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DNA AND/OR RNA EXTRACTION

A microbial profiling analysis has no value if the DNA and/or molecules of the different organisms do not represent the microbial community in the fecal or skin samples from which they were extracted. The method of extraction can have a strong influence on the quantification of the total bacteria and the abundance estimations of specific groups.

BaseClear BiaNomics has invested in optimization and validation of our extraction procedures and offers specific solutions to extract DNA as well as RNA from complex samples, such as feces. However, in case you prefer a certain isolation protocol this is no problem for us. Experts from BaseClear BiaNomics can help you select the most appropriate extraction method for your project.

EVALUATION OF EXTRACTION METHODS

Studies have shown that the DNA or RNA extraction methodology itself can have a strong influence on the quantification of the total bacteria and the abundance estimations of specific groups. 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.

Our scientists 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. Based on this research, we have further optimized our DNA extraction procedures. Now we can offer you specific solutions to extract DNA as well as RNA from complex samples, such as fecal samples.  

Meet Tom van den Bogert!

Tom is responsible for all metagenomics and microbial profiling projects, which are based on our next generation sequencing technologies, and the development of related approaches.

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