III.3. Tools for studying the fungal exposome
Collecting, storing, and conveying environmental or human samples for
fungal assessment are critical steps. This preanalytical stage needs to
be planned and performed according to the desired sample nature
(bioaerosol, house dust, skin, feces), to the environment (temperature,
wind, relative humidity, building material) or personal conditions
(adult vs child, professional vs home exposure), and to the purpose of
the study (e.g. epidemiological study vs examination of a patient’s
case) (61–63).
Environmental samples may be analyzed by culture-dependent and
culture-independent approaches. The former requires in vitrogrowth of fungal samples prior to identification, while the latter
proceeds with spore and sub-spore fragments identification, either
through microscopy analysis or molecular methods. For most environmental
fungal taxa, culture cannot be achieved (64). On the other hand, for
those growing in vitro, their growth rate will depend on the type of
fungal culture, the nutrient media in use (57). Microscopic examination
allows for quantitative assessment of samples and low taxonomical
detection of taxa which is a less precise approach. Immunological
detection of molds using specific enzyme-linked immunoassay (ELISA) is
also possible (65). Alternatively, DNA-based approaches such as
polymerase chain reaction (PCR) targeting taxonomic marker sequences, or
DNA metabarcoding, allow the identification of considerably higher
taxonomic biodiversity within the collected samples (64,66). However,
this new technology also has some shortcomings, including primer bias
which can heavily alter sequencing results (67,68), or the fact that
taxonomic marker sequences are not directly related to the
identification of a fungal species, therefore introducing the need for
operational taxonomic units (64). The usage of DNA-based procedures for
characterizing environmental fungi communities includes application of
PCR amplification of ribosomal RNA genes and DNA fingerprinting methods
such as Denaturing Gradient Gel Electrophoresis (DGGE), which uses a
genetic fingerprinting method to examine microbial communities from
environmental samples. These methods provide a broad quantification of
fungi identified from the environment (69,70).
A third approach gaining momentum addresses fungal exposome using
statistical modeling of airborne particles based on the study of
air-mass movements categorized in spatio-temporal patterns of
connectivity. This approach might alleviate the labor-intensive
classical identification of airborne fungal spores, and eliminate the
potential bias linked to the choice of the air sampling site (71).
Studies on human mycobiota have taken advantage of the culturomics
approach, which can be combined with molecular methods such as
metagenomic deep sequencing, allowing the identification of more fungal
taxa in patients and healthy controls (24,72).
Overview of major mold-related hypersensitivity diseases
Fungus-human host interactions involve a combination of
hypersensitivity, toxicity, and opportunistic infections (26–28,73–76)(Figure 2) . Indoor and outdoor exposure to fungi is ubiquitous
(33,47) and altered by climate change
(29,41,77).