Evaluation of extraction methods for the isolation of dust mites, bacterial, and fungal PCR-quality DNA from indoor environmental dust samples: A new scope for indoors research

Abstract

Dust mites, bacteria, and fungi are ubiquitous organisms found in household dust and have been related to the development of three types of human diseases: hypersensitivity responses (allergic reactions), infections, and toxicosis of the respiratory system. Sometimes, the presence of these organisms cannot be detected by typical methods, which prevents an effective and accurate identification of these pathological sources.

An effective isolation of PCR-quality DNA from indoors environmental samples will allow employing the PCR technology as an indoor detection technique for these biological sources. Several DNA extraction methods have been employed with soil or sediment samples, but their DNA products usually contain organic contaminants, polysaccharides, proteins, and tannins that inhibit the PCR amplification.

We compared for the first time, seven DNA extraction methods to identify the most efficient protocol for obtaining dust mites, bacteria and fungi PCR-quality DNA from indoor settings. The SoilMasterTM DNA Extraction Kit showed a highly sensitive, reproducible and fast (less than an hour) method for obtaining PCR-quality DNA from dust mites, bacteria, and fungi when compared with the other methods studied. An added modification (sample homogenization) to this kit positively influenced the dust mites’ mitochondrial DNA extraction by increasing its ratio over proteins. By using the DNA extraction and PCR approach in indoors-dust samples, non-cultivable indoor biological contaminant organisms can also be identified, contributing to an accurate diagnostic test.