Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research

Area of Science:

• Genomics and Microbiology
• Bioinformatics and Computational Biology

Background:

• Standardized methodologies are crucial for generating comparable data in global research efforts.
• Open-source procedures facilitate data standardization and reproducibility.

Purpose of the Study:

• To present a modular, high-throughput nucleic acid extraction protocol (DREX) standardized within the Earth Hologenome Initiative.
• To enable the generation of both genomic and microbial metagenomic data from vertebrate fecal samples.

Main Methods:

• The DREX protocol allows purification of RNA and DNA in separate fractions (DREX1) or as total nucleic acids (DREX2).
• Effectiveness was demonstrated across fecal samples from amphibians, reptiles, and mammals.
• Performance was benchmarked against a widely used commercial kit for microbiome research.

Main Results:

• Both DREX1 and DREX2 yielded highly similar microbial community profiles and comparable host genome coverages.
• The method showed effectiveness across various vertebrate taxa, with reduced performance on bird guano.
• Benchmarking confirmed comparable recovery of host genomic data and microbial community complexity versus a commercial kit.

Conclusions:

• The open-source DREX method is a robust, cost-effective, scalable, and automation-friendly procedure for high-quality hologenomic data generation.
• It enhances research comparability and reproducibility through standardized, high-throughput, open-access protocols.
• The modular design supports integration into automated pipelines and continuous improvement.