Understanding the Influence of DNA Extraction on Microbial Diversity: Implications for Different Sample Types

Background: Microbiome analyses are essential for understanding microorganism composition and diversity, but interpretation is often challenging due to biological and technical variables. DNA extraction is a critical step that can significantly bias results. Our aim was to determine the extent to which DNA extraction impacts results for different sample types, and assess therein whether the processing of certain sample types could be automated more effectively. Methods: For this study, we assessed the suitability of up to four distinct DNA extraction protocols for four different clinical sample types: stool, cervical swabs, skin swabs, and hospital surface swabs. Results: We found that skin and cervical swab samples had good results with all tested protocols, however, for stool samples we found that the more sophisticated manual extraction protocols with vigorous bead-beating were necessary in order to avoid erroneous taxa proportions on all investigated taxonomic levels and, in particular, false underrepresentation of important genera such as Blautia. Conclusion: Our results suggest that the selection of an appropriate DNA extraction protocol and the level of possible automation depend largely on the sample type. For instance, skin and cervical samples appear easier to automate than stool samples, or at least when a rough assessment of taxonomic abundance is sufficient for the intended purpose.