gut mycobiome of african families

Urbanization probably represents the global change with the highest impact on human lifestyle and consequently on human health. Urbanization produced a series of habits developed to minimize exposure to harmful microorganisms leading to a drastic change in social, food and health care dynamics. These effects are also produced by means of a remodeling of the intestinal microbial communities with the related encoded functions. Over time, these variations have been correlated with an increase in the incidence of chronic degenerative and autoimmune diseases, characterized by a loss of bacterial richness and diversity. A few studies investigated the bacterial fraction of the transitional microbiomes, however, the knowledge about the impact of urbanization on intestinal fungal communities are almost unexplored. Here, we demonstrate the effect of urbanization on the gut human mycobiota, studied between three areas in Burkina Faso with different levels of urbanization and compare the results to Italy, thus following a Western-related gradient. These variations were also studied within family members i.e. mother, father and children. We observed that the rural areas showed a greater intestinal fungal complexity in terms of diversity and composition compared to the more urbanized area of Burkina Faso, the capital Ouagadougou and Italy. Furthermore, urbanization determined a differential abundance gradient in the 33 fungal ASVs detected, in particular we identified 12 fungal species affected by urbanization gradient. These species are known for their immunogenic activity and overall the impact on human health. We also observed that the mycobionts differed within family members only in areas with no urbanization and intermediate level of urbanization. Since the occurrence of non-communicable diseases follows the trend of fungal reduction, our results suggest changes in yeast communities as a legitimate explanation for the hygiene hypothesis.