Characterization of household microbiomes from three unique cities around the world

Characterizing the household bacterial microbiome allows for a stronger understanding of the various microbes to which a person is exposed every day in their home. Exploring household microbiomes in different countries around the world increases our understanding of the impact human behaviour might have on niche microbial communities in the house. The goal of this study was to use shotgun metagenomics to characterize the microbiome from ten locations around the house in ten different houses from three countries (Mysuru, India; Dubai, United Arab Emirates (UAE); and Tucson, USA). There was a significant difference in alpha diversity between the three countries (ANOVA, P<0.001), with homes in Mysuru, India, showing significantly higher bacterial diversity compared with those in Tucson, AZ, USA and Dubai, UAE. Beta diversity analysis of the homes found that bacterial communities differed significantly by geographic location [permutational multivariate analysis of variance (PERMANOVA), P=0.001] and, within cities, by household location (PERMANOVA, P=0.001), with geographic location explaining 5.3% and household location explaining 7.3% of variation. Household location was a strong driver of diversity within each of the three cities individually, accounting for 14-18% of microbiome variation. The highest levels of bacterial diversity across the three cities were found underneath the toilet rim and within bathroom and kitchen sinks. A core microbiome of classes Actinomycetota and Gammaproteobacteria was found in all homes in all three cities. Within each city, a core microbiome was identified at the species level within specific household locations. Many bacterial taxa found in the homes were a part of the human-associated phyla Actinomycetota (e.g. genera Brevibacterium, Mycolicibacterium and Rhodococcus), Pseudomonadota (e.g. genera Acinetobacter, Moraxella, Paracoccus and Pseudomonas) and Bacillota (genus Streptococcus), which is comparable to previous studies. The household microbiome is variable across different locations within the house and on a global scale. Factors such as human activity, cultural practices, climate and surface type and use may drive this diversity. Characterizing the household microbiome on a global scale allows for a better understanding of what drives microbial diversity, increasing our understanding of how microbial communities are shaped by the environment and how humans influence their dynamics, as well as any risks to human health that the built microbiome may potentially pose.