Microbiomes in the human body as well as in the environment determine a lot of immunological and physiological responses. The air we breathe inside our indoor environments is often dominated by various microflora, originating from the sources including occupants, dusts, pets, and moisture-damaged building materials. Studies on indoor microbiomes were previously hindered because of the dependence on mainly culture-based techniques. Moreover, many microorganisms are not culturable in conventional culture media. PCR, FISH (fluorescence in situ hybridization), and microarrays can only identify genes of microorganisms for which probes

have been developed and are not applicable for determining unknown microbial genes. Universal primers for the 16S rRNA gene, DGGE (denaturing gradient gel electrophoresis) and other postPCR techniques can utilize DNA amplified from most of the microorganisms. However, DGGE technique is limited by band resolution and species identity is only detectable for bands that have been individually excised and sequenced. Recent advances in sequencing technology during last few years have increased genome sequencing throughput over 50-fold when compared to Sanger-based sequencing methods. This advancement has enabled us to produce gigabases of

sequencing information in a very short time. Moreover, the cost incurred on each sequencing run has also been considerably reduced. The present article will review the recent applications of high-throughput sequencing technology for understanding the microbiome, particularly in indoor environments, such as home, hospital and office.