Since switching from an agricultural to an urban lifestyle, humans have seen a rise in inflammatory diseases such as allergies and asthma. Some hypotheses suggested that urbanisation has a negative impact on the development of the immune system. One of the most accepted, the “old friends” hypothesis, jointly with the observed “farm effect”, propose that moving to urban areas has left our immune systems weakened by the lack of interactions with microorganisms we have evolved with for thousands of years. In this thesis, the air microbiomes of two farms with different degrees of urbanisation were analysed at all taxonomic levels to uncover their microbial communities and how urbanisation and the built environment might impact them. While microbial diversity was not different between the rural and urban farms, their microbial and viral composition was significantly impacted by farm location and room type. It was shown that differences between farms were due to an increased presence of soil microorganisms in the rural farm, while the urban farm had more human-associated microorganisms. Soil microorganisms like Ornithinimicrobium and Nocardioides were consistently present in the core microbiome of the rural farm as well as significantly more abundant than in the urban farm. Similarly, the rural farm had characteristic archaeal species, such as methanogens, typically associated to cow dwellings, while fungal species, like Aspergillus spp., were more equally distributed across both farms. Combining abundance data from all microbial kingdoms and viruses into co-occurrence networks showed that the rural farm has a more stabilised microbiome than the urban farm and air viruses had the potential to interact with multiple microbial species in both farms. Additionally, environmental parameters like temperature, humidity and CO2 showed the potential to be used as proxies to describe and cluster the air microbiome by room type, as the microbiome in closed rooms was influenced by higher temperatures and CO2, while in animal dwellings the microbiome was influenced by higher humidity values. Finally, it was revealed that specific features of the air composition were shared across rooms of the same type, but another portion of the microbiome was unique to each room type, even inside the same room. This thesis shows that the microbiome and virome of the analysed farms were impacted by their degree of urbanisation and that soil microorganisms and viruses might be key players in rural farms. Additional research is needed to characterise other rural environments to reveal if this pattern is followed in other rural and urban built environments.
- metagenomics
- built environment
- virome
- co-occurrence networks
- diversity
Characterisation of the air microbiome in farms with different degrees of urbanisation
Delgado Corrales, B. (Author). 25 Apr 2024
Student thesis: Doctoral Thesis