Buildings are complex ecological systems that support a high diversity of prokaryotic and eukaryotic communities. Since many of these organisms interact with humans and their activities, and adding the considerable amount of time modern humans spend indoors, it is critical to understand the taxonomic composition of indoor biota as well as the ecological processes and environmental factors that may influence their diversity and composition.

In this thesis, I report on studies where I employed a Next-Generation DNA Sequencing technique, monitored 668 environmental factors and occupants’ activities, conducted advanced multivariate statistical analyses, and demonstrated that community composition of different organisms in indoor environments, including Fungi, Bacteria, and Animals may be influenced by different building characteristics, furnishings, type of occupants as well as their activities. In addition, this is the first study reporting the presence of Archaea in household dust as a common part of the indoor microbiota;​ however, the archaeal abundance in indoor environment was considerably lower than Bacteria, perhaps because of less available sources contributing to indoor Archaea or more environmental filtering preventing archaeal establishment in indoor environments. This also can be interpreted that the indoor archaeal assemblages are probably allochthonous for the most part (passive entrants of archaeal traces from different sources), in contrast, to those of the Bacteria which are a mixture of allochthonous and autochthonous (live and active inhabitants of dust). Finally, in a separate study with samples collected over a 20-year period, I found that the total airborne fungal spore count in outdoor air would likely increase significantly in future years as a result of climate change, indicating a likely rise in indoor fungal spore abundance as well.

Overall, this study as one of the first to look for members of all domains of life in a single cohort study, has advanced our understanding of biological components of residential houses and illustrated how community composition of different organisms in the indoor environment may be influenced by different building characteristics, furnishing, and its occupants. I believe such comprehension of indoor ecology can help researchers design intervention studies to provide public health policy decision makers with new tools to improve the built environment.