Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants

A comprehensive review of microbial contamination in the indoor environment: sources, sampling, health risks, and mitigation strategies

The quality of the indoor environment significantly impacts human health and productivity, especially given the amount of time individuals spend indoors globally. While chemical pollutants have been a focus of indoor air quality research, microbial contaminants also have a significant bearing on indoor air quality. This review provides a comprehensive overview of microbial contamination in built environments, covering sources, sampling strategies, and analysis methods. Microbial contamination has various origins, including human occupants, pets, and the outdoor environment. Sampling strategies for indoor microbial contamination include air, surface, and dust sampling, and various analysis methods are used to assess microbial diversity and complexity in indoor environments. The review also discusses the health risks associated with microbial contaminants, including bacteria, fungi, and viruses, and their products in indoor air, highlighting the need for evidence-based studies that can relate to specific health conditions. The importance of indoor air quality is emphasized from the perspective of the COVID-19 pandemic. A section of the review highlights the knowledge gap related to microbiological burden in indoor environments in developing countries, using India as a representative example. Finally, potential mitigation strategies to improve microbiological indoor air quality are briefly reviewed.

Indoor Airborne Microbiome and Endotoxin: Meteorological Events and Occupant Characteristics Are Important Determinants

Airborne bacteria and endotoxin may affect asthma and allergies. However, there is limited understanding of the environmental determinants that influence them. This study investigated the airborne microbiomes in the homes of 1038 participants from five cities in Northern Europe: Aarhus, Bergen, Reykjavik, Tartu, and Uppsala. Airborne dust particles were sampled with electrostatic dust fall collectors (EDCs) from the participants' bedrooms. The dust washed from the EDCs' clothes was used to extract DNA and endotoxin. The DNA extracts were used for quantitative polymerase chain (qPCR) measurement and 16S rRNA gene sequencing, while endotoxin was measured using the kinetic chromogenic limulus amoebocyte lysate (LAL) assay. The results showed that households in Tartu and Aarhus had a higher bacterial load and diversity than those in Bergen and Reykjavik, possibly due to elevated concentrations of outdoor bacterial taxa associated with low precipitation and high wind speeds. Bergen-Tartu had the highest difference (ANOSIM R = 0.203) in β diversity. Multivariate regression models showed that α diversity indices and bacterial and endotoxin loads were positively associated with the occupants' age, number of occupants, cleaning frequency, presence of dogs, and age of the house. Further studies are needed to understand how meteorological factors influence the indoor bacterial community in light of climate change.

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.

Diversity of Microbial Communities, PAHs, and Metals in Road and Leaf Dust of Functional Zones of Moscow and Murmansk

The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and leaf dust in three urban zones of Murmansk and Moscow with contrasting anthropogenic load were conducted. We found that the structure of bacterial communities affected the functional zoning of the city, biotope type, and geographical components. Fungal communities were instead impacted only by biotope type. Our findings revealed that the structure of fungal communities was mostly impacted by PAHs whereas bacterial communities were sensitive to metals. Bacteria of the genus Sphingomonas in road and leaf dust as indicators of the ecological state of the urban ecosystems were proposed.

Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov

A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.

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.

Assessment of Microbiological Quality of Indoor Air at Different Hospital Sites of Dilla University: A Cross-Sectional Study

BACKGROUND

In both residential and hospital indoor environments, humans can be exposed to airborne microorganisms. The hospital's indoor air may contain a large number of disease-causing agents brought in by patients, staff, students, visitors, ventilation, or the outside. Hospitalized patients are at a higher risk of infection due to confined spaces, crowdedness, and poor infection prevention practices, which can accumulate and create favorable conditions for the growth and multiplication of microorganisms. Therefore, the aim of this study was to evaluate the indoor air bacterial load in Dilla University Hospital, Southern Ethiopia.

METHODS

An institutional-based cross-sectional study design was used to assess the bacterial load in the indoor air at Dilla University Hospital. To determine the bacterial load, a passive air sampling technique was used. The settle plate method was used to collect data, which involved exposing Petri-dishes filled with blood agar media to the indoor air of the sampled rooms for 60 minutes.

RESULT

A total of 72 indoor air samples were collected once a week for 2 weeks at 14-day intervals from 18 rooms in 8 wards, and samples were collected twice a day in the morning and afternoon. The mean bacterial concentrations ranged from 450 to 1585.83 CFU/m³ after 60 minutes of culture media exposure. The mean bacterial concentrations in the obstetrics, surgical, pediatric, gynecology, and medical wards exceeded WHO guidelines. A high indoor air bacterial load was found in 58 (80.6%) of the samples in this study. Gram-positive bacteria in the air were the most common 51 (71%) of the bacterial population measured in all indoor environments. Fungal growth was found in 65 (90.3%) of the samples. Temperatures (26.5°C-28.3°C) and relative humidity (61.1%-67.8%) in the rooms were both above WHO guidelines, creating favorable conditions for bacterial growth and multiplication.

CONCLUSION

The majority of the wards at Dilla University Hospital had bacterial loads in the air that exceeded WHO guidelines. Overcrowding, high temperatures, inadequate ventilation, improper waste management, and a lack of traffic flow control mechanisms could all contribute to a high concentration of bacteria in the indoor air. To control the introduction of microorganisms by patients, students, caregivers, and visitors, it is critical to regularly monitor indoor air bacterial load and implement infection prevention and control measures.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.

Comprehensive health risk assessment of microbial indoor air quality in microenvironments

The higher airborne microbial concentration in indoor areas might be responsible for the adverse indoor air quality, which relates well with poor respiratory and general health effects in the form of Sick building syndromes. The current study aimed to isolate and characterize the seasonal (winter and spring) levels of culturable bio-aerosols from indoor air, implicating human health by using an epidemiological health survey. Microorganisms were identified by standard macro and microbiological methods, followed by biochemical testing and molecular techniques. Sampling results revealed the bacterial and fungal aerosol concentrations ranging between (300–3650 CFU/m³) and (300–4150 CFU/m³) respectively, in different microenvironments during the winter season (December-February). However, in spring (March-May), bacterial and fungal aerosol concentrations were monitored, ranging between (450–5150 CFU/m³) and (350–5070 CFU/m³) respectively. Interestingly, Aspergillus and Cladosporium were the majorly recorded fungi whereas, Staphylococcus, Streptobacillus, and Micrococcus found predominant bacterial genera among all the sites. Taken together, the elevated levels of bioaerosols are the foremost risk factor that can lead to various respiratory and general health issues in additional analysis, the questionnaire survey indicated the headache (28%) and allergy (20%) were significant indoor health concerns. This type of approach will serve as a foundation for assisting residents in taking preventative measures to avoid exposure to dangerous bioaerosols.

The indoor mycobiome of daycare centers is affected by occupancy and climate

Many children spend considerable time in daycare centers and may be influenced by the indoor microorganisms there, including fungi. In this study, we investigate the indoor mycobiomes of 125 daycare centers distributed along strong environmental gradients throughout Norway. Dust samples were collected from doorframes outside and inside buildings using a community science sampling approach. Fungal communities in the dust samples were analyzed using DNA metabarcoding of the internal transcribed spacer 2 (ITS2) region. We observed a marked difference between the outdoor and indoor mycobiomes. The indoor mycobiomes included considerably more yeasts and molds than the outdoor samples, with Saccharomyces, Mucor, Malassezia, and Penicillium being among the most dominant fungal genera. Changes in the indoor fungal richness and composition correlated with numerous variables related to both outdoor and indoor conditions; there was a clear geographic structure in the indoor mycobiome composition that mirrored the outdoor climate, ranging from humid areas in western Norway to drier and colder areas in eastern Norway. Moreover, the number of children in the daycare centers, as well as various building features, influenced the indoor mycobiome composition. We conclude that the indoor mycobiomes in Norwegian daycare centers are structured by multiple factors and are dominated by yeasts and molds. This study exemplifies how community science sampling enables DNA-based analyses of a high number of samples covering wide geographic areas.

IMPORTANCE With an alarming increase in chronic diseases like childhood asthma and allergies, there is an increased focus on the exposure of young children to indoor biological and chemical air pollutants. Our study of 125 daycares throughout Norway demonstrates that the indoor mycobiome not only reflects cooccurring outdoor fungi but also includes a high abundance of yeast and mold fungi with an affinity for indoor environments. A multitude of factors influence the indoor mycobiomes in daycares, including the building type, inhabitants, as well as the outdoor environment. Many of the detected yeasts and molds are likely associated with the human body, where some have been coupled with allergies and respiratory problems. Our results call for further studies investigating the potential impact of the identified daycare-associated mycobiomes on children’s health.

Spatiotemporal variation of the indoor mycobiome in daycare centers

BACKGROUND

Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding.

RESULTS

The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring.

CONCLUSIONS

Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings. Video abstract.

Indoor Particulate Matter in Urban Households: Sources, Pathways, Characteristics, Health Effects, and Exposure Mitigation

Particulate matter (PM) is a complex mixture of solid particles and liquid droplets suspended in the air with varying size, shape, and chemical composition which intensifies significant concern due to severe health effects. Based on the well-established human health effects of outdoor PM, health-based standards for outdoor air have been promoted (e.g., the National Ambient Air Quality Standards formulated by the U.S.). Due to the exchange of indoor and outdoor air, the chemical composition of indoor particulate matter is related to the sources and components of outdoor PM. However, PM in the indoor environment has the potential to exceed outdoor PM levels. Indoor PM includes particles of outdoor origin that drift indoors and particles that originate from indoor activities, which include cooking, fireplaces, smoking, fuel combustion for heating, human activities, and burning incense. Indoor PM can be enriched with inorganic and organic contaminants, including toxic heavy metals and carcinogenic volatile organic compounds. As a potential health hazard, indoor exposure to PM has received increased attention in recent years because people spend most of their time indoors. In addition, as the quantity, quality, and scope of the research have expanded, it is necessary to conduct a systematic review of indoor PM. This review discusses the sources, pathways, characteristics, health effects, and exposure mitigation of indoor PM. Practical solutions and steps to reduce exposure to indoor PM are also discussed.

Elemental and microbiota content in indoor and outdoor air using recuperation unit filters

This paper presents the results of a twelve-month measurement campaign conducted at a rural single-family house in Poland. The external and internal filters of a recuperator used to mechanically ventilate the building were used to separate the total suspended particles (TSPs), and the concentrations of fifteen elements and abundance of fungi and bacteria were determined. Lower annual mean concentrations were observed indoors, and the concentrations of most elements did not significantly change between seasons. There were some differences between winter and summer, which may have resulted from changes in the ventilation regimes in the house. The number of bacteria was similar outdoors and indoors, while the amounts of fungi were higher indoors (p < 0.05). The order of metal concentrations outdoors agreed well with observations in other countries, while indoors the metal concentrations order indicated the individual characteristics of the building. The species diversity of fungi was higher than that of bacteria, and different species were found indoors and outdoors, while bacteria were typically present both indoors and outdoors. Different TSP sources were identified indoors and outdoors, suggesting limited penetration between the two environments. However, both environments were affected by traffic. Mechanical ventilation systems with built-in filters (such as recuperators) were useful in assessing the air quality within the building, and the changeable recuperation filters offer an approach to assess the air quality in several houses without any additional cost or discomfort to the residents.

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.

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.

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.

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.

Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors

Characterizing indoor microbial communities using molecular methods provides insight into bacterial assemblages present in environments that can influence occupants' health. We conducted an environmental assessment as part of an epidemiologic study of 50 elementary schools in a large city in the northeastern USA. We vacuumed dust from the edges of the floor in 500 classrooms accounting for 499 processed dust aliquots for 16S Illumina MiSeq sequencing to characterize bacterial assemblages. DNA sequences were organized into operational taxonomic units (OTUs) and identified using a database derived from the National Center for Biotechnology Information. Bacterial diversity and ecological analyses were performed at the genus level. We identified 29 phyla, 57 classes, 148 orders, 320 families, 1193 genera, and 2045 species in 3073 OTUs. The number of genera per school ranged from 470 to 705. The phylum Proteobacteria was richest of all while Firmicutes was most abundant. The most abundant order included Lactobacillales, Spirulinales, and Clostridiales. Halospirulina was the most abundant genus, which has never been reported from any school studies before. Gram-negative bacteria were more abundant and richer (relative abundance = 0.53; 1632 OTUs) than gram-positive bacteria (0.47; 1441). Outdoor environment-associated genera were identified in greater abundance in the classrooms, in contrast to homes where human-associated bacteria are typically more abundant. Effects of school location, degree of water damage, building condition, number of students, air temperature and humidity, floor material, and classroom's floor level on the bacterial richness or community composition were statistically significant but subtle, indicating relative stability of classroom microbiome from environmental stress. Our study indicates that classroom floor dust had a characteristic bacterial community that is different from typical house dust represented by more gram-positive and human-associated bacteria. Health implications of exposure to the microbiomes in classroom floor dust may be different from those in homes for school staff and students. Video abstract.

Prokaryotic and Fungal Characterization of the Facilities Used to Assemble, Test, and Launch the OSIRIS-REx Spacecraft

To characterize the ATLO (Assembly, Test, and Launch Operations) environment of the OSIRIS-REx spacecraft, we analyzed 17 aluminum witness foils and two blanks for bacterial, archaeal, fungal, and arthropod DNA. Under NASA’s Planetary Protection guidelines, OSIRIS-REx is a Category II outbound, Category V unrestricted sample return mission. As a result, it has no bioburden restrictions. However, the mission does have strict organic contamination requirements to achieve its primary objective of returning pristine carbonaceous asteroid regolith to Earth. Its target, near-Earth asteroid (101955) Bennu, is likely to contain organic compounds that are biologically available. Therefore, it is useful to understand what organisms were present during ATLO as part of the larger contamination knowledge effort—even though it is unlikely that any of the organisms will survive the multi-year deep space journey. Even though these samples of opportunity were not collected or preserved for DNA analysis, we successfully amplified bacterial and archaeal DNA (16S rRNA gene) from 16 of the 17 witness foils containing as few as 7 ± 3 cells per sample. Fungal DNA (ITS1) was detected in 12 of the 17 witness foils. Despite observing arthropods in some of the ATLO facilities, arthropod DNA (COI gene) was not detected. We observed 1,009 bacterial and archaeal sOTUs (sub-operational taxonomic units, 100% unique) and 167 fungal sOTUs across all of our samples (25–84 sOTUs per sample). The most abundant bacterial sOTU belonged to the genus Bacillus. This sOTU was present in blanks and may represent contamination during sample handling or storage. The sample collected from inside the fairing just prior to launch contained several unique bacterial and fungal sOTUs that describe previously uncharacterized potential for contamination during the final phase of ATLO. Additionally, fungal richness (number of sOTUs) negatively correlates with the number of carbon-bearing particles detected on samples. The total number of fungal sequences positively correlates with total amino acid concentration. These results demonstrate that it is possible to use samples of opportunity to characterize the microbiology of low-biomass environments while also revealing the limitations imposed by sample collection and preservation methods not specifically designed with biology in mind.

Bed bugs shape the indoor microbial community composition of infested homes

Indoor pests, and the allergens they produce, adversely affect human health. Surprisingly, however, their effects on indoor microbial communities have not been assessed. Bed bug (Cimex lectularius) infestations pose severe challenges in elderly and low-income housing. They void large amounts of liquid feces into the home environment, which might alter the indoor microbial community composition. In this study, using bed bug-infested and uninfested homes, we showed a strong impact of bed bug infestations on the indoor microbial diversity. Floor dust samples were collected from uninfested and bed bug-infested homes and their microbiomes were analyzed before and after heat interventions that eliminated bed bugs. The microbial communities of bed bug-infested homes were radically different from those of uninfested homes, and the bed bug endosymbiont Wolbachia was the major driver of this difference. After bed bugs were eliminated, the microbial community gradually shifted toward the community composition of uninfested homes, strongly implicating bed bugs in shaping the dust-associated environmental microbiome. Further studies are needed to understand the viability of these microbial communities and the potential risks that bed bug-associated microbes and their metabolites pose to human health.

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait

Kuwait is a country with a very high dust loading; in fact it bears the world's highest particulate matter concentration in the outdoor air. The airborne dust often has associated biological materials, including pathogenic microbes that pose a serious risk to the urban ecosystem and public health. This study has established the baseline taxonomic characterization of microbes associated with dust transported into Kuwait from different trajectories. A high volume air sampler with six-stage cascade impactor was deployed for sample collection at a remote as well as an urban site. Samples from three different seasons (autumn, spring and summer) were subjected to targeted amplicon sequencing. A set of ~ 50 and 60 bacterial and fungal genera, respectively, established the core air microbiome. The predominant bacterial genera (relative abundance ≥ 1%) were Brevundimonas (12.5%), Sphingobium (3.3%), Sphingopyxis (2.7%), Pseudomonas (2.5%), Sphingomonas (2.4%), Massilia (2.3%), Acidovorax (2.0%), Allorhizobium (1.8%), Halomonas (1.3%), and Mesorhizobium (1.1%), and the fungal taxa were Cryptococcus (12%) followed by Alternaria (9%), Aspergillus (7%), Candida (3%), Cladosporium (2.9%), Schizophyllum (1.6%), Fusarium (1.4%), Gleotinia (1.3%) and Penicillium (1.15%). Significant spatio-temporal variations were recorded in terms of relative abundances, α-diversities, and β-diversities of bacterial communities. The dissimilarities were less pronounced and instead the communities were fairly homogenous. Linear discrimant analysis revealed three fungal genera known to be significantly differentially abundant with respect to different size fractions of dust. Our results shed light on the spatio-temporal distribution of airborne microbes and their implications in general health.

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota

BACKGROUND

From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood₂₀₁₀ cohort.

RESULTS

Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa.

CONCLUSIONS

Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child. Video Abstract.

Microorganisms populating the water-related indoor biome

Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies have investigated microorganisms in the air and dust, tap water, another major input of microbial propagules, has received far less attention. The quality of drinking water in developed world is strictly regulated to prevent immediate danger to human health. However, fungi, algae, protists and bacteria of less immediate concern are usually not screened for. These organisms can thus use water as a vector of transmission into the households, especially if they are resistant to various water treatment procedures. Good tolerance of unfavourable abiotic conditions is also important for survival once microbes enter the household. Limitation of water availability, high or low temperatures, application of antimicrobial chemicals and other measures are taken to prevent indoor microbial overgrowth. These conditions, together with a large number of novel chemicals in our homes, shape the diversity and abundance of indoor microbiota through constant selection of the most resilient species, resulting in a substantial overlap in diversity of indoor and natural extreme environments. At least in fungi, extremotolerance has been linked to human pathogenicity, explaining why many species found in novel indoor habitats (such as dishwasher) are notable opportunistic pathogens. As a result, microorganisms that often enter our households with water and are then enriched in novel indoor habitats might have a hitherto underestimated impact on the well-being of the increasingly indoor-bound human population. KEY POINTS: Domestic environment harbours a large diversity of microorganisms. Microbiota of water-related indoor habitats mainly originates from tap water. Bathrooms, kitchens and household appliances select for polyextremotolerant species. Many household-related microorganisms are human opportunistic pathogens.

Indoor dust extracellular vesicles promote cancer lung metastasis by inducing tumour necrosis factor-α

Indoor pollutants are important problems to public health. Among indoor pollutants, indoor dust contains extracellular vesicles (EVs), which are associated with pulmonary inflammation. However, it has not been reported whether indoor dust EVs affect the cancer lung metastasis. In this study, we isolated indoor dust EVs and investigated their roles in cancer lung metastasis. Upon intranasal administration, indoor dust EVs enhanced mouse melanoma lung metastasis in a dose-dependent manner in mice. Pre-treatment or co-treatment of indoor dust EVs significantly promoted melanoma lung metastasis, whereas post-treatment of the EVs did not. In addition, the lung lysates from indoor dust EV-treated mice significantly increased tumour cell migration in vitro. We observed that tumour necrosis factor-α played important roles in indoor dust EV-mediated promotion of tumour cell migration in vitro and cancer lung metastasis in vivo. Furthermore, Pseudomonas EVs, the main components of indoor dust EVs, and indoor dust EVs showed comparable effects in promoting tumour cell migration in vitro and cancer lung metastasis in vivo. Taken together, our results suggest that indoor dust EVs, at least partly contributed by Pseudomonas EVs, are potential promoting agents of cancer lung metastasis.

Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms

This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = −127.05 to −0.25) and wall-to-wall carpet (95% CI = −47.60 to −3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI −179.00 to −44.55) and mechanical ventilation (95% CI = −136.71 to −5.12).

IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

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

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

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

There is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing techniques. Oxford Nanopore’s MinION is the newest third generation sequencing technology on the market. With its many advantages such as portability, user friendliness, simplicity, speed of sequencing and long read length, the technology is now an actual contender to established sequencing platforms. MinION’s main disadvantage is a relatively low read accuracy compared to several other platforms, although this is constantly improving. The present study, which appears to be the first of its kind, provides the results of a preliminary analysis of the microbial communities in indoor environments based on 16S rRNA gene amplicon sequencing, using both the Oxford Nanopore Technologies (ONT) MinIOn and the Illumina MiSeq DNA sequencers. At the level of family and above, there was no significant difference between the microbial compositions as revealed by the two platforms. However, at the genus, and particularly at the species level, the ONT MinION reported greater taxonomic resolution than Illumina MiSeq.

Respiratory dysbiosis and population-wide temporal dynamics in canine chronic bronchitis and non-inflammatory respiratory disease

The lungs of people and companion animals are now recognized to harbor diverse, low biomass bacterial communities. While these communities are difficult to characterize using culture-based approaches, targeted molecular methods such as 16S rRNA amplicon sequencing can do so using DNA extracted from samples such as bronchoalveolar lavage fluid (BALF). Previous studies identified a surprisingly uniform composition of the microbiota in the lungs of healthy research dogs living in a controlled environment, however there are no reports of the lung microbiota of client-owned dogs. Moreover, compositional changes in the lung microbiota depending on disease status have been reported in people, suggesting that similar events may occur in dogs, a species subject to several respiratory disease mechanisms analogous to those seen in people. To address these knowledge gaps, BALF samples from client-owned dogs presenting to the University of Missouri Veterinary Health Center for respiratory signs between 2014 and 2017 were processed for and subjected to 16S rRNA sequencing. Based on specific diagnostic criteria, dogs were categorized as Chronic Bronchitis (CB, n = 53) or non-CB (n = 11). Community structure was compared between groups, as well as to historical data from healthy research dogs (n = 16) of a uniform breed and environment. The lung microbiota detected in all client-owned dogs was markedly different in composition from that previously detected in research dogs and contained increased relative abundance of multiple canine fecal and environmental bacteria, likely due to aspiration associated with their clinical signs. While inter-sample diversity differed significantly between samples from CB and non-CB dogs, the variability within both groups made it difficult to discern reproducible bacterial classifiers of disease. During subsequent analyses to identify other sources of variability within the data however, population-wide temporal dynamics in community structure were observed, with substantial changes occurring in late 2015 and again in early 2017. A review of regional climate data indicated that the first change occurred during a historically warm and wet period, suggesting that changes in environmental conditions may be associated with changes in the respiratory microbiota in the context of respiratory disease. As the lung microbiota in humans and other animals is believed to result from repetitive micro-aspirations during health and in certain disease states associated with dyspnea and laryngeal dysfunction, these data support the increased colonization of the lower airways during compromised airway function, and the potential for temporal effects due to putative factors such as climate.

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

BACKGROUND

The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. To date, mandatory microbial monitoring and observational studies of spacecraft and space stations have been conducted by traditional culture methods, although it is known that many microbes cannot be cultured with standard techniques. To fully appreciate the true number and diversity of microbes that survive in the ISS, molecular and culture-based methods were used to assess microbial communities on ISS surfaces. Samples were taken at eight pre-defined locations during three flight missions spanning 14 months and analyzed upon return to Earth.

RESULTS

The cultivable bacterial and fungal population ranged from 104 to 109 CFU/m2 depending on location and consisted of various bacterial (Actinobacteria, Firmicutes, and Proteobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Amplicon sequencing detected more bacterial phyla when compared to the culture-based analyses, but both methods identified similar numbers of fungal phyla. Changes in bacterial and fungal load (by culture and qPCR) were observed over time but not across locations. Bacterial community composition changed over time, but not across locations, while fungal community remained the same between samplings and locations. There were no significant differences in community composition and richness after propidium monoazide sample treatment, suggesting that the analyzed DNA was extracted from intact/viable organisms. Moreover, approximately 46% of intact/viable bacteria and 40% of intact/viable fungi could be cultured.

CONCLUSIONS

The results reveal a diverse population of bacteria and fungi on ISS environmental surfaces that changed over time but remained similar between locations. The dominant organisms are associated with the human microbiome and may include opportunistic pathogens. This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation. The results of this study can have significant impact on our understanding of other confined built environments on the Earth such as clean rooms used in the pharmaceutical and medical industries.

Indoor damp surfaces harbor molds with clinical significance

Background and Purpose:

Fungal contamination in damp places in buildings has become an increasing problem worldwide. Dampness facilitates the growth of fungi, which can cause adverse effects not only on the buildings but also on their occupants. The aim of this study was to identify indoor mold species in the buildings of Kerman province, Iran.

Materials and Methods:

In this study, 110 samples were obtained from surfaces of damp indoor areas in buildings randomly selected in Kerman province. The identification of fungal species was based on the macroscopic and microscopic characteristics of the isolates, such as colony morphology, hyphae, conidia, and conidiophores, as well as molecular sequence data.

Results:

Based on the results, a total of 218 fungal isolates were obtained. Apart from frequently isolated fungi, such as Alternaria, Aspergillus, and Penicillium, 13 species, including Cladosporium sphaerospermum, Cladosporium herbarum, Cladosporium halotolerans, Engyodontium album, Collariella bostrychodes, Stachybotrys xigazenensis, Ramularia eucalypti, Fusarium merismoides, Fusarium solani, Ochroconis musae, Mucor racemosus, Acremonium zonatum, and Acremonium persicinum were identified, and the selected species were described. Among these 13 species, Cladosporium was the most common species (43%) in indoor surfaces, followed by Ochroconis musae (10.8%) and Engyodontium album (7.4%). To the best of our knowledge, Stachybotrys xigazenensis was reported in the present study for the first time in Iran. In addition, E. album and O. musae were isolated for the first time from indoor surfaces in Iran.

Conclusion:

According to the results, the level of overall fungal richness across indoor surfaces was high. Some of the isolated taxa were clinically significant. It was concluded that the damp residential surfaces were potentially passive collectors of clinically significant molds.

Bedroom Allergen Exposure Beyond House Dust Mites

PURPOSE OF REVIEW

The review provides insight into recent findings on bedroom allergen exposures, primarily focusing on pet, pest, and fungal exposures.

RECENT FINDINGS

Large-scale studies and improved exposure assessment technologies, including measurement of airborne allergens and of multiple allergens simultaneously, have extended our understanding of indoor allergen exposures and their impact on allergic disease. Practical, streamlined methods for exposure reduction have shown promise in some settings, and potential protective effects of early-life exposures have been further elucidated through the investigation of specific bacterial taxa. Advances in molecular allergology have yielded novel data on sensitization profiles and cross-reactivity. The role of indoor allergen exposures in allergic disease is complex and remains incompletely understood. Advancing our knowledge of various co-exposures, including the environmental and host microbiome, that interact with allergens in early life will be crucial for the development of efficacious interventions to reduce the substantial economic and social burden of allergic diseases including asthma.

Characterization of culturable airborne bacteria and antibiotic susceptibility profiles of indoor and immediate-outdoor environments of a research institute in Ghana

Background: The study was conducted to determine the bacterial composition and antibiotic susceptibility profiles of a research institute at the University of Ghana where workers and students spend about 70-85% of their lives in indoor and immediate-outdoor environments. This is imperative as one-third of the recognized infectious diseases are transmitted through airborne-route. Furthermore, the increasing rate of bacterial antimicrobial resistance associated with such environments poses serious public health challenges. Methods: A total of 42 airborne samples were collected from eight major sites at the Department of Biochemistry, Cell and Molecular Biology (BCMB), using passive bacterial sampling techniques. Standard phenotypic microbiological procedures were used to characterize the isolates. Antibiotic susceptibility profiles were determined using standard disk diffusion method and guidelines of Clinical and Laboratory Standards Institute (CLSI). Results: Four groups of bacterial isolates were identified from the total samples collected with Gram positive bacilli as the most common. All the isolates showed resistance to beta lactam and sulfonamide classes of antibiotics with full resistance (100%) to ampicillin and penicillin. In total, seven different anti-biotypes were observed with the highest susceptibility displayed towards tetracycline and gentamycin. Significantly, the various air sampling sites of the institute indicated the presence of bacteria with the majority showing multiple antibiotics resistance. Conclusions: Although the recovery of bacteria from supposed sterile environments calls for attention, the observed low contamination rate as compared to the WHO standard suggests a minimum risk of exposure of students and workers to airborne microbial contamination.

Artemisia pollen is the main vector for airborne endotoxin

BACKGROUND

Endotoxin (LPS) released from gram-negative bacteria causes strong immunologic and inflammatory effects and, when airborne, can contribute to respiratory conditions, such as allergic asthma.

OBJECTIVES

We sought to identify the source of airborne endotoxin and the effect of this endotoxin on allergic sensitization.

METHODS

We determined LPS levels in outdoor air on a daily basis for 4 consecutive years in Munich (Germany) and Davos (Switzerland). Air was sampled as particulate matter (PM) greater than 10 μm (PM > 10) and PM between 2.5 and 10 μm. LPS levels were determined by using the recombinant Factor C assay.

RESULTS

More than 60% of the annual endotoxin exposure was detected in the PM > 10 fraction, showing that bacteria do not aerosolize as independent units or aggregates but adhered to large particles. In Munich 70% of annual exposure was detected between June 12th and August 28th. Multivariate modeling showed that endotoxin levels could be explained by phenological parameters (ie, plant growth). Indeed, days with high airborne endotoxin levels correlated well with the amount of Artemisia pollen in the air. Pollen collected from plants across Europe (100 locations) showed that the highest levels of endotoxin were detected on Artemisia vulgaris (mugwort) pollen, with little on other pollen. Microbiome analysis showed that LPS concentrations on mugwort pollen were related to the presence of Pseudomonas species and Pantoea species communities. In a mouse model of allergic disease, the presence of LPS on mugwort pollen was needed for allergic sensitization.

CONCLUSIONS

The majority of airborne endotoxin stems from bacteria dispersed with pollen of only one plant: mugwort. This LPS was essential for inducing inflammation of the lung and allergic sensitization.

Is the association between pet ownership and indoor endotoxin levels confounded or modified by outdoor residential greenspace?

BACKGROUND

Pet ownership is consistently associated with higher indoor endotoxin concentrations, but may also be related to the amount of greenspace around the home. This study examined whether the association between pet ownership and higher indoor endotoxin concentrations is confounded or modified by residential greenspace.

METHODS

Information on pet ownership was collected at the time of recruitment of the German LISA birth cohort. Endotoxin levels were measured in settled house dust sampled from mothers' mattresses (N=1197) and living room floors (N=390). Greenspace around the home was assessed as the mean Normalized Difference Vegetation Index in 100m, 500m and 1000m buffers around the home, and as the distance to the nearest urban and natural green space. Linear regression models assessed cross-sectional associations between pet ownership and log-transformed endotoxin levels, adjusted for known predictors of endotoxin levels. Confounding by greenspace was assessed by additionally adjusting the models for each greenspace variable. Effect modification was assessed by including interaction terms between pet ownership and each greenspace variable, and by model stratification.

RESULTS

Dog and cat ownership were associated with higher endotoxin levels in mothers' mattresses, whereas only dog ownership was associated with endotoxin levels in the floor samples. All associations were highly robust to further adjustment for greenspace, and there was little evidence to suggest any effect modification (interaction terms had p-values >0.05).

CONCLUSIONS

Residential greenspace did not confound or modify the association between pet ownership and indoor endotoxin levels. Studies should continue investigating whether pets influence the indoor environment only by their presence, or also by acting as transmission vectors of the outdoors.

Exposures Related to House Dust Microbiota in a U.S. Farming Population

BACKGROUND

Environmental factors can influence the house dust microbiota, which may impact health outcomes. Little is known about how farming exposures impact the indoor microbiota.

OBJECTIVE

We aimed to identify exposures related to bacterial communities in house dust in a U.S. farming population.

METHODS

We used 16S rRNA amplicon sequencing to characterize bacterial communities in vacuumed dust samples from the bedrooms of a subset of 879 households of farmers and farmers' spouses enrolled in the Agricultural Lung Health Study (ALHS), a case-control study of asthma nested within the Agricultural Health Study (AHS) in North Carolina and Iowa. Information on current farming (past 12 mo), including both crop and animal farming, and other potential microbial sources was obtained via questionnaires. We used linear regression to evaluate associations between exposures and bacterial diversity within each sample, analysis of similarity (ANOSIM), and permutational multivariate analysis of variance (PERMANOVA) to identify exposures related to diversity between samples, and analysis of composition of microbiome to examine whether exposures related to diversity were also related to differential abundance of specific operational taxonomic units (OTUs).

RESULTS

Current farming was positively associated with bacterial diversity in house dust, with or without adjustment for nonfarm exposures related to diversity, including presence of indoor pets, home condition, and season of dust collection. Many taxa exhibited differential abundance related to farming. Some taxa in the phyla Chloroflexi and Verrucomicrobia were associated [false discovery rate (FDR)<0.05] with farming but not with other nonfarm factors. Many taxa correlated with the concentration of house dust of endotoxin, commonly studied as a general marker of exposure to the farming environment.

CONCLUSIONS

In this farming population, house dust microbiota differed by current farming status. Understanding the determinants of the indoor microbiota is the first step toward understanding potential relationships with health outcomes. https://doi.org/10.1289/EHP3145.

Characterization of culturable airborne bacteria and antibiotic susceptibility profiles of indoor and immediate-outdoor environments of a research institute

Background:The study was conducted to determine the bacterial composition and antibiotic susceptibility profiles of a research institute at the University of Ghana where workers and students spend about 70-85% of their lives in indoor and immediate-outdoor environments. This is imperative as one-third of the recognized infectious diseases are transmitted through airborne-route. Furthermore, the increasing rate of bacterial antimicrobial resistance associated with such environments poses serious public health challenges.Methods:A total of 42 airborne samples were collected from eight major sites at the Department of Biochemistry, Cell and Molecular Biology (BCMB), using passive bacterial sampling techniques. Standard phenotypic microbiological procedures were used to characterize the isolates. Antibiotic susceptibility profiles were determined using standard disk diffusion method and guidelines of Clinical and Laboratory Standards Institute (CLSI).Results:Four groups of bacterial isolates were identified from the total samples collected with Gram positive bacilli as the most common. All the isolates showed resistance to beta lactam and sulfonamide classes of antibiotics with full resistance (100%) to ampicillin and penicillin. In total, seven different anti-biotypes were observed with the highest susceptibility displayed towards tetracycline and gentamycin. Significantly, the various air sampling sites of the institute indicated the presence of bacteria with the majority showing multiple antibiotics resistance.Conclusions:Although the recovery of bacteria from supposed sterile environments calls for attention, the observed low contamination rate as compared to the WHO standard suggests a minimum risk of exposure of students and workers to airborne microbial contamination.

[Epidemiological studies with environmental relevance in Germany]

Our environment is a major factor in determining health and well-being throughout life, from conception into old age. This overview illustrates the most important epidemiological studies and health monitoring systems in Germany, which investigate environmental influences in various population subgroups and estimate related health effects. Environmental factors examined in each study are described. The mentioned studies in children and adults build the basis for predictions and preventive measures. The number of the assessed environmental factors, the depth of the examinations as well as the (phenotypical) characterization of the study participants differ. Still, the obtained data build a base for important future research. However, for this, a permanent and Germany-wide assessment of environmental factors is necessary.The proportion of the European population living in urban areas is projected to increase in the future. Therefore, environmental factors such as air pollution, air temperature, and noise, but also social inequality, are likely to have a negative effect on health and quality of life of the population. The challenge of the aging population as well as potential adaptation processes to the diverse environmental stimuli requires multidisciplinary approaches. From an environmental epidemiology view, the collected data from the described studies are of immense value because only with this data can associations between environment and health be investigated and public health-relevant preventive measures be identified.The NAKO health study will be the largest resource of health data and should therefore be included in future activities related to the investigation of environmental health effects in Germany.

A comparison of methods used to unveil the genetic and metabolic pool in the built environment

BACKGROUND

A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting.

RESULTS

We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community.

CONCLUSIONS

Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.

Temperature-controlled laminar airflow (TLA) device in the treatment of children with severe atopic eczema: Open-label, proof-of-concept study

BACKGROUND

Children with severe, persistent atopic eczema (AE) have limited treatment options, often requiring systemic immunosuppression.

OBJECTIVE

To evaluate the effect of the temperature-controlled laminar airflow (TLA) treatment in children/adolescents with severe AE.

METHODS

We recruited 15 children aged 2-16 years with long-standing, severe AE and sensitization to ≥1 perennial inhalant allergen. Run-in period of 6-10 weeks (3 visits) was followed by 12-month treatment with overnight TLA (Airsonett^® , Sweden). The primary outcome was eczema severity (SCORAD-Index and Investigator Global Assessment-IGA). Secondary outcomes included child/family dermatology quality of life and family impact questionnaires (CDQLI, FDQLI, DFI), patient-oriented eczema measure (POEM), medication requirements and healthcare contacts. The study is registered as ISRCTN65865773.

RESULTS

There was a significant reduction in AE severity ascertained by SCORAD and IGA during the 12-month intervention period (P < .001). SCORAD was reduced from a median of 34.9 [interquartile range 28.75-45.15] at Baseline to 17.2 [12.95-32.3] at the final visit, and IGA improved significantly from 4 [3-4] to 2 [1-3]. We observed a significant improvement in FDQLI (16.0 [12.25-19.0] to 12 [8-18], P = .023) and DFI (P = .011), but not CDQLI or POEM. Compared to 6-month period prior to enrolment, there was a significant reduction at six months after the start of the intervention in potent topical corticosteroids (P = .033). The exploratory cluster analysis revealed two strongly divergent patterns of response, with 9 patients classified as responders, and 6 as non-responders.

CONCLUSION AND CLINICAL RELEVANCE

Addition of TLA device to standard pharmacological treatment may be an effective add-on to the management of difficult-to-control AE.

Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing

Diverse bacterial and fungal communities inhabit human-occupied buildings and circulate in indoor air; however, viral diversity in these man-made environments remains largely unknown. Here we investigated DNA and RNA viruses circulating in the air of 12 university dormitory rooms by analyzing dust accumulated over a one-year period on heating, ventilation, and air conditioning (HVAC) filters. A metagenomic sequencing approach was used to determine the identity and diversity of viral particles extracted from the HVAC filters. We detected a broad diversity of viruses associated with a range of hosts, including animals, arthropods, bacteria, fungi, humans, plants, and protists, suggesting that disparate organisms can contribute to indoor airborne viral communities. Viral community composition and the distribution of human-infecting papillomaviruses and polyomaviruses were distinct in the different dormitory rooms, indicating that airborne viral communities are variable in human-occupied spaces and appear to reflect differential rates of viral shedding from room occupants. This work significantly expands the known airborne viral diversity found indoors, enabling the design of sensitive and quantitative assays to further investigate specific viruses of interest and providing new insight into the likely sources of viruses found in indoor air.

Urban upbringing and childhood respiratory and allergic conditions: A multi-country holistic study

OBJECTIVE

We integratively assessed the effect of different indoor and outdoor environmental exposures early in life on respiratory and allergic health conditions among children from (sub-) urban areas.

METHODS

This study included children participating in four ongoing European birth cohorts located in three different geographical regions: INMA (Spain), LISAplus (Germany), GINIplus (Germany) and BAMSE (Sweden). Wheezing, bronchitis, asthma and allergic rhinitis throughout childhood were assessed using parental-completed questionnaires. We designed "environmental scores" corresponding to different indoor, green- and grey-related exposures (main analysis, a-priori-approach). Cohort-specific associations between these environmental scores and the respiratory health outcomes were assessed using random-effects meta-analyses. In addition, a factor analysis was performed based on the same exposure information used to develop the environmental scores (confirmatory analysis, data-driven-approach).

RESULTS

A higher early exposure to the indoor environmental score increased the risk for wheezing and bronchitis within the first year of life (combined adjusted odds ratio: 1.20 [95% confidence interval: 1.13-1.27] and 1.28 [1.18-1.39], respectively). In contrast, there was an inverse association with allergic rhinitis between 6 and 8 years (0.85 [0.79-0.92]). There were no statistically significant associations for the outdoor related environmental scores in relation to any of the health outcomes tested. The factor analysis conducted confirmed these trends.

CONCLUSION

Although a higher exposure to indoor related exposure through occupants was associated with an increased risk for wheezing and bronchitis within the 1st year, it might serve as a preventive mechanism against later childhood allergic respiratory outcomes in urbanized environments through enhanced shared contact with microbial agents.

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms

The aim of this study was to investigate the fate of nine potential indicator antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, intI1) and the diversity of bacterial communities in response to poultry manure applications to arable soil over a 90 day period. Quantitative real time PCR and Illumina high-throughput sequencing of 16S rDNA gene were used to quantify and trace ARG fate. The levels of all genes dramatically decreased over time and intI1, sul1, sul2 and tetM always had the greatest abundance and lowest dissipation rates. This indicated that more effort should be focused on the ARG elimination from manure rather than waiting for subsequent attenuation in the environment. Our sequencing results documented dramatic changes in the microbial community structure and diversity during these experiments. In poultry manure groups, Bacteroidetes and Actinobacteria were the two dominant phyla while Acidobacteria dominated the control groups. Moreover, the relative abundance of genera Corynebacterium, Pseudomonas, Ochrobactrum, Actinomadura and Bacillus, which contained potential opportunistic pathogens, changed over time suggesting that poultry manure not only strongly influenced bacterial community composition, but also selected specific bacterial communities. This study provides a glimpse of ARG fates and bacterial community diversity in soil after the application of poultry manure.

Airborne bacterial assemblage in a zero carbon building: A case study

Currently, there is little information pertaining to the airborne bacterial communities of green buildings. In this case study, the air bacterial community of a zero carbon building (ZCB) in Hong Kong was characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment dominated the indoor airborne bacterial assemblage, with a modest contribution from bacteria associated with human skin. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties were detected, which may have been driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighted UniFrac distances) differed depending on the season and sampling location. A Bayesian source-tracking approach further supported the importance of adjacent outdoor air bacterial assemblage in sourcing the ZCB indoor bioaerosol. Despite the unique building attributes, the ZCB microbial assemblage detected and its temporal characteristics were not dissimilar to that of conventional built environments investigated previously. Future controlled experiments and microbial assemblage investigations of other ZCBs will undoubtedly uncover additional knowledge related to how airborne bacteria in green buildings may be influenced by their distinctive architectural attributes.

Floor dust bacteria and fungi and their coexistence with PAHs in Jordanian indoor environments

Floor dust samples were collected from Jordanian indoor environments (eight dwellings and an educational building) in Amman. Quantitative PCR (qPCR) analyses of selected fungal and bacterial groups were performed. The bacterial and fungal concentrations were also correlated with PAHs concentrations, which were previously measured in the same samples by using GC-MS. The bacterial and fungal concentrations varied significantly among and within the tested indoor environments. Based on the collected samples in the entrance area of the dwellings, the largest variation was found in Gram-negative bacteria and total fungi concentration. The lowest bacterial and fungal concentrations were found in the dwelling that was least occupied and the most recently built. At the educational building, the Gram-positive bacteria concentrations were lower than those observed in the dwellings. Unlike for bacteria, we observed significant negative correlation with some polycyclic aromatic hydrocarbons (PAHs). This calls for further studies investigating biodegradation of PAHs in house dust and presence of potentially health hazardous PAH metabolites. Since biocontamination in floor dust has been given relatively little to no attention in the MENA region we recommend that more extensive measurements be conducted in the future with chemical and biological analysis of floor dust contaminants and their exposure indoors.

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed.

City-scale distribution and dispersal routes of mycobiome in residences

BACKGROUND

Pathogenic and allergenic bacteria and fungi within the indoors can bring detrimental health effects on the occupants. We previously studied the bacterial communities found in households located throughout Hong Kong as well as the skin surfaces of the occupants. As a complementary study, here, we investigated the fungal communities (mycobiome) in the same residences and occupants and identified factors that are important in shaping their diversity, composition, distribution, and dispersal patterns.

RESULTS

We observed that common skin and environmental fungal taxa dominated air, surface, and skin samples. Individual and touch frequency strongly and respectively shaped the fungal community structure on occupant skin and residential surfaces. Cross-domain analysis revealed positive correlations between bacterial and fungal community diversity and composition, especially for skin samples. SourceTracker prediction suggested that some fungi can be transferred bidirectionally between surfaces and skin sites, but bacteria showed a stronger dispersal potential. In addition, we detected a modest but significant association between indoor airborne bacterial composition and geographic distance on a city-wide scale, a pattern not observed for fungi. However, the distance-decay effects were more pronounced at shorter local scale for both communities, and airflow might play a prominent role in driving the spatial variation of the indoor airborne mycobiome.

CONCLUSIONS

Our study suggests that occupants exert a weaker influence on surface fungal communities compared to bacterial communities, and local environmental factors, including air currents, appear to be stronger determinants of indoor airborne mycobiome than ventilation strategy, human occupancy, and room type.