Although we spend the majority of our lives indoors, the airborne microbial content of enclosed spaces still remains inadequately described. The objective of this study was to characterize the bacterial diversity of indoor air in three different enclosed spaces with three levels of occupancy, and, in particular, to highlight the 'core' species, the opportunistic pathogens and their origins. Our findings provide an overall description of bacterial diversity in these indoor environments. Data gathered from the three enclosed spaces revealed the presence of a common indoor signature (60% of total sequences in common). This work will provide a clearer understanding of the dominant groups of bacteria encountered in enclosed spaces: Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. Thus, certain evidence revealed a connection between 'core' species and the human micro-environment (20% of phylotypes and 12% of sequences of human origin). Overall PCA analysis showed that the indoor environment is influenced mainly by the microbial diversity from nose and skin. Among the 'core species' found during this study, a large number (72% of all pathogen-related sequences were concentrated in 'core species') of genera and species are known to be responsible for opportunistic or nosocomial diseases or to include human commensal bacteria such as Mycobacterium sp., Acinetobacter baumanii, Aerococcus viridians, Thermoactinomyces vulgaris or Clostridium perfringens.