A good start is half the battle. This is also true in genomics research. Each sequencing methodology depends heavily on the quality of the acquired nucleic acids that are used as starting material. For any DNA-based technique, it is essential that the DNA in the sample is in an adequate concentration, of high-molecular weight and of sufficient quality. For microbial profiling and -omics-related approaches, there appear to be additional criteria. The first criterion is that the nucleic acids that are present represent the microbial community in the environmental samples (e.g. water, soil, feces, and food) from which they were extracted. Studies have shown that the DNA extraction methodology itself can have a strong influence on the quantification of the total bacteria and the abundance estimations of specific groups. Experts from BaseClear can help you select the appropriate extraction method for your sequencing project.
It is far from simple to determine which extraction method yields the nucleic acid fraction that most accurately represents the true microbial composition. Each extraction method differs in its manner of obtaining nucleic acids from samples and thereby in its applicability for different purposes. The extraction methods differ for example in the degree of homogenization, the cell lysis method (chemical, enzymatic or mechanical) and the nucleic acid recovery principle (e.g., by precipitation or column based). Chemical and enzymatic lysis methods appear to be gentler, but they do not fully access all microbial populations. Mechanical lysis by bead beating has the advantage that the lysis buffer better penetrates through the complete sample. However, this method may result in a higher degree of DNA shearing, which is detrimental for whole genome sequencing where high molecular weight DNA is required. It has been shown that it is possible to minimize DNA shearing by removing the aqueous phase after each round of bead beating.
Scientists from BaseClear have investigated the different extraction methods that are available and compared them in terms of costs, hands-on time, nucleic acid yield and quality and the microbial diversity. Their evaluation revealed, for example, that the bead beating apparatus used as well as the homogenization time has a profound influence on the DNA yield. They also found that the choice of the DNA extraction method influences how much starting material is required and affects the practical progress of the sequencing project in terms of speed. Based on this research, the scientists were able to further optimize our DNA extraction procedures. Thus we can now offer you specific solutions to extract DNA as well as RNA from complex samples, such as fecal samples.