Metabarcoding to track indoor fungi

Environmental microbes can have both beneficial and harmful effects on health, e.g. bacterial biodiversity is discussed as a factor influencing immuntolerance. This might explain the lower incidence of allergic diseases in children living in rural environments in contrast to children living in urban environments. Rural environments are usually more diverse and researchers are particularly looking at the effect of environmental microbiota on the commensal microbiota. The latter has been shown to have a strong influence on human immuncompetence.

People spend most of their time in indoor environments, which contain a variety of microbes. Serious problems may develop in buildings with long-lasting dampness, where the moisture supports the growth of bacteria and fungi (i.e., mould). Based on epidemiological studies, mould in buildings is positively associated with several allergic and respiratory effects, and certain moulds are toxigenic, meaning that they can produce mycotoxins. There are estimates that allergic diseases caused by plant, animal, and fungal allergens affect more than 30% of the population in industrialized countries, and there is increasing awareness and concern over exposure to moulds in indoor environments. The phenomenon has become known as Sick Building Syndrome (SBS), where the occupants describe a complex range of vague and often subjective health complaints. 

The most widely used methods to identify indoor fungi are culture dependent which means that they are inherently biased. We know that among the thousands of microbial species that populate the world, only a few have been characterized by more than just a DNA sequence due to our inability to grow them in the laboratory. A very good reason to switch to DNA based methods as two researchers of the University of Helsinki just did. They utilized metabarcoding to determine the fungal diversity in samples collected from five buildings: two at the university, two from nursery schools in the city, and an old inhabited farmhouse in a more rural setting.

The study represents an important proof of concept as it shows quite promising depth of results but also the potential pitfalls. Having identified the latter will allow for reliable high quality applications. The total number of fungal genera found during the study was 585 but when comparing fungal diversities and taxonomic composition between different types of buildings, no obvious differences or patters were found.

Of the 78 fungal genera listed to have been shown to induce allergies in persons that are hypersensitive to allergens, 51 were found in this study, although mostly at very low frequencies. 

The authors make clear that given the experimental design of their study there are clear limitations to what can be concluded: We discovered that making explicit conclusions on the relationship between the indoor air quality and mycoflora is complicated by the lack of appropriate indicators for air quality and by the occurrence of wide spatial and temporal changes in diversity and compositions among samples.