Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development

Associations of indoor airborne microbiome with lung function: evidence from a randomized, double-blind, crossover study of microbial intervention

Microorganisms constitute an essential component of the indoor ecosystem and may pose potential health risks after inhalation. However, evidence regarding the impact of indoor airborne microbiome on general respiratory health is scarce. Additionally, while air purification has been shown to be an effective strategy for controlling culturable bioaerosols, its impact on indoor airborne microbiome remains unclear. To determine the impact of indoor airborne microbial exposure on lung function, and whether and how air purification can modify indoor airborne microbiome, we conducted a randomized, double-blind, crossover study employing air purification intervention among 68 healthy young adults in Beijing, China. Indoor airborne bacteria and fungi were characterized using amplicon sequencing technology and quantified by qPCR. Our results indicated positive associations between indoor airborne microbial α-diversity and lung function indices; however, adverse effects from total microbial load were observed. Males were more susceptible to microbial exposure than females. Beneficial effects from richness in Actinobacteria, Bacteroidia, Oxyphotobacteria, Bacilli, Clostridia, Alphaproteobacteria, Gammaproteobacteria, Dothideomycetes, and Sordariomycetes, and detrimental effects from five Proteobacteria genera, including Dechloromonas, Hydrogenophaga, Klebsiella, Pseudomonas, and Tolumonas, were also identified. Air purification contributed to decreased fungal diversity and total fungal load, but not the overall microbial community structure. Our study demonstrates the significant role of indoor airborne microbiome in regulating human respiratory health and provides inspiration for improving health through manipulation of indoor microbiome. Meanwhile, our study also underscores the importance of balancing the potential benefits from decreased microbial load and the underlying risks from reduced microbial diversity while applying environmental microbial interventions.

Height-Resolved Analysis of Indoor Airborne Microbiome: Comparison with Floor Dust-Borne Microbiome and the Significance of Shoe Sole Dust

Exposure to the indoor airborne microbiome is closely related to the air that individuals breathe. However, the floor dust-borne microbiome is commonly used as a proxy for indoor airborne microbiome, and the spatial distribution of indoor airborne microbiome is less well understood. This study aimed to characterize indoor airborne microorganisms at varying heights and compare them with those in floor dust. An assembly of three horizontally and three vertically positioned Petri dishes coated with mineral oil was applied for passive air sampling continuously at three heights without interruption. The airborne microbiomes at the three different heights showed slight stratification and differed significantly from those found in the floor dust. Based on the apportionment results from the fast expectation-maximization algorithm (FEAST), shoe sole dust contributed approximately 4% to indoor airborne bacteria and 14% to airborne fungi, a contribution that is comparable to that from the floor dust-borne microbiome. The results indicated that floor dust may not be a reliable proxy for indoor airborne microbiome. Moreover, the study highlights the need for height-resolved studies of indoor airborne microbiomes among humans in different activity modes and life states. Additionally, shoe sole-dust-associated microorganisms could potentially be a source to "re-wild" the indoor microbiota.

Childhood asthma and mould in homes-A meta-analysis

Asthma is a multifaceted and multicausal disease. Childhood asthma is strongly influenced by genetic traits and is characterized by hyperreactivity of the airways so that also unspecific triggers including moulds can trigger an asthma attack. Therefore, it is undisputed that moulds in the home can cause asthma attacks in asthmatic children. It is, however, unclear if mould in homes also induce the development of asthma. Because more and more severe attacks in asthmatic children living in mouldy homes might speed up the diagnosis of asthma, cross-sectional studies are not well-suited to differentiate between mould as a causative or only as a precipitating factor. Cross-sectional studies show an increased asthma risk and poorer lung function in children living in mouldy homes. To better understand the causal role of mould in homes, a systematic review was performed with random effects meta-analysis focusing on cohort and case-control studies only.We found 21 case-control and 11 cohort studies examining the association between mould at home and later advent of childhood asthma. According to the case-control studies, mouldy homes increase the risk of asthma by 53% (95 confidence interval [CI]: 42-65%) with no evidence of heterogeneity or publication bias. Risk estimates based on cohort studies were smaller with 15% (1-31%). The cohort studies also showed no publication bias but substantial heterogeneity (I2 = 60.5, p = 0.005). Heterogeneity could be partly explained by percentage of male children, age of participants, and publication year, but was not affected by study quality.In conclusion, living in mouldy homes during childhood seems to increase the risk of later developing bronchial asthma.

Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space

Human occupied built environments are no longer confined to Earth. In fact, there have been humans living and working in low-Earth orbit on the International Space Station (ISS) since November 2000. With NASA's Artemis missions and the age of commercial space stations set to begin, more human-occupied spacecraft than ever will be in Earth's orbit and beyond. On Earth and in the ISS, microbes, especially fungi, can be found in dust and grow when unexpected, elevated moisture conditions occur. However, we do not yet know how indoor microbiomes in Earth-based homes and in the ISS differ due to their unique set of environmental conditions. Here we show that bacterial and fungal communities are different in dust collected from vacuum bags on Earth and the ISS, with Earth-based homes being more diverse (465 fungal OTUs and 237 bacterial ASVs) compared to the ISS (102 fungal OTUs and 102 bacterial ASVs). When dust from these locations were exposed to varying equilibrium relative humidity conditions (ERH), there were also significant fungal community composition changes as ERH and time elevated increased (Bray Curtis: R2 = 0.35, P = 0.001). These findings can inform future spacecraft design to promote healthy indoor microbiomes that support crew health, spacecraft integrity, and planetary protection.

Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting

Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Fungal diversity in homes and asthma morbidity among school-age children in New York City

BACKGROUND

Asthma development has been inversely associated with exposure to fungal diversity. However, the influence of fungi on measures of asthma morbidity is not well understood.

OBJECTIVES

This study aimed to test the hypothesis that fungal diversity is inversely associated with neighborhood asthma prevalence and identify specific fungal species associated with asthma morbidity.

METHODS

Children aged 7-8 years (n = 347) living in higher (11-18%) and lower (3-9%) asthma prevalence neighborhoods were recruited within an asthma case-control study. Fungal communities were analyzed from floor dust using high-throughput DNA sequencing. A subset of asthmatic children (n = 140) was followed to age 10-11 to determine asthma persistence.

RESULTS

Neighborhood asthma prevalence was inversely associated with fungal species richness (P = 0.010) and Shannon diversity (P = 0.059). Associations between neighborhood asthma prevalence and diversity indices were driven by differences in building type and presence of bedroom carpet. Among children with asthma at age 7-8 years, Shannon fungal diversity was inversely associated with frequent asthma symptoms at that age (OR 0.57, P = 0.025) and with asthma persistence to age 10-11 (OR 0.48, P = 0.043). Analyses of individual fungal species did not show significant associations with asthma outcomes when adjusted for false discovery rates.

DISCUSSION

Lower fungal diversity was associated with asthma symptoms in this urban setting. Individual fungal species associated with asthma morbidity were not detected. Further research is warranted into building type, carpeting, and other environmental characteristics which influence fungal exposures in homes.

Fungi in Early-Life House Dust Samples and the Development of Asthma: A Birth Cohort Study

Rationale: Fungal exposure has been associated with predisposing and protective effects on the development of childhood asthma. Objectives: To study whether early-life house dust mycobiota composition is associated with the development of asthma. Methods: Mycobiota were determined by amplicon sequencing from 382 dust samples collected from living room floors 2 months after birth in homes of the LUKAS cohort. Asthma status by 10.5 years of age was defined from questionnaires and assigned as ever asthma (n = 68) or current asthma (n = 27). Inhalant atopy was clinically determined at the same age. β-composition was analyzed using PERMANOVA-S, and asthma and atopy analyses were performed using discrete time hazard models and logistic regression, respectively. Results: The house dust mycobiota composition based on Bray-Curtis distance was different in the homes of children who later did or did not develop asthma. The first and the fourth axes scores of principal coordinates analysis based on Bray-Curtis were associated with ever asthma. Of the genera with the strongest correlation with these axes, the relative abundance of Boeremia, Cladosporium, Microdochium, Mycosphaerella, and Pyrenochaetopsis showed protective associations with asthma. None of these associations remained significant after mutual adjustment among the five genera or when mutually adjusted for other microbial cell wall markers and previously identified asthma-protective bacterial indices. Neither fungal α-diversity nor load was associated with asthma in the whole population, but higher fungal richness was a risk factor among children on farms. Higher fungal loads (measured via quantitative polymerase chain reaction) in house dust were associated with the risk of inhalant atopy. Conclusions: The results of our analyses from this well-characterized birth cohort suggest that the early-life house dust mycobiota in Finnish homes, characterized via DNA amplicon sequencing, do not have strong predisposing or protective effects on asthma development.

Assessment of indoor bioaerosol exposure using direct-reading versus traditional methods-potential application to home health care

Home healthcare workers (HHCWs) can be occupationally exposed to bioaerosols in their clients' homes. However, choosing the appropriate method to measure bioaerosol exposures remains a challenge. Therefore, a systematic comparison of existing measurement approaches is essential. Bioaerosol measurements with a real-time, fluorescence-based Wideband Integrated Bioaerosol Sensor (WIBS) were compared to measurements with four traditional off-line methods (TOLMs). The TOLMS included optical microscopic counting of spore trap samples, microbial cultivation of impactor samples, qPCR, and next-generation sequencing (NGS) of filter samples. Measurements were conducted in an occupied apartment simulating the environments that HHCWs could encounter in their patients' homes. Descriptive statistics and Spearman's correlation test were computed to compare the real-time measurement with those of each TOLM. The results showed that the geometric mean number concentrations of the total fluorescent aerosol particles (TFAPs) detected with the WIBS were several orders of magnitude higher than those of total fungi or bacteria measured with the TOLMs. Among the TOLMs, concentrations obtained with qPCR and NGS were the closest to the WIBS detections. Correlations between the results obtained with the WIBS and TOLMs were not consistent. No correlation was found between the concentrations of fungi detected using microscopic counting and any of the WIBS fluorescent aerosol particle (FAP) types, either indoors or outdoors. In contrast, the total concentrations detected with microbial cultivation correlated with the WIBS TFAP results, both indoors and outdoors. Outdoors, the total concentration of culturable bacteria correlated with FAP-type AC. In addition, fungal and bacterial concentrations obtained with qPCR correlated with FAP types AB and AC. For a continuous, high-time resolution but broad scope, the real-time WIBS could be considered, whereas a TOLM would be the best choice for specific and more accurate microbial characterization. HHCWs' activities tend to re-aerosolize bioaerosols causing wide temporal variation in bioparticle concentrations. Thus, the advantage of using the real-time instrument is to capture those variations. This study lays a foundation for future exposure assessment studies targeting HHCWs.

Childhood lower respiratory tract infections linked to residential airborne bacterial and fungal microbiota

Residential microbial composition likely contributes to the development of lower respiratory tract infections (LRTI) among children, but the association is poorly understood. We aimed to study the relationship between the indoor airborne dust bacterial and fungal microbiota and childhood LRTI in Ibadan, Nigeria. Ninety-eight children under the age of five years hospitalized with LRTI were recruited and matched by age (±3 months), sex, and geographical location to 99 community-based controls without LRTI. Participants' homes were visited and sampled over a 14-day period for airborne house dust using electrostatic dustfall collectors (EDC). In airborne dust samples, the composition of bacterial and fungal communities was characterized by a meta-barcoding approach using amplicons targeting simultaneously the bacterial 16S rRNA gene and the internal-transcribed-spacer (ITS) region-1 of fungi in association with the SILVA and UNITE database respectively. A 100-unit change in house dust bacterial, but not fungal, richness (OR 1.06; 95%CI 1.03-1.10) and a 1-unit change in Shannon diversity (OR 1.92; 95%CI 1.28-3.01) were both independently associated with childhood LRTI after adjusting for other indoor environmental risk factors. Beta-diversity analysis showed that bacterial (PERMANOVA p < 0.001, R² = 0.036) and fungal (PERMANOVA p < 0.001, R² = 0.028) community composition differed significantly between homes of cases and controls. Pair-wise differential abundance analysis using both DESEq2 and MaAsLin2 consistently identified the bacterial phyla Deinococcota (Benjamini-Hochberg (BH) adjusted p-value <0.001) and Bacteriodota (BH-adjusted p-value = 0.004) to be negatively associated with LRTI. Within the fungal microbiota, phylum Ascomycota abundance (BH adjusted p-value <0.001) was observed to be directly associated with LRTI, while Basidiomycota abundance (BH adjusted p-value <0.001) was negatively associated with LRTI. Our study suggests that early-life exposure to certain airborne bacterial and fungal communities is associated with LRTI among children under the age of five years.

The Moderating Role of Housing Quality on Concentrated Poverty and Asthma-Related Emergency Department Visits Among Hispanics/Latinos

Background. Rates of asthma-related emergency department visits have been shown to vary significantly by place (i.e., neighborhood) and race/ethnicity. The moderating factors of asthmatic events among Hispanic/Latino-specific populations are known to a much lesser degree. Objective. To assess the extent to which housing moderates the effect of poverty on Hispanic/Latino-specific asthma-related emergency department (ED) visits at an ecological level. Methods. Using data from the Office of Statewide Health Planning and Development (OSHPD) and the 2016-2017 U.S. Census, a cross-sectional ecological analysis at the census tract-level was conducted. Crosswalk files from the U.S. Department of Housing and Urban Development were used to associate zip codes to census tracts. Negative binomial regression was used to estimate rate ratios. Results. The effect of poverty on asthma-related ED visits was significantly moderated by the median year of housing structures built. The effect of mid-level poverty (RR= 1.57, 95% CI 1.27, 1.95) and high-level poverty (RR= 1.47, 95% CI 1.22, 1.78) in comparison to low-level poverty, was significantly greater among census tracts with housing built prior to 1965 in comparison to census tract with housing built between 1965-2020. Conclusion. Communities with older housing structures tend to be associated with increased Hispanic/Latino ED visits apart from affluent communities.

Persisting Cryptococcus yeast species Vishniacozyma victoriae and Cryptococcus neoformans elicit unique airway inflammation in mice following repeated exposure

Background

Allergic airway disease (AAD) is a growing concern in industrialized nations and can be influenced by fungal exposures. Basidiomycota yeast species such as Cryptococcus neoformans are known to exacerbate allergic airway disease; however, recent indoor assessments have identified other Basidiomycota yeasts, including Vishniacozyma victoriae (syn. Cryptococcus victoriae), to be prevalent and potentially associated with asthma. Until now, the murine pulmonary immune response to repeated V. victoriae exposure was previously unexplored.

Objective

This study aimed to compare the immunological impact of repeated pulmonary exposure to Cryptococcus yeasts.

Methods

Mice were repeatedly exposed to an immunogenic dose of C. neoformans or V. victoriae via oropharyngeal aspiration. Bronchoalveolar lavage fluid (BALF) and lungs were collected to examine airway remodeling, inflammation, mucous production, cellular influx, and cytokine responses at 1 day and 21 days post final exposure. The responses to C. neoformans and V. victoriae were analyzed and compared.

Results

Following repeated exposure, both C. neoformans and V. victoriae cells were still detectable in the lungs 21 days post final exposure. Repeated C. neoformans exposure initiated myeloid and lymphoid cellular infiltration into the lung that worsened over time, as well as an IL-4 and IL-5 response compared to PBS-exposed controls. In contrast, repeated V. victoriae exposure induced a strong CD4+ T cell-driven lymphoid response that started to resolve by 21 days post final exposure.

Discussion

C. neoformans remained in the lungs and exacerbated the pulmonary immune responses as expected following repeated exposure. The persistence of V. victoriae in the lung and strong lymphoid response following repeated exposure were unexpected given its lack of reported involvement in AAD. Given the abundance in indoor environments and industrial utilization of V. victoriae, these results highlight the importance to investigate the impact of frequently detected fungal organisms on the pulmonary response following inhalational exposure. Moreover, it is important to continue to address the knowledge gap involving Basidiomycota yeasts and their impact on AAD.

Optimization of bacterial DNA and endotoxin extraction from settled airborne dust

Collecting and obtaining sufficient amount of airborne particles for multiple microbial component assessments can be challenging. A passive dust sampling device, the electrostatic dust fall collector (EDC) has been established for assessing airborne exposures including endotoxin and glucans. Recently, with advances in next-generation sequencing techniques, EDCs were used to collect microbial cells for DNA sequencing analysis to promote the study of airborne bacterial and fungal communities. However, low DNA yields have been problematic when employing passive sampling with EDC. To address this challenge, we attempted to increase the efficiency of extraction. We compared DNA extraction efficiency of bacterial components from EDCs captured on filters through filtration using five extraction techniques. By measuring the abundance, diversity and structure of bacterial communities using qPCR and amplicon sequencing targeting 16S rRNA genes, we found that two techniques outperformed the rest. Furthermore, we developed protocols to simultaneously extract both DNA and endotoxin from a single EDC cloth. Our technique promotes a high quality to price ratio and may be employed in large epidemiological studies addressing airborne bacterial exposure where a large number of samples is needed.

Indoor bacterial and fungal aerosols as predictors of lower respiratory tract infections among under-five children in Ibadan, Nigeria

BACKGROUND

This study aimed to investigate the association between exposure to diverse indoor microbial aerosols and lower respiratory tract infections (LRTI) among children aged 1 to 59 months in Ibadan, Nigeria.

METHODS

One hundred and seventy-eight (178) hospital-based LRTI cases among under-five children were matched for age (± 3 months), sex and geographical location with 180 community-based controls (under-five children without LRTI). Following consent from caregivers of eligible participants, a child's health questionnaire, clinical proforma and standardized home-walkthrough checklist were used to collect data. Participant homes were visited and sampled for indoor microbial exposures using active sampling approach by Anderson sampler. Indoor microbial count (IMC), total bacterial count (TBC), and total fungal count (TFC) were estimated and dichotomized into high (> median) and low (≤ median) exposures. Alpha diversity measures including richness (R), Shannon (H) and Simpson (D) indices were also estimated. Conditional logistic regression models were used to test association between exposure to indoor microbial aerosols and LRTI risk among under-five children.

RESULTS

Significantly higher bacterial and fungal diversities were found in homes of cases (R = 3.00; H = 1.04; D = 2.67 and R = 2.56; H = 0.82; D = 2.33) than homes of controls (R = 2.00; H = 0.64; D = 1.80 and R = 1.89; H = 0.55; D = 1.88) p < 0.001, respectively. In the multivariate models, higher categories of exposure to IMC (aOR = 2.67, 95% CI 1.44-4.97), TBC (aOR = 2.51, 95% CI 1.36-4.65), TFC (aOR = 2.75, 95% CI 1.54-4.89), bacterial diversity (aOR = 1.87, 95% CI 1.08-3.24) and fungal diversity (aOR = 3.00, 95% CI 1.55-5.79) were independently associated with LRTI risk among under-five children.

CONCLUSIONS

This study suggests an increased risk of LRTI when children under the age of five years are exposed to high levels of indoor microbial aerosols.

Spring is associated with increased total and allergenic fungal concentrations in house dust from a pediatric asthma cohort in New York City

Introduction

Asthma and allergy symptoms vary seasonally due to exposure to environmental sources of allergen, including fungi. However, we need an improved understanding of seasonal influence on fungal exposures in the indoor environment. We hypothesized that concentrations of total fungi and allergenic species in vacuumed dust vary significantly by season.

Objective

Assess seasonal variation of indoor fungi with greater implications related to seasonal asthma control.

Methods

We combined next-generation sequencing with quantitative polymerase chain reaction (qPCR) to measure concentrations of fungal DNA in indoor floor dust samples (n = 298) collected from homes participating in the New York City Neighborhood Asthma and Allergy Study (NAAS).

Results

Total fungal concentration in spring was significantly higher than the other three seasons (p ≤ 0.005). Mean concentrations for 78% of fungal species were elevated in the spring (26% were significantly highest in spring, p < 0.05). Concentrations of 8 allergenic fungal species were significantly (p < 0.5) higher in spring compared to at least two other seasons. Indoor relative humidity and temperature were significantly highest in spring (p < 0.05) and were associated with total fungal concentration (R2 = 0.049, R2 = 0.11, respectively).

Conclusion

There is significant seasonal variation in total fungal concentration and concentration of select allergenic species. Indoor relative humidity and temperature may underlie these associations.

Determinants of bacterial and fungal microbiota in Finnish home dust: Impact of environmental biodiversity, pets, and occupants

The indoors is where many humans spend most of their time, and are strongly exposed to indoor microbiota, which may have multifaceted effects on health. Therefore, a comprehensive understanding of the determinants of indoor microbiota is necessary. We collected dust samples from 295 homes of families with young children in the Helsinki region of Finland and analyzed the bacterial and fungal composition based on the 16S rRNA and ITS DNA sequences. Microbial profiles were combined with extensive survey data on family structure, daily life, and physical characteristics of the home, as well as additional external environmental information, such as land use, and vegetational biodiversity near the home. Using permutational multivariate analysis of variance we explained 18% of the variation of the relative abundance between samples within bacterial composition, and 17% of the fungal composition with the explanatory variables. The fungal community was dominated by the phyla Basidiomycota, and Ascomycota; the bacterial phyla Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria were dominant. The presence of dogs, multiple children, and firewood were significantly associated with both the fungal and bacterial composition. Additionally, fungal communities were associated with land use, biodiversity in the area, and the type of building, while bacterial communities were associated with the human inhabitants and cleaning practices. A distinction emerged between members of Ascomycota and Basidiomycota, Ascomycota being more abundant in homes with greater surrounding natural environment, and potential contact with the environment. The results suggest that the fungal composition is strongly dependent on the transport of outdoor environmental fungi into homes, while bacteria are largely derived from the inhabitants.

Season, Vegetation Proximity and Building Age Shape the Indoor Fungal Communities' Composition at City-Scale

Exposure to particular microbiome compositions in the built environment can affect human health and well-being. Identifying the drivers of these indoor microbial assemblages is key to controlling the microbiota of the built environment. In the present study, we used culture and metabarcoding of the fungal Internal Transcribed Spacer ribosomal RNA region to assess whether small-scale variation in the built environment influences the diversity, composition and structure of indoor air fungal communities between a heating and an unheated season. Passive dust collectors were used to collect airborne fungi from 259 dwellings representative of three major building periods and five building environments in one city-Lausanne (Vaud, Switzerland)-over a heating and an unheated period. A homogenous population (one or two people with an average age of 75 years) inhabited the households. Geographic information systems were used to assess detailed site characteristics (altitude, proximity to forest, fields and parks, proximity to the lake, and density of buildings and roads) for each building. Our analysis indicated that season was the factor that explained most of the variation in colonies forming unit (CFU) concentration and indoor mycobiome composition, followed by the period of building construction. Fungal assemblages were more diverse during the heating season than during the unheated season. Buildings with effective insulation had distinct mycobiome compositions from those built before 1975 - regardless of whether they were constructed with pre-1945 technology and materials or 1945 - 1974 ones. The urban landscape-as a whole-was a significant predictor of cultivable Penicillium load-the closer the building was to the lake, the higher the Penicillium load-but not of fungal community composition. Nevertheless, the relative abundance of eleven fungal taxa detected by metabarcoding decreased significantly with the urbanization gradient. When urban landscape descriptors were analyzed separately, the explanatory power of proximity to vegetation in shaping fungal assemblages become significant, indicating that land cover type had an influence on fungal community structure that was obscured by the effects of building age and sampling season. In conclusion, indoor mycobiomes are strongly modulated by season, and their assemblages are shaped by the effectiveness of building insulation, but are weakly influenced by the urban landscape.

Indoor microbiome and allergic diseases: From theoretical advances to prevention strategies

The prevalence of allergic diseases, such as asthma, rhinitis, eczema, and sick building syndrome (SBS), has increased drastically in the past few decades. Current medications can only relieve the symptoms but not cure these diseases whose development is suggested to be greatly impacted by the indoor microbiome. However, no study comprehensively summarizes the progress and general rules in the field, impeding subsequent translational application. To close knowledge gaps between theoretical research and practical application, we conducted a comprehensive literature review to summarize the epidemiological, environmental, and molecular evidence of indoor microbiome studies. Epidemiological evidence shows that the potential protective indoor microorganisms for asthma are mainly from the phyla Actinobacteria and Proteobacteria, and the risk microorganisms are mainly from Bacilli, Clostridia, and Bacteroidia. Due to extremely high microbial diversity and geographic variation, different health-associated species/genera are detected in different regions. Compared with indoor microbial composition, indoor metabolites show more consistent associations with health, including microbial volatile organic compounds (MVOCs), lipopolysaccharides (LPS), indole derivatives, and flavonoids. Therefore, indoor metabolites could be a better indicator than indoor microbial taxa for environmental assessments and health outcome prediction. The interaction between the indoor microbiome and environmental characteristics (surrounding greenness, relative humidity, building confinement, and CO2 concentration) and immunology effects of indoor microorganisms (inflammatory cytokines and pattern recognition receptors) are briefly reviewed to provide new insights for disease prevention and treatment. Widely used tools in indoor microbiome studies are introduced to facilitate standard practice and the precise identification of health-related targets.

The Environmental Microbiome, Allergic Disease, and Asthma

The environmental microbiome represents the entirety of the microbes and their metabolites that we encounter in our environments. A growing body of evidence supports the role of the environmental microbiome in risk for and severity of allergic diseases and asthma. The environmental microbiome represents a ubiquitous, lifelong exposure to non-self antigens. During the critical window between birth and 1 year of life, interactions between our early immune system and the environmental microbiome have 2 consequences: our individual microbiome is populated by environmental microbes, and our immune system is trained regarding which antigens to tolerate. During this time, a diversity of exposures appears largely protective, dramatically decreasing the risk of developing allergic diseases and asthma. As we grow older, our interactions with the environmental microbiome change. While it continues to exert influence over the composition of the human microbiome, the environmental microbiome becomes increasingly a source for antigenic stimulation and infection. The same microbial exposure protective against disease development may exacerbate disease severity. Although much has been learned about the importance of the environmental microbiome in allergic disease, much more remains to be understood about these complicated interactions between our environment, our microbiome, our immune system, and disease.

Characteristics of annual mold variations and association with childhood allergic symptoms/diseases via combining surveys and home visit measurements

The presence of dampness and visible molds leads to concerns of poor indoor air quality which has been consistently linked with increased exacerbation and development of allergy and respiratory diseases. Due to the limitations of epidemiological surveys, the actual fungal exposure characteristics in residences has not been sufficiently understood. This study aimed to characterize household fungal diversity and its annual temporal and spatial variations. We developed combined cross-sectional survey, repeated air sampling around a year, and DNA sequencing methods. The questionnaire survey was conducted in 2019, and 4943 valid cases were received from parents; a follow-up case-control study (11 cases and 12 controls) was designed, and onsite measurements of indoor environments were repeated in typical summer, transient season, and winter; dust from floor and beddings in children's room were collected and ITS based DNA sequencing of totally 68 samples was conducted. Results from 3361 children without changes to their residences since birth verified the significant associations of indoor dampness/mold indicators and prevalence of children-reported diseases, with increased adjusted odd ratios (aORs) >1 for studied asthma, wheeze, allergic rhinitis, and eczema. The airborne fungal concentrations from air sampling were higher than 1000 CFU/m³ in summer, regardless of indoors and outdoors, indicating an intermediate pollution level. The DNA sequencing for dust showed the Aspergillus was the predominant at genus level and the Aspergillus_penicillioides was the most common at species level; while the fungal community and composition varied significantly in different homes and seasons, according to α and β diversity analyses. The comprehensive research methods contribute to a holistic understanding of indoor fungal exposure, including the concentrations, seasonal variations, community, and diversity, and verifies the relations with children's adverse health outcomes. The study further elucidates the role of microbiome in human health, which helps setting health-protective thresholds and managing mold treatments in buildings, to promote indoor air quality and human well-beings.

Mycobiota and the Contribution of Yeasts in Floor Dust of 50 Elementary Schools Characterized with Sequencing Internal Transcribed Spacer Region of Ribosomal DNA

The assemblage of fungi including unicellular yeasts in schools is understudied. We conducted an environmental study to characterize fungal communities in classroom floor dust. We collected 500 samples from 50 elementary schools in Philadelphia, PA, and evaluated room dampness/mold conditions. Genomic DNA from dust was extracted for internal transcribed spacer 1 Illumina MiSeq sequencing to identify operational taxonomic units (OTUs) organized from DNA sequences. Differential abundance analyses were performed to examine significant differences in abundance among groups. We identified 724 genera from 1490 OTUs. The genus Epicoccum was not diverse but the most abundant (relative abundance = 18.9%). Fungi were less diverse but most dissimilar in composition in the most water-damaged classrooms compared to the least water-damaged, indicating differential effects of individual classroom water-damage on fungal compositions. We identified 62 yeast genera, representing 19.6% of DNA sequences. Cyberlindnera was the most abundant (6.1%), followed by Cryptococcus, Aureobasidium, Rhodotorula, and Candida. The average relative abundance of yeasts tended to increase with increasing dampness and mold score and was significantly (p-value = 0.048) higher in the most water-damaged classrooms (22.4%) than the least water-damaged classrooms (18.2%). Our study suggests the need for further research on the potential health effects associated with exposures to yeasts in schools.

Fungal Spore Richness in School Classrooms is Related to Surrounding Forest in a Season-Dependent Manner

Airborne fungal spores are important aeroallergens that are remarkably diverse in terms of taxonomic richness. Indoor fungal richness is dominated by outdoor fungi and is geographically patterned, but the influence of natural landscape is unclear. We aimed to elucidate the relationship between indoor fungal spore richness and natural landscape by examining the amount of surrounding forest cover. Passive sampling of airborne fungal spores was conducted in 24 schools in Taiwan during hot and cool seasons, and amplicon sequencing was used to study fungal spore (genus) richness targeting the internal transcribed spacer 2 (ITS2) region. In total, 693 fungal genera were identified, 12 of which were ubiquitous. Despite overall similarity of fungal spore richness between seasons, Basidiomycota and Ascomycota richness increased during the hot and cool seasons, respectively. Fungal spore richness in schools had a strong positive correlation with the amount of surrounding forest cover during the cool season, but not during the hot season. Fungal assemblages in schools were more similar during the hot season due to the increased ubiquity of Agaricomycetes genera. These observations indicate dispersal limitation at the kilometer scale during the cool season and increased long-distance dispersal during the hot season. Several allergenic fungi were commonly identified in schools, including some previously overlooked by conventional methods, which may be targeted as sensitizing agents in future investigations into atopic conditions. More generally, the relative importance of fungal spore richness in the development, chronicity, and severity of atopic conditions in children requires investigation.

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

A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.

Environmental and Human Microbiome for Health

Microorganisms are an essential part of life on the earth and can exist in association with virtually any living thing. The environmental microbiome is much more diverse than the human microbiome. It is reported that most microbes existing in the environment are difficult to culture in the laboratory. Whereas both pathogenic and beneficial microbes may be prevailing in the environment, the human body can have three categories of microbes- beneficial, pathogenic, and opportunistic pathogenic. With at least 10-fold more cells than human cells, microbes as normal flora are critical for human survival. The microbes present in the human body play a crucial role in maintaining human health, and the environmental microbiome influences the human microbiome makeup. The interaction between the environmental and human microbiome highly influences human health, however it is poorly understood. In addition, as an established infection is associated with health-seeking behavior, a large number of studies have focused on the transmission and dynamics of infectious microorganisms than the noninfectious or beneficial ones. This review will summarize how the interaction between the environmental and human microbiome affects human health and identify approaches that might be beneficial for humans to improve health by being exposed to the natural environment.

Residential bacteria and fungi identified by high-throughput sequencing and childhood respiratory health

The objective of this study was to examine and compare environmental microbiota from dust and children's respiratory health outcomes at ages seven and twelve. At age seven, in-home visits were conducted for children enrolled in the Cincinnati Childhood Allergy and Air Pollution Study (CCAAPS). Floor dust was collected and analyzed for bacterial (16 S rRNA gene) and fungal (internal transcribed spacer region) microbiota. Respiratory outcomes, including physician-diagnosed asthma, wheeze, rhinitis, and aeroallergen sensitivity were assessed by physical examination and caregiver-report at ages seven and twelve. The associations between dust microbiota and respiratory outcomes were evaluated using Permanova, DESeq, and weighted quantile sum (WQS) regression models. Four types of WQS regression models were run to identify mixtures of fungi or bacteria that were associated with the absence or presence of health outcomes. For alpha or beta diversity of fungi and bacteria, no significant associations were found with respiratory health outcomes. DESeq identified specific bacterial and fungal indicator taxa that were higher or lower with the presence of different health outcomes. Most individual indicator fungal species were lower with asthma and wheeze and higher with aeroallergen positivity and rhinitis, whereas bacterial data was less consistent. WQS regression models demonstrated that a combination of species might influence health outcomes. Several heavily weighted species had a strong influence on the models, and therefore, created a microbial community that was associated with the absence or presence of asthma, wheeze, rhinitis, and aeroallergen+. Weights for specific species within WQS regression models supported indicator taxa findings. Health outcomes might be more influenced by the composition of a complex mixture of bacterial and fungal species in the indoor environment than by the absence or presence of individual species. This study demonstrates that WQS is a useful tool in evaluating mixtures in relation to potential health effects.

Indoor green can modify the indoor dust microbial communities

Little is known about the potential role of indoor plants in shaping the indoor microbiota. Within the ENVIRONAGE birth cohort, we collected settled dust and performed 16S and ITS amplicon sequencing and qPCR measurements to characterize the indoor microbiota, including bacterial and fungal loads and Chao1 richness, Shannon, and Simpson diversity indices. For 155 households, we obtained information on the number of indoor plants. We performed linear regression models adjusted for several a priori chosen covariables. Overall, an increase in indoor plants and density was associated with increased microbial diversity, but not load. For example, we found an increase of 64 (95%CI:3;125) and 26 (95%CI:4;48) units of bacterial and fungal taxa richness, respectively, in households with more than three plants compared to no plants. Our results support the hypothesis that indoor plants can enrich indoor microbial diversity, while impacts on microbial loads are not obvious.

BioMateriOME: To understand microbe-material interactions within sustainable, living architectures

BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively. This review summarizes the BioMateriOME prototype and its use as a tool in combining microbiology, design, architecture and social science. The use of microbiology and biological components in the fabrication of biomaterials is provided, together with an appreciation of the microbial communities common to conventional indoor surfaces, and how these communities may change in response to the implementation of living materials in our homes. Societal perceptions of microbiomes and biomaterials, are considered within the framework of healthy architecture. Finally, features of architectural design with microbes in mind are introduced, with the possibility of codifying microbial surveillance into design and construction benchmarks, standards and regulations toward healthier buildings and their occupants.

Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK

Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10453-022-09760-9.

Vishniacozyma victoriae (syn. Cryptococcus victoriae) in the homes of asthmatic and non-asthmatic children in New York City

BACKGROUND

Indoor environments contain a broad diversity of non-pathogenic Basidiomycota yeasts, but their role in exacerbating adverse health effects has remained unclear.

OBJECTIVE

To understand the role of Vishniacozyma victoriae exposure and its impact on human health.

METHODS

A qPCR assay was developed to detect and quantify an abundant indoor yeast species, Vishniacozyma victoriae (syn. Cryptococcus victoriae), from homes participating in the New York City Neighborhood Asthma and Allergy Study (NAAS). We evaluated the associations between V. victoriae, housing characteristics, and asthma relevant health endpoints.

RESULTS

V. victoriae was quantified in 236 of the 256 bedroom floor dust samples ranging from less than 300-45,918 cell equivalents/mg of dust. Higher concentrations of V. victoriae were significantly associated with carpeted bedroom floors (P = 0.044), mean specific humidity (P = 0.004), winter (P < 0.0001) and spring (P = 0.001) seasons, and the presence of dog (P = 0.010) and dog allergen Can f 1 (P = 0.027). V. victoriae concentrations were lower in homes of children with asthma vs. without asthma (P = 0.027), an association observed only among the non-seroatopic children.

City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types

Currently, there is a lack of understanding on the variations of the indoor airborne microbiotas of different building types within a city, and how operational taxonomic unit (OTU)- and amplicon sequence variant (ASV)-based analyses of the 16S rRNA gene sequences affect interpretation of the indoor airborne microbiota results. Therefore, in this study, the indoor airborne bacterial microbiotas between commercial buildings, residences, and subways within the same city were compared using both OTU- and ASV-based analytic methods. Our findings suggested that indoor airborne bacterial microbiota compositions were significantly different between building types regardless of the bioinformatics method used. The processes of ecological drift and random dispersal consistently played significant roles in the assembly of the indoor microbiota across building types. Abundant taxa tended to be more centralized in the correlation network of each building type, highlighting their importance. Taxonomic changes between the microbiotas of different building types were also linked to changes in their inferred metabolic function capabilities. Overall, the results imply that customized strategies are necessary to manage indoor airborne bacterial microbiotas for each building type or even within each specific building.

Microbial exposures in moisture-damaged schools and associations with respiratory symptoms in students: A multi-country environmental exposure study

Moisture-damaged buildings are associated with respiratory symptoms and underlying diseases among building occupants, but the causative agent(s) remain a mystery. We first identified specific fungal and bacterial taxa in classrooms with moisture damage in Finnish and Dutch primary schools. We then investigated associations of the identified moisture damage indicators with respiratory symptoms in more than 2700 students. Finally, we explored whether exposure to specific taxa within the indoor microbiota may explain the association between moisture damage and respiratory health. Schools were assessed for moisture damage through detailed inspections, and the microbial composition of settled dust in electrostatic dustfall collectors was determined using marker-gene analysis. In Finland, there were several positive associations between particular microbial indicators (diversity, richness, individual taxa) and a respiratory symptom score, while in the Netherlands, the associations tended to be mostly inverse and statistically non-significant. In Finland, abundance of the Sphingomonas bacterial genus and endotoxin levels partially explained the associations between moisture damage and symptom score. A few microbial taxa explained part of the associations with health, but overall, the observed associations between damage-associated individual taxa and respiratory health were limited.

Childhood asthma- pathogenesis and phenotypes

In the pathogenesis of asthma in children there is a pivotal role for a type 2 inflammatory response to early life exposures or events. Interactions between infections, atopy, genetic susceptibility, and environmental exposures (such as farmyard environment, air pollution, tobacco smoke exposure) influence the development of wheezing illness and the risk for progression to asthma. The immune system, lung function and the microbiome in gut and airways develop in parallel and dysbiosis of the microbiome may be a critical factor in asthma development. Increased infant weight gain and preterm birth are other risk factors for development of asthma and reduced lung function. The complex interplay between these factors explains the heterogeneity of asthma in children. Subgroups of patients can be identified as phenotypes based on clinical parameters, or endotypes, based on a specific pathophysiological mechanism. Paediatric asthma phenotypes and endotypes may ultimately help to improve diagnosis of asthma, prediction of asthma development and treatment of individual children, based on clinical, temporal, developmental or inflammatory characteristics. Unbiased, data-driven clustering, using a multidimensional or systems biology approach may be needed to better define phenotypes. The present knowledge on inflammatory phenotypes of childhood asthma has now been successfully applied in the treatment with biologicals of children with severe therapy resistant asthma, and it is to be expected that more personalized treatment options may become available.

Microbial growth and volatile organic compound (VOC) emissions from carpet and drywall under elevated relative humidity conditions

BACKGROUND

Microbes can grow in indoor environments if moisture is available, and we need an improved understanding of how this growth contributes to emissions of microbial volatile organic compounds (mVOCs). The goal of this study was to measure how moisture levels, building material type, collection site, and microbial species composition impact microbial growth and emissions of mVOCs. We subjected two common building materials, drywall, and carpet, to treatments with varying moisture availability and measured microbial communities and mVOC emissions.

RESULTS

Fungal growth occurred in samples at >75% equilibrium relative humidity (ERH) for carpet with dust and >85% ERH for inoculated painted drywall. In addition to incubated relative humidity level, dust sample collection site (adonis p=0.001) and material type (drywall, carpet, adonis p=0.001) drove fungal and bacterial species composition. Increased relative humidity was associated with decreased microbial species diversity in samples of carpet with dust (adonis p= 0.005). Abundant volatile organic compounds (VOCs) that accounted for >1% emissions were likely released from building materials and the dust itself. However, certain mVOCs were associated with microbial growth from carpet with dust such as C10H16H+ (monoterpenes) and C2H6SH+ (dimethyl sulfide and ethanethiol). CO2 production from samples of carpet with dust at 95% ERH averaged 5.92 mg hr-1 kg-1, while the average for carpet without dust at 95% ERH was 2.55 mg hr-1 kg-1.

CONCLUSION

Microbial growth and mVOC emissions occur at lower relative humidity in carpet and floor dust compared to drywall, which has important implications for human exposure. Even under elevated relative humidity conditions, the VOC emissions profile is dominated by non-microbial VOCs, although potential mVOCs may dominate odor production. Video Abstract.

Residential green space can shape the indoor microbial environment

BACKGROUND

The influence of outdoor green space on microbial communities indoors has scarcely been investigated. Here, we study the associations between nearby residential green space and residential indoor microbiota.

METHODS

We collected settled dust from 176 living rooms of participants of the ENVIRONAGE birth cohort. We performed 16S and ITS amplicon sequencing, and quantitative PCR measurements of total bacterial and fungal loads to calculate bacterial and fungal diversity measures (Chao1 richness, Shannon and Simpson diversity indices) and relative abundance of individual taxa. Green spaces were estimated within 50m and 100m buffers around the residential address. We defined total residential green space using high-resolution land-cover data, further stratified in low-growing (height<3m) and high-growing green (height>3m). We used land-use data to calculate the residential nature. We ran linear regression models, adjusting for confounders and other potential determinants. Results are expressed as units change for an interquartile range (IQR) increase in residential green space and their 95% confidence intervals (CI).

RESULTS

After adjustment, we observed statistically significant associations between the indoor microbial diversity indices and nearby residential green space. For bacteria, the Shannon index was directly associated with residential nature (e.g. 0.08 units increase (CI:0.02,0.13) per IQR increase in nature within a 50m buffer). Fungal diversity was directly associated with high-growing residential green and inversely with low-growing green. For example, an IQR increase in high-growing green within a 50m buffer was associated with increases in 0.14 (CI:0.01,0.27) and 0.02 (CI:0.008,0.04) units in the Shannon and Simpson indices, respectively.

CONCLUSIONS

Nearby green space determines the diversity of indoor environment microbiota, and the type of green differently impacts bacterial and fungal diversity. Further research is needed to investigate in more detail possible microbial taxa compositions underlying the observed changes in indoor microbiota diversity and to explore their contribution to beneficial health effects associated with green space exposure.

Germaphobia! Does Our Relationship With and Knowledge of Biodiversity Affect Our Attitudes Toward Microbes?

Germaphobia – a pathological aversion to microorganisms – could be contributing to an explosion in human immune-related disorders via mass sterilization of surfaces and reduced exposure to biodiversity. Loss of biodiversity and people’s weaker connection to nature, along with poor microbial literacy may be augmenting the negative consequences of germaphobia on ecosystem health. In this study, we created an online questionnaire to acquire data on attitudes toward, and knowledge of microbes. We collected data on nature connectedness and interactions with nature and explored the relationships between these variables. Although the study had an international reach (n = 1,184), the majority of responses came from England, United Kingdom (n = 993). We found a significant association between attitudes toward microbes and both duration and frequency of visits to natural environments. A higher frequency of visits to nature per week, and a longer duration spent in nature per visit, was significantly associated with positive attitudes toward microbes. We found no association between nature connectedness and attitudes toward microbes. We found a significant relationship between knowledge of “lesser known” microbial groups (e.g., identifying that fungi, algae, protozoa, and archaea are microbes) and positive attitudes toward microbes. However, we also found that people who identified viruses as being microbes expressed less positive views of microbes overall–this could potentially be attributed to a “COVID-19 effect.” Our results suggest that basic microbial literacy and nature engagement may be important in reducing/preventing germaphobia-associated attitudes. The results also suggest that a virus-centric phenomenon (e.g., COVID-19) could increase broader germaphobia-associated attitudes. As the rise of immune-related disorders and mental health conditions have been linked to germaphobia, reduced biodiversity, and non-targeted sterilization, our findings point to a feasible strategy to potentially help ameliorate these negative consequences. Further research is needed, but greater emphasis on microbial literacy and promoting time spent in nature could potentially be useful in promoting resilience in human health and more positive/constructive attitudes toward the foundations of our ecosystems—the microorganisms.

Analysing indoor mycobiomes through a large-scale citizen science study in Norway

In the built environment, fungi can cause important deterioration of building materials and have adverse health effects on occupants. Increased knowledge about indoor mycobiomes from different regions of the world, and their main environmental determinants, will enable improved indoor air quality management and identification of health risks. This is the first citizen science study of indoor mycobiomes at a large geographical scale in Europe, including 271 houses from Norway and 807 dust samples from three house compartments: outside of the building, living room and bathroom. The fungal community composition determined by DNA metabarcoding was clearly different between indoor and outdoor samples, but there were no significant differences between the two indoor compartments. The 32 selected variables, related to the outdoor environment, building features and occupant characteristics, accounted for 15% of the overall variation in community composition, with the house compartment as the key factor (7.6%). Next, climate was the main driver of the dust mycobiomes (4.2%), while building and occupant variables had significant but minor influences (1.4% and 1.1%, respectively). The house-dust mycobiomes were dominated by ascomycetes (⁓70%) with Capnodiales and Eurotiales as the most abundant orders. Compared to the outdoor samples, the indoor mycobiomes showed higher species richness, which is probably due to the mixture of fungi from outdoor and indoor sources. The main indoor indicator fungi belonged to two ecological groups with allergenic potential: xerophilic moulds and skin-associated yeasts. Our results suggest that citizen science is a successful approach for unravelling the built microbiome at large geographical scales.

Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity

Exposure to biodiverse aerobiomes supports human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have reported aerobiome vertical stratification in different urban green spaces. We used columnar sampling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate urban green space aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial diversity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha diversity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide novel insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace. This has important implications for managing urban landscapes for the regulation of aerobiome exposure.

Microbial diversity in homes and the risk of allergic rhinitis and inhalant atopy in two European birth cohorts

BACKGROUND

Microbial exposures in early childhood direct the development of the immune system and their diversity may influence the risk of allergy development. We aimed to determine whether the indoor microbial diversity at early-life is associated with the development of allergic rhinitis and inhalant atopy.

METHODS

The study population included children within two birth cohorts: Finnish rural-suburban LUKAS (N = 312), and German urban LISA from Munich and Leipzig study centers (N = 248). The indoor microbiota diversity (Chao1 richness and Shannon entropy) was characterized from floor dust samples collected at the child age of 2-3 months by Illumina MiSeq sequencing of bacterial and fungal DNA amplicons. Allergic rhinitis and inhalant atopy were determined at the age of 10 years and analyzed using logistic regression models.

RESULTS

High bacterial richness (aOR 0.19, 95%CI 0.09-0.42 for middle and aOR 0.12, 95%CI 0.05-0.29 for highest vs. lowest tertile) and Shannon entropy were associated with lower risk of allergic rhinitis in LISA, and similar trend was seen in LUKAS. We observed some significant associations between bacterial and fungal diversity measured and the risk of inhalant atopy, but the associations were inconsistent between the two cohorts. High bacterial diversity tended to be associated with increased risk of inhalant atopy in rural areas, but lower risk in more urban areas. Fungal diversity tended to be associated with increased risk of inhalant atopy only in LISA.

CONCLUSIONS

Our study suggests that a higher bacterial diversity may reduce the risk of allergic rhinitis later in childhood. The environment-dependent heterogeneity in the associations with inhalant atopy - visible here as inconsistent results between two differing cohorts - suggests that specific constituents of the diversity may be relevant.

Associations of observed home dampness and mold with the fungal and bacterial dust microbiomes

The objective of this analysis was to examine and compare quantitative metrics of observed dampness and mold, including visible mold and moisture damage, and fungal and bacterial microbiomes. In-home visits were conducted at age 7 for children enrolled in the Cincinnati Childhood Allergy and Air Pollution Study. Trained study staff evaluated the primary residence and measured total areas of visible moisture and mold damage in the home. Floor dust was collected and archived. Archived dust samples collected from each home (n = 178) were extracted and analyzed using bacterial (16S rRNA gene) and fungal (internal transcribed spacer region) sequencing. Fungi were also divided into moisture requirement categories of xerophiles, mesophiles, and hydrophiles. Data analyses used Spearman's correlation, Kruskal-Wallis, Permanova, DESeq, and negative binomial regression models. Comparing high moisture or mold damage to no damage, five fungal species and two bacterial species had higher concentrations (absolute abundance) and six fungal species and three bacterial species had lower concentrations. Hydrophilic and mesophilic fungi showed significant dose-related increases with increasing moisture damage and mold damage, respectively. When comparing alpha or beta diversity of fungi and bacteria across mold and moisture damage levels, no significant associations or differences were found. Mold and moisture damage did not affect diversity of fungal and bacterial microbiomes. Instead, both kinds of damage were associated with changes in species composition of both bacterial and fungal microbiomes, indicating that fungal and bacterial communities in the home might be influenced by one another as well as by mold or moisture in the home.

The mycobiomes and bacteriomes of sputum, saliva, and home dust

Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.

Derived habitats of indoor microbes are associated with asthma symptoms in Chinese university dormitories

Increasing evidence from the home environment indicates that indoor microbiome exposure is associated with asthma development. However, indoor microbiome composition can be highly diverse and dynamic, and thus current studies fail to produce consistent results. Chinese university dormitories are special high-density dwellings with similar building and occupants characteristics, which facilitate to disentangle the complex interactions between microbes, environmental characteristics and asthma. Settled air dust and floor dust was collected from 87 dormitory rooms in Shanxi University. Bacterial communities were characterized by 16 S rRNA amplicon sequencing. Students (n = 357) were surveyed for asthma symptoms and measured for fractional exhaled nitric oxide (FeNO). Asthma was not associated with the overall bacterial richness but associated with specific phylogenetic classes. Taxa richness and abundance in Clostridia, including Ruminococcus, Blautia, Clostridium and Subdoligranulum, were positively associated with asthma (p < 0.05), and these taxa were mainly derived from the human gut. Taxa richness in Alphaproteobacteria and Actinobacteria were marginally protectively associated with asthma, and these taxa were mainly derived from the outdoor environment. Bacterial richness and abundance were not associated with FeNO levels. Building age was associated with overall bacterial community variation in air and floor dust (p < 0.05), but not associated with the asthma-related microorganisms. Our data shows that taxa from different phylogenetic classes and derived habitats have different health effects, indicating the importance of incorporating phylogenetic and ecological concepts in revealing patterns in the microbiome asthma association analysis.

Indoor Microbial Exposures and Chronic Lung Disease: From Microbial Toxins to the Microbiome

Effects of environmental microbial exposures on human health have long been of interest. Microbes were historically assumed to be harmful, but data have suggested that microbial exposures can modulate the immune system. We focus on the effects of indoor environmental microbial exposure on chronic lung diseases. We found contradictory data in bacterial studies using endotoxin as a surrogate for bacterial exposure. Contradictory data also exist in studies of fungal exposure. Many factors may modulate the effect of environmental microbial exposures on lung health, including coexposures. Future studies need to clarify which method of assessing environmental microbial exposures is most relevant.

Next Generation Exome Sequencing of Pediatric Asthma Identifies Rare and Novel Variants in Candidate Genes

Multiple genes have been implicated to have a role in asthma predisposition by association studies. Pediatric patients often manifest a more extensive form of this disease and a particularly severe disease course. It is likely that genetic predisposition could play a more substantial role in this group. This study is aimed at identifying the spectrum of rare and novel variation in known pediatric asthma susceptibility genes using whole exome sequencing analysis in nine individual cases of childhood onset allergic asthma. DNA samples from the nine children with a history of bronchial asthma diagnosis underwent whole exome sequencing on Ion Proton. For each patient, the entire complement of rare variation within strongly associated candidate genes was catalogued. The analysis showed 21 variants in the subjects, 13 had been previously identified, and 8 were novel. Also, among of which, nineteen were nonsynonymous and 2 were nonsense. With regard to the novel variants, the 2 nonsynonymous variants in the PRKG1 gene (PRKG1: p.C519W and PRKG1: p.G520W) were presented in 4 cases, and a nonsynonymous variant in the MAVS gene (MAVS: p.A45V) was identified in 3 cases. The variants we found in this study will enrich the variant spectrum and build up the database in the Saudi population. Novel eight variants were identified in the study which provides more evidence in the genetic susceptibility in asthma among Saudi children, providing a genetic screening map for the molecular genetic determinants of allergic disease in Saudi children, with the goal of reducing the impact of chronic diseases on the health and the economy. We believe that the advanced specified statistical filtration/annotation programs used in this study succeeded to release such results in a preliminary study, exploring the genetic map of that disease in Saudi children.

Particle Resuspension Dynamics in the Infant Near-Floor Microenvironment

Carpet dust contains microbial and chemical material that can impact early childhood health. Infants may be exposed to greater quantities of resuspended dust, given their close proximity to floor surfaces. Chamber experiments with a robotic infant were integrated with a material balance model to provide new fundamental insights into the size-dependency of infant crawling-induced particle resuspension and exposure. The robotic infant was exposed to resuspended particle concentrations from 10⁵ to 10⁶ m^-3 in the near-floor (NF) microzone during crawling, with concentrations generally decreasing following vacuum cleaning of the carpets. A pronounced vertical variation in particle concentrations was observed between the NF microzone and bulk air. Resuspension fractions for crawling are similar to those for adult walking, with values ranging from 10^-6 to 10^-1 and increasing with particle size. Meaningful amounts of dust are resuspended during crawling, with emission rates of 0.1 to 2 × 10⁴ μg h^-1. Size-resolved inhalation intake fractions ranged from 5 to 8 × 10³ inhaled particles per million resuspended particles, demonstrating that a significant fraction of resuspended particles can be inhaled. A new exposure metric, the dust-to-breathing zone transport efficiency, was introduced to characterize the overall probability of a settled particle being resuspended and delivered to the respiratory airways. Values ranged from less than 0.1 to over 200 inhaled particles per million settled particles, increased with particle size, and varied by over 2 orders of magnitude among 12 carpet types.

Association between indoor microbiome exposure and sick building syndrome (SBS) in junior high schools of Johor Bahru, Malaysia

Sick building syndrome (SBS) is a collection of nonspecific syndromes linked with the built environment. The occurrence of SBS is associated with humidity, ventilation, moulds and microbial compounds exposure. However, no study has reported the association between indoor microbiome and SBS. In this study, 308 students were surveyed for SBS symptoms from 21 classrooms of 7 junior high schools from Johor Bahru, Malaysia, and vacuum dust from floor, desks and chairs was collected. High throughput amplicon sequencing (16S rRNA gene and ITS region) and quantitative PCR were conducted to characterize the absolute concentration of bacteria and fungi taxa. In total, 326 bacterial and 255 fungal genera were detected in dust with large compositional variation among classrooms. Also, half of these samples showed low compositional similarity to microbiome data deposited in the public database. The number of observed OTUs in Gammaproteobacteria was positively associated with SBS (p = 0.004). Eight microbial genera were associated with SBS (p < 0.01). Bacterial genera, Rhodomicrobium, Scytonema and Microcoleus, were protectively (negatively) associated with ocular and throat symptoms and tiredness, and Izhakiella and an unclassified genus from Euzebyaceae were positively associated with the throat and ocular symptoms. Three fungal genera, Polychaeton, Gympopus and an unclassified genus from Microbotryaceae, were mainly positively associated with tiredness. The associations differed with our previous study in microbial compounds (endotoxin and ergosterol) and SBS in the same population, in which nasal and dermal symptoms were affected. A higher indoor relative humidity and visible dampness or mould in classrooms were associated with a higher concentration of potential risk bacteria and a lower concentration of potential protective bacteria (p < 0.01). This is the first study to characterize the SBS-associated microorganisms in the indoor environment, revealing complex interactions between microbiome, SBS symptoms and environmental characteristics.

Ten questions concerning occupant health in buildings during normal operations and extreme events including the COVID-19 pandemic

Even before the COVID-19 pandemic, people spent on average around 90% of their time indoors. Now more than ever, with work-from-home orders in place, it is crucial that we radically rethink the design and operation of buildings. Indoor Environmental Quality (IEQ) directly affects the comfort and well-being of occupants. When IEQ is compromised, occupants are at increased risk for many diseases that are exacerbated by both social and economic forces. In the U.S. alone, the annual cost attributed to sick building syndrome in commercial workplaces is estimated to be between $10 billion to $70 billion. It is imperative to understand how parameters that drive IEQ can be designed properly and how buildings can be operated to provide ideal IEQ to safeguard health. While IEQ is a fertile area of scholarship, there is a pressing need for a systematic understanding of how IEQ factors impact occupant health. During extreme events, such as a global pandemic, designers, facility managers, and occupants need pragmatic guidance on reducing health risks in buildings. This paper answers ten questions that explore the effects of buildings on the health of occupants. The study establishes a foundation for future work and provides insights for new research directions and discoveries.

Decoding personal biotic and abiotic airborne exposome

The complexity and dynamics of human diseases are driven by the interactions between internal molecular activities and external environmental exposures. Although advances in omics technology have dramatically broadened the understanding of internal molecular and cellular mechanisms, understanding of the external environmental exposures, especially at the personal level, is still rudimentary in comparison. This is largely owing to our limited ability to efficiently collect the personal environmental exposome (PEE) and extract the nucleic acids and chemicals from PEE. Here we describe a protocol that integrates hardware and experimental pipelines to collect and decode biotic and abiotic external exposome at the individual level. The described protocol has several advantages over conventional approaches, such as exposome monitoring at the personal level, decontamination steps to increase sensitivity and simultaneous capture and high-throughput profiling of biotic and abiotic exposures. The protocol takes ~18 h of bench time over 2-3 d to prepare samples for high-throughput profiling and up to a couple of weeks of instrumental time to analyze, depending on the number of samples. Hundreds to thousands of species and organic compounds could be detected in the airborne particulate samples using this protocol. The composition and complexity of the biotic and abiotic substances are heavily influenced by the sampling spatiotemporal factors. Basic skillsets in molecular biology and analytical chemistry are required to carry out this protocol. This protocol could be modified to decode biotic and abiotic substances in other types of low or ultra-low input samples.

DNA Sequence-Based Approach for Classifying the Mold Status of Buildings

Dampness or water damage in buildings and human exposure to the resultant mold growth is an ever-present public health concern. This study provides quantitative evidence that the airborne fungal ecology of homes with known mold growth ("moldy") differs from the normal airborne fungal ecology of homes with no history of dampness, water damage, or visible mold ("no mold"). Settled dust from indoor air and outdoor air and direct samples from building materials with mold growth were examined in homes from 11 cities across dry, temperate, and continental climate regions within the United States. Community analysis based on the sequence of the internal transcribed spacer region of fungal ribosomal RNA encoding genes demonstrated consistent and quantifiable differences between the fungal ecology of settled dust in homes with inspector-verified water damage and visible mold versus the settled dust of homes with no history of dampness, water damage, or visible mold. These differences include lower community richness (p_adj = 0.01) in the settled dust of moldy homes versus no mold homes, as well as distinct community taxonomic structures between moldy and no mold homes (ANOSIM, R = 0.15, p = 0.001). We identified 11 Ascomycota taxa that were more highly enriched in moldy homes and 14 taxa from Ascomycota, Basidiomycota, and Zygomycota that were more highly enriched in no mold homes. The indoor air differences between moldy versus no mold homes were significant for all three climate regions considered. These distinct but complex differences between settled dust samples from moldy and no homes were used to train a machine learning-based model to classify the mold status of a home. The model was able to accurately classify 100% of moldy homes and 90% of no mold homes. The integration of DNA-based fungal ecology with advanced computational approaches can be used to accurately classify the presence of mold growth in homes, assist with inspection and remediation decisions, and potentially lead to reduced exposure to hazardous microbes indoors.

Construction of a nomogram for predicting the risk of allergic rhinitis among employees of long-distance bus stations in China

This study examined indoor air pollutants and their health effects on allergic rhinitis in 3194 employees of 226 bus station halls and then constructed a nomogram model to predict allergic rhinitis risk in those employees. Indoor air temperature, relative humidity, PM₁₀ , PM_2.5 , total bacteria, and total fungi were measured, and questionnaires were used to collect basic station information and employee health information. The results revealed that the over-standard rates of PM₁₀ , PM_2.5 , total bacteria, and total fungi were 18.16%, 31.13%, 2.22%, and 55.89%, respectively. Seasonal variations were found in temperature, relative humidity, and PM_2.5 . Passenger flow could affect temperature, and total bacteria. Central air conditioning could affect total bacteria. A total of 15.90% of the employees were diagnosed as allergic rhinitis by physicians. Relative humidity, fungi, self-reported allergic rhinitis symptoms, and exposure to smoking were the influencing factors for allergic rhinitis. These four variables were incorporated to construct a nomogram. The concordance index of the nomogram was 0.775 (95% CI: 0.745-0.806) and 0.749 (95% CI: 0.715-0.783) for the training cohort and test cohort, respectively. The calibration plot revealed that the nomogram model exhibited good discrimination and consistency. This nomogram model may help predict the occurrence of allergic rhinitis.

Type 2-high asthma is associated with a specific indoor mycobiome and microbiome

Background

The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters.

Objective

The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA).

Methods

A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during “stable” or pulmonary “exacerbation” periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes.

Results

Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation.

Conclusion

These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.