Bacterial Diversity in House Dust: Characterization of a Core Indoor Microbiome

Our indoor microbiome consists of a wide range of microbial taxa. Whilst many of these microbes are benign, some are beneficial, some harmful, yet our knowledge of the spatial heterogeneity of bacterial assemblages in our residential environment remains limited. To investigate the existence of a common core house dust bacterial microbiome we selected household vacuum dusts, collected through a citizen science approach, from homes across two bioclimatic regions (UK, Oceanic/Maritime and Greece, Mediterranean). Following the extraction of DNA from each dust sample, we targeted the bacterial 16S rRNA gene using Illumina NextSeq sequencing. PERMANOVA analysis of the microbial communities at family level grouped samples within their distinct bioclimatic region and SIMPER analysis at genus level identified the statistically significant taxa responsible for driving diversity between these groups. A “common to all” core house dust microbiome consisted of Acinetobacter, Massalia, Rubellimicrobium, Sphingomonas and Staphylococcus; genera typically associated with human occupancy and common environmental sources. Additionally, a “unique location specific” microbiome was identified, reflective of the bioclimatic region. The Greek dusts indicated a lower average diversity than the UK house dusts, with a high abundance of Rhizobiaceae in the Greek samples. Our study highlights citizen science as a powerful approach to access the indoor residential environment, at scale, and establishes the existence of a “core” house dust microbiome independent of bioclimatic region.

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

Background Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries. Methods Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms. Results Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut. Conclusions We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects.

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

Pathogens are commonly presented in the human respiratory tract, but symptoms are varied among individuals. The interactions between pathogens, commensal microorganisms and host immune systems are important in shaping the...

THE PHYLLOSPHERE, INDOOR MICROBIOME AND HUMAN HEALTH Authors

A healthy indoor environment is very vital as humans spend a greater percentage of their life within built environments. A healthy and quality environment is determined by the biodiversity of and features of the natural environment. The indoor environment just like every other environment possesses a unique community of microorganism which depends on the level of contact between the environment and natural sources. Plants are significant sources of microbial diversity in an environment. There is an interplay between the phyllosphere and the troposphere where the microorganisms released from the phyllosphere perform several beneficial effects consequently, improving human health. The indoor environment must however be enriched with natural sources of microbial release to enhance its biodiversity. This paper therefore focuses on the phyllosphere as a natural source for enhancing indoor biodiversity, the interplay between the phyllosphere and its surrounding environment and its implication on human health.