The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

Conclusion Our understanding of the human gut microbiome role in health and disease depends on obtaining reliable and comparable microbial data of both bacterial and fungal communities. To achieve this goal, using an appropriate methodology is an important step. Previous efforts in standardizing methodology for bacterial microbiome research lead to the recommendation of using the IHMS protocol Q worldwide, to ensure data reproducibility and comparability. In this study, we evaluated and compared the impact of five different DNA extraction methods including the IHMS protocol Q, on the representation of fecal bacterial and fungal communities, with an emphasis on applying the method for use on both communities. In our experimental design, the evaluated DNA extraction methods significantly differed in the efficiency and quality of the isolated DNA, which affected the identified stool microbiome composition. We also discussed the impact of fungal contaminations revealed in kit reagents. Overall, based on the data obtained, we suggest using the DNA extraction protocol “IHMS protocol Q,” which is suitable for simultaneously analyzing both the bacterial and fungal gut community. Ethics Statement This study was carried out in accordance with the recommendations of Committee of the Centre for Cardiovascular Surgery and Transplantation (Protocol no. 201603), with written informed consent from all subjects. All subjects gave written informed consent in accordance with th...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research