Doctoral dissertation in Lahti

The effect of living environment and environmental exposure on the composition of microbial community in soil, on human skin and in the gut

A member of Nature-Based Solutions Research Group Anirudra Parajuli, M.Sc. will defend the doctoral dissertation entitled "THE EFFECT OF LIVING ENVIRONMENT AND ENVIRONMENTAL EXPOSURE ON THE COMPOSITION OF MICROBIAL COMMUNITY IN SOIL, ON HUMAN SKIN AND IN THE GUT" in the Faculty of Biological and Environmental Sciences, University of Helsinki, on 18 January 2019 at 12:00. The public examination will take place at the following address: Aalto auditorium, Niemenkatu 73, Lahti.

Professor Gabriele Berg, Graz University of Technology, will serve as the opponent, and Professor Stephan Pflugmacher Lima as the custos.


Microbes play important roles in the development of the human immune system. Human commensal microbiota of the gut and skin have been shown to modulate the immune system, and high diversity of this microbiota is likely to confer protection against immune-mediated diseases. However, sufficient contacts with the diverse microbiota in our environment have also been thought to be equally important. It is suggested that the rising incidences of immune-mediated diseases such as allergies and asthma in the western urban society having less proportion of natural environment could be due to insufficient contacts with environmental microbes. This thesis aimed to find out the effect of living environment, including the coverage of built area, vegetation type and pollution, on environmental microbiota, their human exposure as well as the composition of human commensal microbiota. This thesis also aimed to study whether applying soil and plant based materials on skin is effective in establishing better contact with microbes.

The effect of pollution on the composition of the environmental microbiota was studied by contaminating four different types of soils with polyaromatic hydrocarbons (PAHs). It was found that PAH-pollution altered the community composition of bacteria, increased the abundance of bacterial phyla shown to be unfavorable and reduced the abundance of those recognized to be favorable for the human immune system. Since exposure to environmental microbes affects human microbiota and the immune function, pollutants such as PAHs likely affect human exposure to environmental microbes and also lead to disturbances in the composition of the human commensal microbiota.

The effect of land cover type on indoor exposure to environmental microbes was investigated by studying the composition of bacteria in the debris deposited in experimental doormats installed inside the main door of urban and rural houses in southern Finland. The quantity of environmental litter and bacterial diversity was significantly less in the doormats of houses in heavily built urban area compared to those in sparsely built rural areas. Stool samples from elderly volunteers living in those houses were analyzed to investigate the effect of land cover type and garden vegetation diversity on the composition of gut microbiota. The number of shrub and non-woody flowering plant species in the yard were associated with an increased abundance of several bacterial taxa known to promote the human immune system. The effect of built area was similar to the shifts in the gut microbiota observed in urban inhabitants from highly industrialized areas relative to rural hunter-gatherer population in previous studies suggesting that high incidences of immune disorders in western population could be associated with a greater coverage of built area.

Urban volunteers were asked to apply soil and plant-based materials on their hands to see if the use of natural ingredients is effective in changing the composition of bacteria on the skin. This led to a significant increase in the diversity and biomass as well as the relative abundance of several bacterial taxa suggesting that microbial exposure via skin could potentially be employed as a route for preventing or even treating immune-mediated disorders by increasing the diversity of skin microbiota, which needs to be investigated.

This thesis concludes that urban living environment characterized by increasing proportion of built areas and high pollution levels could lead to adverse changes in the environmental microbes, reduced indoor exposure to those microbes as well as unfavorable shifts in the composition of the gut microbiota. Shrubs and flowering plants could contribute positively to gut microbial homeostasis. Likewise, a direct contact with soil and plant based materials can be effective in increasing the diversity of the skin microbiota.