From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome

Investigating the culturable atmospheric fungal and bacterial microbiome in West Texas: implication of dust storms and origins of the air parcels

Individuals often experience ailments such as allergies, asthma and respiratory tract infections throughout the year. Weather reports often include estimations of common allergens that can affect these individuals. To describe the local 'atmospheric microbiome' in Lubbock, Texas, USA, we examined the culturable fungal and bacterial microbiome present in the air on calm and dust storm days using internal transcribed spacer (ITS)-1 and 16S rRNA amplicon sequencing, respectively. While some types of airborne fungi were frequently present throughout the year, distinct differences were also observed between calm and dust storm days. We also observed the influence of the origin of air parcels and wind elevation of the air trajectory. The most abundant genera of fungi identified during the study period were Cryptococcus, Aureobasidium, Alternaria, Cladosporium and Filobasidium. This observation was not surprising considering the agricultural intensive environment of West Texas. Interestingly, Cladosporium, a common allergenic mold, was increased during days with dust storm events. The predominant bacterial genera observed were Bacillus, Pseudomonas, Psychrobacter, Massilia and Exiguobacterium. The relative abundance of the psychrophiles, Psychrobacter and Exiguobacterium, was surprising, given the semi-aridity of West Texas. Coupling our observations with back trajectories of the wind (Hybrid Single-Particle Lagrangian Integrated Trajectory models) demonstrated that dust storms, regional anthropogenic activity and origin of air parcels are important influences on the diversity and temporal presence of the atmospheric microbiome.

Characteristics of airborne bacterial communities in indoor and outdoor environments during continuous haze events in Beijing: Implications for health care

There is solid evidence that haze pollution threatens human health owing to the abiotic pollutants it contains. However, the characteristics of airborne bacterial communities in indoor and outdoor environments exhibiting haze occurrence are still unknown. Thus, we examined variations in both indoor and outdoor airborne bacterial communities in Beijing from December 9-27, 2016, a period which included three haze events. The outdoor airborne bacterial communities were clustered into two main groups (Groups I and II), and they shifted between two typical bacterial communities regardless of the haze event. The Chao1, Shannon, and phylogenetic diversity indexes and abundance of dominant classes changed significantly, as did airborne bacterial community type. The indoor airborne bacterial community closely tracked the outdoor bacterial community type, forming two obvious groups supported by Adonis analysis, changes in dominant classes, and bacterial diversity compared to the outdoor group. Furthermore, we found that the airborne bacterial community type could affect the morbidity of respiratory diseases. Daily pneumonia cases were significantly higher in Group I (p = 0.035), whereas daily amygdalitis cases were significantly higher in Group II (p = 0.025). Interestingly, the enriched classes in the indoor environment were quite different from those in the typical airborne bacterial community environment, except for Clostridia, which had significantly higher abundance in both indoor environments. In conclusion, we found that the two indoor and outdoor airborne bacterial community types changed independently of haze events, and the special airborne bacterial community type was closely related to the incidence of pneumonia in the heavy haze season.

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.

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.