Indoor microbiome, environmental characteristics and asthma among junior high school students in Johor Bahru, Malaysia

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.

The indoors microbiome and human health

Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.

Children's food allergy: Effects of environmental influences and antibiotic use across critical developmental windows

BACKGROUND

Increasing studies linked outdoor air pollution (OAP), indoor environmental factors (IEFs), and antibiotics use (AU) with the first wave of allergies (i.e., asthma, allergic rhinitis, and eczema), yet the role of their exposures on children's second wave of allergy (i.e., food allergy) are unknown.

OBJECTIVES

To investigate the association between exposure to OAP and IEFs and childhood doctor-diagnosed food allergy (DFA) during the pre-pregnancy, prenatal, early postnatal, and current periods, and to further explore the effect of OAP and IEFs on DFA in children co-exposed to antibiotics.

METHODS

A retrospective cohort study involving 8689 preschoolers was carried out in Changsha, China. Data on the health outcomes, antibiotic use, and home environment of each child were collected through a questionnaire. Temperature and air pollutants data were obtained from 8 and 10 monitoring stations in Changsha, respectively. Exposure levels to temperature and air pollutants at individual home addresses were calculated by the inverse distance weighted (IDW) method. Multiple logistic regression models were employed to assess the associations of childhood DFA with exposure to OAP, IEF, and AU.

RESULTS

Childhood ever doctor-diagnosed food allergy (DFA) was linked to postnatal PM10 exposure with OR (95% CI) of 1.18 (1.03-1.36), especially for CO and O3 exposure during the first year with ORs (95% CI) = 1.08 (1.00-1.16) and 1.07 (1.00-1.14), as well as SO2 exposure during the previous year with OR (95% CI) of 1.13 (1.02-1.25). The role of postnatal air pollution is more important for the risk of egg, milk and other food allergies. Renovation-related IAP (new furniture) and dampness-related indoor allergens exposures throughout all time windows significantly increased the risk of childhood DFA, with ORs ranging from 1.23 (1.03-1.46) to 1.54 (1.29-1.83). Furthermore, smoke-related IAP (environmental tobacco smoke [ETS], parental and grandparental smoking) exposure during pregnancy, first year, and previous year was related to DFA. Additionally, exposure to pet-related indoor allergens (cats) during first year and total plant-related allergens (particularly nonflowering plants) during previous year were associated with DFA. Moreover, exposure to plant-related allergy during first and previous year was specifically associated with milk allergy, while keeping cats during first year increased the risk of fruits/vegetables allergy. Life-time and early-life AU was associated with the increased risk of childhood DFA with ORs (95% CI) = 1.57 (1.32-1.87) and 1.46 (1.27-1.67), including different types food allergies except fruit/vegetable allergy.

CONCLUSIONS

Postnatal OAP, life-time and early-life IEFs and AU exposure played a vital role in the development of DFA, supporting the "fetal origin of childhood FA" hypothesis.

Unveiling the airborne microbial menace: Novel insights into pathogenic bacteria and fungi in bioaerosols from nursery schools to universities

Bacterial and fungal aerosol pollution is widespread in indoor school environments, and poses potential health risks to students and staff. Understanding the distribution and diversity of microbial communities within aerosols is crucial to mitigate their adverse effects. Existing knowledge regarding the composition of bacterial and fungal aerosols, particularly the presence of potential pathogenic microorganisms in fine particulate matter (PM2.5) from nursery schools to universities, is limited. To bridge this knowledge gap, in the present study, we collected PM2.5 samples from five types of schools (i.e., nursery schools, primary schools, junior schools, and high schools and universities) in China. We used advanced single-molecule real-time sequencing to analyze the species-level diversity of bacterial and fungal components in PM2.5 samples based on 16S and ITS ribosomal genes, respectively. We found significant differences in microbial diversity and community composition among the samples obtained from different educational institutions and pollution levels. In particularly, junior schools exhibited higher PM2.5 concentrations (62.2-86.6 μg/m3) than other schools (14.4-48.4 μg/m3). Moreover, microbial variations in PM2.5 samples were associated with institution type. Notably, the prevailing pathogenic microorganisms included Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Streptococcus pneumoniae, and Schizophyllum commune, all of which were identified as Class II Pathogenic Microorganisms in school settings. Four potentially novel strains of S. commune were identified in PM2.5 samples collected from the university; the four strains showed 92.4 %-94.1 % ITS sequence similarity to known Schizophyllum isolates. To the best of our knowledge, this is the first study to explore bacterial and fungal diversity within PM2.5 samples from nursery schools to universities. Overall, these findings contribute to the existing knowledge of school environmental microbiology to ensure the health and safety of students and staff and impacting public health.

Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border

We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, housing structure, and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs. 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from Mexican homes was enriched with Alishewanella, Paracoccus, Rheinheimera genera and Intrasporangiaceae family. A predictive metagenomics analysis identified 68 significantly differentially abundant functional pathways between US and MX. This study documented multiple structural, environmental, and demographic differences between homes in the US and MX that may contribute to significantly different microbial composition of dust observed in these two countries.

The Role of Biodiversity in the Development of Asthma and Allergic Sensitization: A State-of-the-Science Review

BACKGROUND

Changes in land use and climate change have been reported to reduce biodiversity of both the environment and human microbiota. These reductions in biodiversity may lead to inadequate and unbalanced stimulation of immunoregulatory circuits and, ultimately, to clinical diseases, such as asthma and allergies.

OBJECTIVE

We summarized available empirical evidence on the role of inner (gut, skin, and airways) and outer (air, soil, natural waters, plants, and animals) layers of biodiversity in the development of asthma, wheezing, and allergic sensitization.

METHODS

We conducted a systematic search in SciVerse Scopus, PubMed MEDLINE, and Web of Science up to 5 March 2024 to identify relevant human studies assessing the relationships between inner and outer layers of biodiversity and the risk of asthma, wheezing, or allergic sensitization. The protocol was registered in PROSPERO (CRD42022381725).

RESULTS

A total of 2,419 studies were screened and, after exclusions and a full-text review of 447 studies, 82 studies were included in the comprehensive, final review. Twenty-nine studies reported a protective effect of outer layer biodiversity in the development of asthma, wheezing, or allergic sensitization. There were also 16 studies suggesting an effect of outer layer biodiversity on increasing asthma, wheezing, or allergic sensitization. However, there was no clear evidence on the role of inner layer biodiversity in the development of asthma, wheezing, and allergic sensitization (13 studies reported a protective effect and 15 reported evidence of an increased risk).

CONCLUSIONS

Based on the reviewed literature, a future systematic review could focus more specifically on outer layer biodiversity and asthma. It is unlikely that association with inner layer biodiversity would have enough evidence for systematic review. Based on this comprehensive review, there is a need for population-based longitudinal studies to identify critical periods of exposure in the life course into adulthood and to better understand mechanisms linking environmental exposures and changes in microbiome composition, diversity, and/or function to development of asthma and allergic sensitization. https://doi.org/10.1289/EHP13948.

A preliminary report on the exploration of salivary bacterial diversity by the multiplex SNaPshot assay

Salivary bacterial community composition is associated with the host's internal and environmental factors, which have potential applications in forensic practice. The 16S rRNA gene sequencing is the most commonly used strategy for detecting salivary bacterial diversity; however, its platforms are not compatible with capillary electrophoresis (CE) platforms commonly used for forensic applications. Therefore, we attempted to detect the salivary bacterial diversity using a single nucleotide polymorphism (SNP) assay. Salivary bacterial diversity varies among diverse geographic locations, making it a potential supplementary biomarker for forensic geographic sourcing. To evaluate the performance of the multiplex SNaPshot assay, saliva samples from three geographic locations in China were analyzed using the multiplex SNaPshot assay and 16S rRNA gene sequencing. We screened SNPs from two high-relative-abundance salivary genera (Streptococcus and Veillonella) to construct a multiplex SNaPshot system that can be used on the CE platform. The stability and sensitivity of the multiplex SNaPshot system were also tested. A random forest classification model was used to classify samples from different regions to explore the ability of salivary bacteria to discriminate between geographic sources. Six bacterial SNPs were screened and a multiplex SNaPshot system was constructed. The stability results showed that the typing of salivary stains that were placed indoors for different days was not affected in this study. Two-thirds of mocked salivary stain samples showed more than 90% of typing results obtained for salivary stain samples with an input of 0.1 µl saliva. The results of principal coordinate analysis based on salivary bacterial diversity showed significant differences between samples from the three different geographic locations. The accuracy of the random forest classification was 66.67% based on the multiplex SNaPshot assay and 83.33% based on the 16S rRNA gene sequencing. In conclusion, this is the first attempt to detect salivary bacterial diversity using a multiplex SNaPshot bacterial SNP assay. The geographic difference in human salivary bacterial community composition was significant, as revealed by the multiplex SNaPshot assay; however, its performance in discriminating geographic sources was lower than that of 16S rRNA gene sequencing. This strategy based on bacterial SNP loci may favor the detection of human bacterial diversity in common forensic laboratories but requires further exploration in larger sample sizes and more bacterial SNP loci.

Association of exposure to indoor molds and dampness with allergic diseases at water-damaged dwellings in Korea

This study aims to characterize levels of molds, bacteria, and environmental pollutants, identify the associations between indoor mold and dampness exposures and childhood allergic diseases, including asthma, allergic rhinitis, atopic dermatitis, using three different exposure assessment tools. A total of 50 children with their parents who registered in Seoul and Gyeonggi-do in Korea participated in this study. We collated the information on demographic and housing characteristics, environmental conditions, and lifestyle factors using the Korean version of the International Study of Asthma and Allergies in Childhood questionnaire. We also collected environmental monitoring samples of airborne molds and bacteria, total volatile organic compounds, formaldehyde, and particulate matter less than 10 µm. We evaluated and determined water damage, hidden dampness, and mold growth in dwellings using an infrared (IR) thermal camera and field inspection. Univariate and multivariate regression analyses were performed to evaluate the associations between prevalent allergic diseases and exposure to indoor mold and dampness. Indoor mold and bacterial levels were related to the presence of water damage in dwellings, and the mean levels of indoor molds (93.4 ± 73.5 CFU/m3) and bacteria (221.5 ± 124.2 CFU/m3) in water-damaged homes were significantly higher than those for molds (82.0 ± 58.7 CFU/m3) and for bacteria (152.7 ± 82.1 CFU/m3) in non-damaged dwellings (p < 0.05). The crude odds ratios (ORs) of atopic dermatitis were associated with < 6th floor (OR = 3.80), and higher indoor mold (OR = 6.42) and bacterial levels (OR = 6.00). The crude ORs of allergic diseases, defined as a group of cases who ever suffered from two out of three allergic diseases, e.g., asthma and allergic rhinitis, and allergic rhinitis were also increased by 3.8 and 9.3 times as large, respectively, with water damage (+) determined by IR camera (p < 0.05). The adjusted OR of allergic rhinitis was significantly elevated by 10.4 times in the water-damaged dwellings after adjusting age, sex, and secondhand smoke. Therefore, a longitudinal study is needed to characterize dominant mold species using DNA/RNA-based sequencing techniques and identify a causal relationship between mold exposure and allergic diseases in the future.

Indoor metabolites and chemicals outperform microbiome in classifying childhood asthma and allergic rhinitis

Indoor microorganisms impact asthma and allergic rhinitis (AR), but the associated microbial taxa often vary extensively due to climate and geographical variations. To provide more consistent environmental assessments, new perspectives on microbial exposure for asthma and AR are needed. Home dust from 97 cases (32 asthma alone, 37 AR alone, 28 comorbidity) and 52 age- and gender-matched controls in Shanghai, China, were analyzed using high-throughput shotgun metagenomic sequencing and liquid chromatography-mass spectrometry. Homes of healthy children were enriched with environmental microbes, including Paracoccus, Pseudomonas, and Psychrobacter, and metabolites like keto acids, indoles, pyridines, and flavonoids (astragalin, hesperidin) (False Discovery Rate < 0.05). A neural network co-occurrence probability analysis revealed that environmental microorganisms were involved in producing these keto acids, indoles, and pyridines. Conversely, homes of diseased children were enriched with mycotoxins and synthetic chemicals, including herbicides, insecticides, and food/cosmetic additives. Using a random forest model, characteristic metabolites and microorganisms in Shanghai homes were used to classify high and low prevalence of asthma/AR in an independent dataset in Malaysian schools (N = 1290). Indoor metabolites achieved an average accuracy of 74.9% and 77.1% in differentiating schools with high and low prevalence of asthma and AR, respectively, whereas indoor microorganisms only achieved 51.0% and 59.5%, respectively. These results suggest that indoor metabolites and chemicals rather than indoor microbiome are potentially superior environmental indicators for childhood asthma and AR. This study extends the traditional risk assessment focusing on allergens or air pollutants in childhood asthma and AR, thereby revealing potential novel intervention strategies for these diseases.

Microbes within the building envelope-a case study on the patterns of colonization and potential sampling bias

Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces.

Impact of environmental characteristics on children's gut microbiota - A pilot study in assessing the role of indoor microbiome and metabolites

BACKGROUND

A diverse and balanced human gut microbiota is crucial for maintaining normal human physiological functions. However, the impact of indoor microbiome and metabolites on gut microbiota is not well understood.

METHODS

A self-administered questionnaire was used to collect information on more than 40 personal and environmental characteristics and dietary habits from 56 children in Shanghai, China. Shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS) were used to characterize the indoor microbiome and metabolomic/chemical exposure in children's living rooms. PacBio full-length 16 S rRNA sequencing was used to characterize children's gut microbiota. Associations between environmental characteristics and gut microbiota diversity/composition were assessed using PERMANOVA and regression.

RESULTS

In total, 6247 and 318 indoor and gut microbial species and 1442 indoor metabolites were characterized. Age of children (R2 = 0.033, p = 0.008), age start kindergarten (R2 = 0.029, p = 0.03), living adjacent to heavy traffic (R2 = 0.031, p = 0.01) and drinking soft drinks (R2 = 0.028, p = 0.04) significantly impacted overall gut microbial composition, consistent with previous studies. Having pets/plants and frequent vegetable intake were positively associated with gut microbiota diversity and the Gut Microbiome Health Index (GMHI), while frequent juice and fries intake decreased gut microbiota diversity (p < 0.05). The abundance of indoor Clostridia and Bacilli was positively associated with gut microbial diversity and GMHI (p < 0.01). Total indoor indole derivatives and 6 indole metabolites (L-tryptophan, indole, 3-methylindole, indole-3-acetate, 5-hydroxy-L-tryptophan and indolelactic acid, p < 0.05) were positively associated with the abundance of total protective gut bacteria, suggesting a potential role in promoting gut health. Neural network analysis revealed that these indole derivatives were derived from indoor microorganisms.

CONCLUSIONS

The study is the first to report associations between indoor microbiome/metabolites and gut microbiota, highlighting the potential role of indoor microbiome in shaping human gut microbiota.

The Role of Indoor Microbiome and Metabolites in Shaping Children's Nasal and Oral Microbiota: A Pilot Multi-Omic Analysis

Maintaining a diverse and well-balanced nasal and oral microbiota is vital for human health. However, the impact of indoor microbiome and metabolites on nasal and oral microbiota remains largely unknown. Fifty-six children in Shanghai were surveyed to complete a questionnaire about their personal and environmental characteristics. The indoor microbiome and metabolites from vacuumed indoor dust were profiled via shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS). The nasal and oral microbiota in children was characterized using full-length 16S rRNA sequencing from PacBio. Associations between personal/environmental characteristics and the nasal/oral microbiota were calculated using PERMANOVA and regression analyses. We identified 6247, 431, and 342 microbial species in the indoor dust, nasal, and oral cavities, respectively. The overall nasal and oral microbial composition showed significant associations with environmental tobacco smoke (ETS) exposure during pregnancy and early childhood (p = 0.005 and 0.03, respectively), and the abundance of total indoor flavonoids and two mycotoxins (deoxynivalenol and nivalenol) (p = 0.01, 0.02, and 0.03, respectively). Notably, the abundance of several flavonoids, such as baicalein, eupatilin, isoliquiritigenin, tangeritin, and hesperidin, showed positive correlations with alpha diversity and the abundance of protective microbial taxa in nasal and oral cavities (p < 0.02), suggesting their potential beneficial roles in promoting nasal/oral health. Conversely, high carbohydrate/fat food intake and ETS exposure diminished protective microorganisms while augmenting risky microorganisms in the nasal/oral cavities. Further, potential microbial transfer was observed from the indoor environment to the childhood oral cavity (Moraxella catarrhalis, Streptococcus mitis, and Streptococcus salivarius), which could potentially increase virulence factors related to adherence and immune modulation and vancomycin resistance genes in children. This is the first study to reveal the association between the indoor microbiome/metabolites and nasal/oral microbiota using multi-omic approaches. These findings reveal potential protective and risk factors related to the indoor microbial environment.

Immunologic, genetic, and ecological interplay of factors involved in allergic diseases

An allergic or type I hypersensitivity reaction involves a misdirected immune overreaction to innocuous environmental and dietary antigens called allergens. The genetic predisposition to allergic disease, referred to as atopy, can be expressed as a variety of manifestations-e.g., allergic rhinitis, allergic conjunctivitis, atopic dermatitis, allergic asthma, anaphylaxis. Globally, allergic diseases are one the most common types of chronic conditions. Several factors have been identified to contribute to the pathogenesis and progression of the disease, leading to distinctively variable clinical symptoms. The factors which can attenuate or exacerbate allergic reactions can range from genetic heterozygosity, the prominence of various comorbid infections, and other factors such as pollution, climate, and interactions with other organisms and organism-derived products, and the surrounding environment. As a result, the effective prevention and control of allergies remains to be one of the most prominent public health problems. Therefore, to contextualize the current knowledge about allergic reactions, this review paper attempts to synthesize different aspects of an allergic response to describe its significance in the global health scheme. Specifically, the review shall characterize the biomolecular mechanisms of the pathophysiology of the disease based on underlying disease theories and current findings on ecologic interactions and describe prevention and control strategies being utilized. An integrated perspective that considers the underlying genetic, immunologic, and ecologic aspects of the disease would enable the development of more effective and targeted diagnostic tools and therapeutic strategies for the management and control of allergic diseases.

Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study

BACKGROUND

Indoor dust particles are an everyday source of human exposure to microorganisms and their inhalation may directly affect the microbiota of the respiratory tract. We aimed to characterize the changes in human nasopharyngeal bacteriome after short-term exposure to indoor (workplace) environments.

METHODS

In this pilot study, nasopharyngeal swabs were taken from 22 participants in the morning and after 8 h of their presence at the workplace. At the same time points, indoor dust samples were collected from the participants' households (16 from flats and 6 from houses) and workplaces (8 from a maternity hospital - NEO, 6 from a pediatric hospital - ENT, and 8 from a research center - RCX). 16S rRNA sequencing analysis was performed on these human and environmental matrices.

RESULTS

Staphylococcus and Corynebacterium were the most abundant genera in both indoor dust and nasopharyngeal samples. The analysis indicated lower bacterial diversity in indoor dust samples from flats compared to houses, NEO, ENT, and RCX (p < 0.05). Participants working in the NEO had the highest nasopharyngeal bacterial diversity of all groups (p < 0.05). After 8 h of exposure to the workplace environment, enrichment of the nasopharynx with several new bacterial genera present in the indoor dust was observed in 76% of study participants; however, no significant changes were observed at the level of the nasopharyngeal bacterial diversity (p > 0.05, Shannon index). These "enriching" bacterial genera overlapped between the hospital workplaces - NEO and ENT but differed from those in the research center - RCX.

CONCLUSIONS

The results suggest that although the composition of nasopharyngeal bacteriome is relatively stable during the day. Short-term exposure to the indoor environment can result in the enrichment of the nasopharynx with bacterial DNA from indoor dust; the bacterial composition, however, varies by the indoor workplace environment.

Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional, and structural differences

Around 155 million people worldwide suffer from asthma. In Chile, the prevalence of this disease in children is around 15% and has a high impact in the health system. Studies suggest that asthma is caused by multiple factors, including host genetics, antibiotic use, and the development of the airway microbiota. Here, we used 16S rRNA high-throughput sequencing to characterize the nasal and oral mucosae of 63 asthmatic and 89 healthy children (152 samples) from Santiago, Chile. We found that the nasal mucosa was dominated by a high abundance of Moraxella, Dolosigranulum, Haemophilus, Corynebacterium, Streptococcus, and Staphylococcus. In turn, the oral mucosa was characterized by a high abundance of Streptococcus, Haemophilus, Gemella, Veillonella, Neisseria, and Porphyromonas. Our results showed significantly (P < 0.001) lower alpha diversity and an over-abundance of Streptococcus (P < 0.01) in nasal samples from asthmatics compared to samples from healthy subjects. Community structure, as revealed by co-occurrence networks, showed different microbial interactions in asthmatic and healthy subjects, particularly in the nasal microbiota. The networks revealed keystone genera in each body site, including Prevotella, Leptotrichia, and Porphyromonas in the nasal microbiota, and Streptococcus, Granulicatella, and Veillonella in the oral microbiota. We also detected 51 functional pathways differentially abundant on the nasal mucosa of asthmatic subjects, although only 13 pathways were overrepresented in the asthmatic subjects (P < 0.05). We did not find any significant differences in microbial taxonomic (composition and structure) and functional diversity between the oral mucosa of asthmatic and healthy subjects. This study explores for the first time the relationships between the upper respiratory airways bacteriome and asthma in Chile. It demonstrates that the nasal cavity of children from Santiago harbors unique bacterial communities and identifies potential taxonomic and functional biomarkers of pediatric asthma.

Deciphering the distribution of microbial communities and potential pathogens in the household dust

The reliance of modern society on indoor environments increasing has made them crucial sites for human exposure to microbes. Extensive research has identified ecological drivers that influence indoor microbial assemblages. However, few studies have examined the dispersion of microbes in different locations of identical indoor environments. In this study, we employed PacBio Sequel full-length amplicon sequencing to examine the distribution of microbes at distinct locations in a single home and to identify the potential pathogens and microbial functions. Microbial communities differed considerably among the indoor sampling sites (P < 0.05). In addition, bacterial diversity was influenced by human activities and contact with the external environment at different sites, whereas fungal diversity did not significantly differ among the sites. Potential pathogens, including bacteria and fungi, were significantly enriched on the door handle (P < 0.05), suggesting that door handles may be hotpots for potential pathogens in the household. A high proportion of fungal allergens (34.37 %-56.50 %), which can cause skin diseases and asthma, were observed. Co-occurrence network analysis revealed the essential ecological role of microbial interactions in the development of a healthy immune system. Overall, we revealed the differences in microbial communities at different sampling sites within a single indoor environment, highlighting the distribution of potential pathogens and ecological functions of microbes, and providing a new perspective and information for assessing indoor health from a microbiological viewpoint.

Associations between environmental characteristics, high-resolution indoor microbiome, metabolome and allergic and non-allergic rhinitis symptoms for junior high school students

Rhinitis is one of the most prevalent chronic diseases globally. Microbiome exposure affects the occurrence of rhinitis. However, previous studies did not differentiate allergic rhinitis (AR) and non-allergic rhinitis (NAR) in the microbial association analysis. In this study, we investigate 347 students in 8 junior high schools, Terengganu, Malaysia, who were categorized as healthy (70.9%), AR (13.8%) and NAR (15.3%) based on a self-administered questionnaire and skin prick tests of pollen, pet, mould and house dust mite allergens. Classroom microbial and metabolite exposure in vacuumed dust was characterized by PacBio long-read amplicon sequencing, quantitative PCR and LC-MS-based untargeted metabolomics. Our findings indicate a similar microbial association pattern between AR and NAR. The richness in Gammaproteobacteria was negatively associated with AR and NAR symptoms, whereas total fungal richness was positively associated with AR and NAR symptoms (p < 0.05). Brasilonema bromeliae and Aeromonas enteropelogenes were negatively associated with AR and NAR, and Deinococcus was positively associated with AR and NAR (p < 0.01). Pipecolic acid was protectively associated with AR and NAR symptoms (OR = 0.06 and 0.13, p = 0.009 and 0.045). A neural network analysis showed that B. bromeliae was co-occurring with pipecolic acid, suggesting that the protective role of this species may be mediated by releasing pipecolic acid. Indoor relative humidity and the weight of vacuum dust were associated with AR and NAR, respectively (p < 0.05), but the health effects were mediated by two protective bacterial species, Aliinostoc morphoplasticum and Ilumatobacter fluminis. Overall, our study reported a similar microbial association pattern between AR and NAR and also revealed the complex interactions between microbial species, environmental characteristics, and rhinitis symptoms.

Fungi composition in settled dust associated with fractional exhaled nitric oxide in school children with asthma

Fungi exposure has been significantly linked to respiratory illness. However, numerous fungi taxa that are potentially allergenic still undocumented and leave a barrier to establishing a clear connection between exposure and health risks. This study aimed to evaluate the association of fungi composition in settled dust with fractional exhaled nitric oxide (FeNO) levels among school children with doctor-diagnosed asthma. A cross-sectional study was undertaken among secondary school students in eight schools in the urban area of Hulu Langat, Selangor, Malaysia. A total of 470 school children (aged 14 years old) were randomly selected and their FeNO levels were measured and allergic skin prick tests were conducted. The settled dust samples were collected and analysed by using metagenomic technique to determine the fungi composition. The general linear regression with complex sampling was employed to determine the interrelationship. In total, 2645 fungal operational taxonomic units (OTUs) were characterised from the sequencing process which belongs to Ascomycota (60.7 %), Basidiomycota (36.4 %), Glomeromycota (2.9 %) and Chytridiomycota (0.04 %). The top five mostly abundance in all dust samples were Aspergillus clavatus (27.2 %), followed by Hyphoderma multicystidium (12.2 %), Verrucoconiothyrium prosopidis (9.4 %), Ganoderma tuberculosum (9.2 %), and Heterochaete shearii (7.2 %). The regression results indicated that A. clavatus, Brycekendrickomyces acaciae, Candida parapsilosis, Hazslinszkyomyces aloes, H. multicystidium, H. shearii, Starmerella meliponinorum, V. prosopidis were associated in increased of FeNO levels among the asthmatic group at 0.992 ppb (95 % CI = 0.34-1.68), 2.887 ppb (95 % CI = 2.09-3.76), 0.809 ppb (95 % CI = 0.14-1.49), 0.647 ppb (95 % CI = 0.36-0.94), 1.442 ppb (95 % CI = 0.29-2.61), 1.757 ppb (95 % CI = 0.59-2.87), 1.092 ppb (95 % CI = 0.43-1.75) and 1.088 ppb (95 % CI = 0.51-1.62), respectively. To our knowledge, this is a new finding. The findings pointed out that metagenomics profiling of fungi could enhance our understanding of a complex interrelation between rare and unculturable fungi with airway inflammation.

Asthma, allergic rhinitis and atopic dermatitis in association with home environment - The RHINE study

We studied home environment exposures in relation to asthma, allergic rhinitis and atopic dermatitis among offspring of participants (parents) in the Respiratory Health in Northern Europe (RHINE) study (age ≤ 30 y). Totally 17,881 offspring from Iceland, Norway, Sweden, Denmark and Estonia were included. Home environment exposures, including dampness and mold, type of dwelling, construction year and indoor painting were registered through a questionnaire answered by parents in the first follow up (RHINE II). The parents reported ten years later with in the frame of RHINE III offspring's birth year and offspring's asthma, allergic rhinitis, atopic dermatitis. They also reported dampness and mold at home from RHINE II to RHINE III. The prevalence of offspring's asthma before 10 y, asthma after 10 y, allergic rhinitis at any age and atopic dermatitis at any age were 9.7 %, 4.3 %, 15.6 % and 17.3 %, respectively. Asthma before 10 y was related to any indoor painting at RHINE II (OR = 1.14, 95%CI (1.02, 1.29)). Asthma after 10 y was associated with dampness/mold at home (OR = 1.33-1.62) and living in the newest buildings (constructed in 1986-2001) (OR = 1.30, 95%CI (1.02, 1.66)). Allergic rhinitis was associated with living in newer buildings (constructed in 1961-2001) (OR = 1.16-1.24). Atopic dermatitis was associated with visible mold (OR = 1.35, 95%CI(1.12, 1.62)), dampness/mold at home (OR = 1.18-1.38), living in apartments (OR = 1.22, 95%CI(1.10, 1.35)) and living in newer buildings (constructed in 1961-2001) (OR = 1.14-1.25). There were dose-response effects of dampness and mold on offspring's asthma after 10 y and atopic dermatitis (20 years exposure vs. 10 years exposure). Older offspring had increased risk of developing asthma after 10 y and atopic dermatitis. In conclusion, home dampness and mold, living in apartments, living in newer buildings and indoor painting were associated with offspring's asthma or allergic diseases. Stronger health effects were found among offspring with prolonged exposure of dampness/mold.

Detection of airborne pathogens with single photon counting and a real-time spectrometer on microfluidics

The common practice for monitoring pathogenic bioaerosols is to collect bioaerosols from air and then detect them, which lacks timeliness and accuracy. In order to improve the detection speed, here we demonstrate an innovative airflow-based optical detection method for directly identifying aerosol pathogens, and built a microfluidic-based counter composite spectrometer detection platform, which simplifies sample preparation and collection detection from two steps to one step. The method is based on principal component analysis and partial least squares discriminant analysis for particle species identification and dynamic transmission spectroscopy analysis, and single-photon measurement is used for particle counting. Compared with traditional microscopic counting and identification methods, the particle counting accuracy is high, the standard deviation is small, and the counting accuracy exceeds 92.2%. The setup of dynamic transmission spectroscopy analysis provides high-precision real-time particle identification with an accuracy rate of 93.75%. As the system is further refined, we also foresee potential applications of this method in agricultural disease control, environmental control, and infectious disease control in aerosol pathogen detection.

Microbial regulation of offspring diseases mediated by maternal-associated microbial metabolites

The microbiota plays a crucial role in individuals’ early and long-term health. Previous studies indicated that the microbial regulation of health may start before birth. As the in utero environment is (nearly) sterile, the regulation is probably be originated from maternal microbiota and mediated by their metabolites transferred across the placenta. After the birth, various metabolites are continuously delivered to offspring through human milk feeding. Meanwhile, some components, for example, human milk oligosaccharides, in human milk can only be fermented by microbes, which brings beneficial effects on offspring health. Hence, we speculated that human milk-derived metabolites may also play roles in microbial regulation. However, reports between maternal-associated microbial metabolites and offspring diseases are still lacking and sparsely distributed in several fields. Also, the definition of the maternal-associated microbial metabolite is still unclear. Thus, it would be beneficial to comb through the current knowledge of these metabolites related to diseases for assisting our goals of early prediction, early diagnosis, early prevention, or early treatment through actions only on mothers. Therefore, this review aims to present studies showing how researchers came to the path of investigating these metabolites and then to present studies linking them to the development of offspring asthma, type 1 diabetes mellitus, food allergy, neonatal necrotizing enterocolitis, or autism spectrum disorder. Potential English articles were collected from PubMed by searching terms of disease(s), maternal, and a list of microbial metabolites. Articles published within 5 years were preferred.

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.

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.

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.

Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas

Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a part of environmental microbiotas. However, the expiratory microbiota community and its associations with environmental microbiotas remain poorly understood. Here, expiratory bacteria and fungi and the corresponding microbiotas from the living environments were characterized by DNA amplicon sequencing of residents' exhaled breath condensate (EBC) and environmental samples collected from 14 residences in Nanjing, China. The microbiotas of EBC samples, with a substantial heterogeneity, were found to be as diverse as those of skin, floor dust, and airborne microbiotas. Model fitting results demonstrated the role of stochastic processes in the assembly of the expiratory microbiota. Using a fast expectation-maximization algorithm, microbial community analysis revealed that expiratory microbiotas were differentially associated with other types of microbiotas in a type-dependent and residence-specific manner. Importantly, the expiratory bacteria showed a composition similarity with airborne bacteria in the bathroom and kitchen environments with an average of 12.60%, while the expiratory fungi showed a 53.99% composition similarity with the floor dust fungi. These differential patterns indicate different relationships between expiratory microbiotas and the airborne microbiotas and floor dust microbiotas. The results here illustrated for the first time the associations between expiratory microbiotas and indoor microbiotas, showing a potential microbial exchange between the respiratory tract and indoor environment. Thus, improved hygiene and ventilation practices can be implemented to optimize the indoor microbial exposome, especially in indoor bathrooms and kitchens.

A microbiome study reveals the potential relationship between the bacterial diversity of a gymnastics hall and human health

Currently, investigations on the microbiota of sports centers and related facilities have been carried out in some countries, which showed that Microsporum gypseum, Trichophyton mentagrophytes and T. tonsurans are important dermatoprotofungi. In China, some research on athletes and sports equipment between the fungal community and public health has made some interesting achievements. However, the bacterial group among them has not been reported. Therefore, The aim of this study was to uncover (I) gymnastic equipment is there potential pathogenic factors and (ii) is there any difference in the biomarker of bacterial in different types of gymnastic room? The samples were collected from the gymnastics halls of one university in western China and main sports equipment, including gymnastics carpets, moving barres, hoops and balls, as well as wall bars, parallel bars and horizontal bars. The 16S rDNA of all the samples was sequenced, and the analyses were performed using FaproTax, Bug base function prediction and Line Discriminant Analysis (LDA) Effect Size. A 16S rDNA sequence analysis revealed abundant bacterial species biodiversity on gymnasts and apparatuses from two gymnastics halls at a university in western China. An analysis using the FaproTax and Bugbase functional prediction platforms showed that there were some opportunistic pathogens on the athletes and equipment from the Rhythmic Gymnastics (RG) and Artistic Gymnastics (AG) halls, such as Staphylococcus and Corynebacteiaceae. Infectious agents associated with cancer induction and development, such as Ruminococcaceae, Veillonellaceae and Moraxellaceae, as well as microbial toxin producers with a potential impact on human health, were also detected. According to a line discriminant analysis (LDA effect size), the bacterial biomarker groups of the two gymnasiums were different at the phylum-genus level: for RG, Erysipelatoclostridium, Lachnospiraceae and Bacteroidales, while for AG, Rhizobiales. Based on the results of the investigation, we suggest that more comprehensive consideration should be given to indoor microbial biodiversity and related public health problems in school gymnasiums.

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.

Associations of early-life factors and indoor environmental exposure with asthma among children: a case-control study in Chongqing, China

BACKGROUND

Childhood asthma has substantial effects on children's health. It is important to identify influencing factors in early life in the development of childhood asthma. We aim to evaluate the effects of early-life factors and indoor environmental exposure on childhood asthma in Chongqing, China.

METHOD

We designed a case-control study to enrol children with asthma aged 3 to < 14 years old and controls in Chongqing, China. The "Children's Early Life and Indoor Environment Survey" was used to collect the early-life factors and indoor environmental exposure of foetuses in utero and of infants during the first 3 years of life. A multivariate logistic regression model was used to evaluate the association between independent variables and childhood asthma and the interaction of early-life factors and environmental exposure.

RESULTS

A total of 160 asthma cases and 247 controls were included in this study. The mean ages of the cases and controls were 5.53 ± 1.88 and 5.72 ± 2.34 years, respectively (P = 0.192). Early-life factors and indoor environmental exposure were independently associated with childhood asthma. Infectious diseases of the respiratory system in children under 3 years old [adjusted odds ratio (OR) = 5.76, 95% confidence interval (CI) 2.49-13.30], bedroom air conditioner use (adjusted OR = 4.61, 95% CI 1.45-14.64), and bedroom dampness/mould (adjusted OR = 2.98, 95% CI 1.54-5.75) ranked as the three most significant exposures associated with the risk of childhood asthma. Other factors associated with an increased risk of childhood asthma included second-hand smoke exposure in early life (adjusted OR = 1.93, 95% CI 1.24-3.00), neonatal pneumonia (adjusted OR = 1.90, 95% CI 1.05-3.42) and maternal allergic diseases during pregnancy (adjusted OR = 2.13, 95% CI 1.10-4.10). The interaction effects of child second-hand smoke exposure with other covariates were not found to be statistically significant.

CONCLUSIONS

Early-life factors and indoor environmental exposure are closely related to childhood asthma in Chongqing, China. Further interventions and management in the early life of children should be considered to prevent and control childhood asthma in Chongqing and similar cities.

Indoor microbiome, air pollutants and asthma, rhinitis and eczema in preschool children - A repeated cross-sectional study

BACKGROUND

Indoor microbiome exposure is associated with asthma, rhinitis and eczema. However, no studies report the interactions between environmental characteristics, indoor microbiome and health effects in a repeated cross-sectional framework.

METHODS

1,279 and 1,121 preschool children in an industrial city (Taiyuan) of China were assessed for asthma, rhinitis and eczema symptoms in 2012 and 2019 by self-administered questionnaires, respectively. Bacteria and fungi in classroom vacuum dust were characterized by culture-independent amplicon sequencing. Multi-level logistic/linear regression was performed in two cross-sectional and two combined models to assess the associations.

RESULTS

The number of observed species in bacterial and fungal communities in classrooms increased significantly from 2012 to 2019, and the compositions of the microbial communities were drastically changed (p < 0.001). The temporal microbiome variation was significantly larger than the spatial variation within the city (p < 0.001). Annual average outdoor SO₂ concentration decreased by 60.7%, whereas NO₂ and PM₁₀ concentrations increased by 63.3% and 40.0% from 2012 to 2019, which were both associated with indoor microbiome variation (PERMANOVA p < 0.001). The prevalence of asthma (2.0% to 3.3%, p = 0.06) and rhinitis (28.0% to 25.3%, p = 0.13) were not significantly changed, but the prevalence of eczema was increased (3.6% to 7.0%; p < 0.001). Aspergillus subversicolor, Collinsella and Cutibacterium were positively associated with asthma, rhinitis and eczema, respectively (p < 0.01). Prevotella, Lactobacillus iners and Dolosigranulum were protectively (negatively) associated with rhinitis (p < 0.01), consistent with previous studies in the human respiratory tract. NO₂ and PM₁₀ concentrations were negatively associated with rhinitis in a bivariate model, but a multivariate mediation analysis revealed that Prevotella fully mediated the health effects.

CONCLUSIONS

This is the first study to report the interactions between environmental characteristics, indoor microbiome and health in a repeated cross-sectional framework. The mediating effects of indoor microorganisms suggest incorporating biological with chemical exposure for a comprehensive exposure assessment.

Eczema, facial erythema, and seborrheic dermatitis symptoms among young adults in China in relation to ambient air pollution, climate, and home environment

A questionnaire survey on dermal symptoms and home environment was performed in eight Chinese cities (40 279 participants). Data on city level temperature, precipitation, PM₁₀ , NO_2, and gross domestic product (GDP) per capita were collected. In total, 2.2% had eczema, 2.4% facial erythema (FE) and 2.6% seborrheic dermatitis symptoms (SD). Higher temperature was associated with eczema (OR = 1.09). Higher GDP per capita was related to less SD. Higher PM₁₀ was related to SD. Suburban living was protective for eczema (OR = 0.77) (vs. urban). Living in old buildings (built before 1991) was related to eczema (OR = 1.42). Living near heavily trafficked roads was related to FE (OR = 1.33) and SD (OR = 1.35). Having new furniture was related to all symptoms (OR = 1.26-1.47). Burning mosquito coils (OR = 1.37-1.57) and incense (OR = 1.33-1.37) were associated with eczema, FE, or SD. Presence of cockroaches and rats/mice was associated with FE or SD (OR = 1.31-1.40). Using air conditioner, daily cleaning and frequently exposing bedding to sunshine were protective (OR = 0.60-0.83). In conclusion, higher temperature, higher PM₁₀ , urban living, living near heavily trafficked roads, old buildings, new furniture, burning mosquito coils and incense, and presence of cockroaches/rats/mice increased the risk of eczema, FE, or SD. Higher GDP, air conditioner, daily cleaning, and exposing bedding to sunshine were protective.

The decay of airborne bacteria and fungi in a constant temperature and humidity test chamber

Despite substantial research to profile the microbial characteristics in the atmosphere, the changing metabolism underpinning microbial successional dynamics remains ambiguous. Herein, we applied qPCR, high-throughput sequencing of the genes encoding 16S and ITS rRNA to render the bacterial/fungal dynamics of ambient PM_2.5 filters maintained at constant conditions of temperature (20 ± 2 °C) and humidity (50 ± 5%). The incubation experiments which lasted for 50 days aim to simulate a metabolic process of microbe in two types PM_2.5 (polluted and non-polluted). The results show that microbial community species in polluted PM_2.5 had faster decay rates, more bacterial diversity and less fungal community compared to the non-polluted ones. For bacteria, the proportion of anaerobic species is higher than aerobic ones, and their performance of contain mobile elements, form-biofilms, and pathogenic risks declined rapidly as times went by. Whereas for fungi, saprotroph species occupied about 70% of the population, resulting in a specified peak of abundance due to the adequacy nutrients supplied by the apoptosis cells. Combining the classified microbial species, we found stable community structure and the volatile ones related to the various metabolic survival strategies during different time. Without the input of peripheral environment, the health risks of airborne microbe descend to a healthy level after 20 days, implying their biologic effectiveness was about 20 days no matter the air is polluted or not. This study provided new insights into the different metabolic survival of airborne microorganisms in ideal and stable conditions.

Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools - Potential roles of indoor microbial amino acids and vitamin metabolites

Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multi-level linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial α-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (β-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.

Metagenomic characterization of indoor dust fungal associated with allergy and lung inflammation among school children

The exposure of school children to indoor air pollutants has increased allergy and respiratory diseases. The objective of this study were to determine the toxicodynamic interaction of indoor pollutants exposure, biological and chemical with expression of adhesion molecules on eosinophil and neutrophil. A self-administered questionnaire, allergy skin test, and fractional exhaled nitric oxide (FeNO) analyser were used to collect information on health status, sensitization to allergens and respiratory inflammation, respectively among school children at age of 14 years. The sputum induced were analysed to determine the expression of CD11b, CD35, CD63 and CD66b on eosinophil and neutrophil by using flow cytometry technique. The particulate matter (PM_2.5 and PM₁₀), NO₂, CO₂, and formaldehyde, temperature, and relative humidity were measured inside the classrooms. The fungal DNA were extracted from settled dust collected from classrooms and evaluated using metagenomic techniques. We applied chemometric and regression in statistical analysis. A total of 1869 unique of operational taxonomic units (OTUs) of fungi were identified with dominated at genus level by Aspergillus (15.8%), Verrucoconiothyrium (5.5%), and Ganoderma (4.6%). Chemometric and regression results revealed that relative abundance of T. asahii were associated with down regulation of CD66b expressed on eosinophil, and elevation of FeNO levels in predicting asthmatic children with model accuracy of 63.6%. Meanwhile, upregulation of CD11b expressed on eosinophil were associated with relative abundance of A. clavatus and regulated by PM_2.5. There were significant association of P. bandonii with upregulation of CD63 expressed on neutrophil and exposure to NO₂. Our findings indicate that exposure to PM_2.5, NO₂, T. asahii, P.bandonii and A.clavatus are likely interrelated with upregulation of activation and degranulation markers on both eosinophil and neutrophil.

Associations between the indoor microbiome, environmental characteristics and respiratory infections in junior high school students of Johor Bahru, Malaysia

Pathogens are commonly present in the human respiratory tract, but symptoms are varied among individuals. The interactions between pathogens, commensal microorganisms and host immune systems are important in shaping the susceptibility, development and severity of respiratory diseases. Compared to the extensive studies on the human microbiota, few studies reported the association between indoor microbiome exposure and respiratory infections. In this study, 308 students from 21 classrooms were randomly selected to survey the occurrence of respiratory infections in junior high schools of Johor Bahru, Malaysia. Vacuum dust was collected from the floor, chairs and desks of these classrooms, and high-throughput amplicon sequencing (16S rRNA and ITS) and quantitative PCR were conducted to characterize the absolute concentration of the indoor microorganisms. Fifteen bacterial genera in the classes Actinobacteria, Alphaproteobacteria, and Cyanobacteria were protectively associated with respiratory infections (p < 0.01), and these bacteria were mainly derived from the outdoor environment. Previous studies also reported that outdoor environmental bacteria were protectively associated with chronic respiratory diseases, such as asthma, but the genera identified were different between acute and chronic respiratory diseases. Four fungal genera from Ascomycota, including Devriesia, Endocarpon, Sarcinomyces and an unclassified genus from Herpotrichillaceae, were protectively associated with respiratory infections (p < 0.01). House dust mite (HDM) allergens and outdoor NO₂ concentration were associated with respiratory infections and infection-related microorganisms. A causal mediation analysis revealed that the health effects of HDM and NO₂ were partially or fully mediated by the indoor microorganisms. This is the first study to explore the association between environmental characteristics, microbiome exposure and respiratory infections in a public indoor environment, expanding our understanding of the complex interactions among these factors.

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China-association with asthma, rhinitis and rhinoconjunctivitis in high school students

BACKGROUND

Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries.

METHODS

Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms.

RESULTS

Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut.

CONCLUSIONS

We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects. Video abstract.

Assessment of bio-contaminants during COVID-19 outbreak from the indoor environment of Hail city, Kingdom of Saudi Arabia

Biocontaminants are minute particles derived from different biological materials. Indoor biocontaminants are associated with major public health problems. In Gulf countries, it is more precarious due to the harsh climatic conditions, including high ambient temperatures and relative humidity. In addition, due to COVID-19 pandemic, most of the time public is inside their home. Therefore, the aim of the study was to determine the load of biocontaminants in the indoor environment of Hail city. The results showed that most of the bacteria are gram-positive and higher in polymicrobial (87.1%) than monomicrobial (62.7%) association. There was no significant association with sample collection time and types of isolates. The most abundant microbes found in all samples were Staphylococcus aureus followed by Bacillus spp. Among Gram-negative bacterial isolates, E. coli was most common in tested indoor air samples. The study will be useful to find the biocontaminants associated with risk factors and their impact on human health in indoor environment, especially during the COVID-19 pandemic. These results indicate the need to implement health care awareness programs in the region to improve indoor air quality.

Experimental parameters defining ultra-low biomass bioaerosol analysis

Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.

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.

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.

A prospective study on the role of smoking, environmental tobacco smoke, indoor painting and living in old or new buildings on asthma, rhinitis and respiratory symptoms

We studied associations between tobacco smoke, home environment and respiratory health in a 10 year follow up of a cohort of 11,506 adults in Northern Europe. Multilevel logistic regression models were applied to estimate onset and remission of symptoms. Current smokers at baseline developed more respiratory symptoms (OR = 1.39-4.43) and rhinitis symptoms (OR = 1.35). Starting smoking during follow up increased the risk of new respiratory symptoms (OR = 1.54-1.97) and quitting smoking decreased the risk (OR = 0.34-0.60). ETS at baseline increased the risk of wheeze (OR = 1.26). Combined ETS at baseline or follow up increased the risk of wheeze (OR = 1.27) and nocturnal cough (OR = 1.22). Wood painting at baseline reduced remission of asthma (OR 95%CI: 0.61, 0.38-0.99). Floor painting at home increased productive cough (OR 95%CI: 1.64, 1.15-2.34) and decreased remission of wheeze (OR 95%CI: 0.63, 0.40-0.996). Indoor painting (OR 95%CI: 1.43, 1.16-1.75) and floor painting (OR 95%CI: 1.77, 1.11-2.82) increased remission of allergic rhinitis. Living in the oldest buildings (constructed before 1960) was associated with higher onset of nocturnal cough and doctor diagnosed asthma. Living in the newest buildings (constructed 1986-2001) was associated with higher onset of nocturnal breathlessness (OR = 1.39) and rhinitis (OR = 1.34). In conclusion, smoking, ETS and painting indoor can be risk factors for respiratory symptoms. Wood painting and floor painting can reduce remission of respiratory symptoms. Smoking can increase rhinitis. Living in older buildings can be a risk factor for nocturnal cough and doctor diagnosed asthma. Living in new buildings can increase nocturnal dyspnoea and rhinitis.

The Environmental Relative Moldiness Index reveals changes in mold contamination in United States homes over time

The Environmental Relative Moldiness Index (ERMI) is a scale created to compare mold contamination levels in U.S. homes. The ERMI was developed as a result of the Department of Housing and Urban Development's (HUD) first American Healthy Homes Survey (AHHS I), which sampled 1,096 homes selected to be representative of the U.S. housing stock. In AHHS I, a dust sample from each home was analyzed using quantitative PCR assays (qPCR) for 36 common indoor molds: 26 Group 1 molds, which were associated with water damage in homes and 10 Group 2 molds, which primarily enter the home from the outside environment. In 2019, HUD completed AHHS II by sampling 695 homes. Because lead was banned from paint in 1978, a larger proportion of homes selected for AHHS II had been built before 1978 compared to AHHS I. The 36 ERMI molds were analyzed in AHHS II exactly as in AHHS I. For the 36-ERMI molds, the rates of detection, average concentrations, and geometric means were in significant concordance (p < 0.001) between AHHS I and II, indicating that the ERMI methodology was stable over time. However, the average ERMI value in AHHS II homes was greater than in AHHS I. The reason for the difference was investigated by examining the Group 1 and 2 mold populations. The average summed logs of Group 1 molds were significantly greater in homes built before 1978 than the average for homes built later. Conversely, the average summed logs of Group 2 mold populations were the same in homes built before 1978 and homes built later. Since the summed logs of Group 2 mold is subtracted from the summed logs of Group 1 molds in the ERMI calculation, the average ERMI value was higher in AHHS II homes than AHHS I. In conclusion, by using the ERMI metric, we were able to demonstrate that water damage and mold growth were more likely to occur as homes get older.

Exposure to indoor air contaminants in school buildings with and without reported indoor air quality problems

Reported indoor air quality (IAQ) complaints are common even in relatively new or renovated school buildings in Finland. However, detecting the causes for complaints with commonly used indoor air measurements is difficult. This study presents data on perceived and measured IAQ in six comprehensive school buildings in Finland. The aim of this study was to discover the possible differences of perceived and measured IAQ between schools with reported IAQ complaints and schools without reported IAQ complaints. The initial categorisation of schools with ('problematic schools') and without ('comparison schools') complaints was ensured via a validated indoor climate survey and a recently developed online questionnaire, which were completed by 186 teachers and 1268 students from the six schools. IAQ measurements of physical parameters, gaseous pollutants, particulate matter and bioaerosols were conducted in four problematic school buildings (26 classrooms) and two comparison school buildings (12 classrooms). Using air sampling as well as exhaust air filters and classroom settled dust to detect the presence of elevated concentrations of airborne cultivable microbes and pathogenic, toxigenic and mycoparasitic Trichoderma strains were the most indicative methods in distinguishing problematic schools from comparison schools. Other IAQ-related measurements did not detect clear differences between problematic and comparison schools, as the concentration levels were very low. The results indicate that the complaints reported by occupants could have been related to excess moisture or mould problems that had not been found or repaired. Ventilation pressure condition investigations and simultaneous exhaust and supply air filter dust culture should be addressed precisely in future studies.