Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France

Abstract

The indoor microbial community is a mixture of microorganisms resulting from outdoor ecosystems that seed the built environment. However, the biogeography of the indoor microbial community is still inadequately studied. Dust from more than 3000 dwellings across France was analyzed by qPCR using 17 targets: 10 molds, 3 bacteria groups, and 4 mites. Thus, the first spatial description of the main indoor microbial allergens on the French territory, in relation with biogeographical factors influencing the distribution of microorganisms, was realized in this study. Ten microorganisms out of 17 exhibited increasing abundance profiles across the country: Five microorganisms (Dermatophagoïdes pteronyssinus, Dermatophagoïdes spp., Streptomyces spp., Cladosporium sphaerospermum, Epicoccum nigrum) from northeast to southwest, two (Cryptococcus spp., Alternaria alternata) from northwest to southeast, Mycobacteria from east to west, Aspergillus fumigatus from south to north, and Penicillium chrysogenum from south to northeast. These geographical patterns were partly linked to climate and land cover. Multivariate analysis showed that composition of communities seemed to depend on landscapes, with species related to closed and rather cold and humid landscapes (forests, located in the northeast) and others to more open, hot, and dry landscapes (herbaceous and coastal regions, located in the west). This study highlights the importance of geographical location and outdoor factors that shape communities. In order to study the effect of microorganisms on human health (allergic diseases in particular), it is important to identify biogeographic factors that structure microbial communities on large spatial scales and to quantify the exposure with quantitative tools, such as the multi-qPCR approach.

Species-resolved sequencing of low-biomass microbiomes by 2bRAD-M

“…was transferred from human, given the likely high contact frequency between the skin and these indoor environmental surfaces. Conversely, Alternaria alteranta was mostly found in the indoor environments but absence in the underarm which is in agreement with existing reports28,29 . Thus the fungi profiles derived from 2bRAD-M are consistent with literature, demonstrating the ability to reliably profile fungi (simultaneously with bacteria) in low-biomass samples.Taking advantage of 2bRAD-M's capability in profiling bacterial and fungal species simultaneously, occurrence-network analysis revealed negative correlation between the human skin commensal yeast of Malassezia globosa (which is associated with Seborrheic Dermatitis 30 ) and the aforementioned S. epidermidis (recently proposed as a gatekeeper of healthy skin 31 ; Spearman coefficient of -0.569;…”

Urban Life as Risk Factor for Aspergillosis

“…architecture, furnishing or exposure to air pollution including particulate matter. A French study previously described Af distribution: Urbanized areas and heterogeneous agricultural areas were mentioned to be positively related to Af (Rocchi et al, 2020). Particularly, large cities seem to have negative effects.…”

“…Infections require inhalation of fungal spores from the environment (Harun et al, 2010). Aspergillus is among the most common life-threatening airborne opportunistic fungus found indoors (Rocchi et al, 2020). The presence of Af in CF sputum is associated with worse respiratory quality of life in CF (Hong et al, 2020) and chronic Af is associated with more frequent pulmonary exacerbation dependent hospitalizations (Hong et al, 2018).…”

“…Therefore, the impact of simultaneous exposure to multiple contaminants (other fungi, bacteria) has not been observed. Some species showed differences in concentrations according to geographic locations and the distribution of fungal spores is not homogeneous in the atmosphere (Rocchi et al, 2020). Regional or geographical patterns as well as different outdoor parameters or indoor characteristics (thermoisolation, ventilation, architecture) were not considered in this study.…”

The indoor environment - a potential source for intact human-associated anaerobes

“…This maturation process (including its speed and quality) depends on various factors, including birth mode (Caesarean section vs. vaginal birth), type of feeding (breast-fed vs. formula-fed), medication (e.g. antibiotics), time point of introduction of solid food, quality of social interactions and contact to animals and nature (Guaraldi & Salvatori, 2012; Moossavi & Azad, 2020; Pasolli et al, 2019; Rocchi et al, 2020). During maturation of the intestinal microbiome, facultative anaerobic microorganisms, which initially thrive in the gastrointestinal tract (GIT) after birth, are subsequently replaced by obligate anaerobes, which support the optimal fermentation of solid food (Browne et al, 2017).…”