What is the importance of DNA extraction techniques in Whole-Genome Shotgun Metagenomic Sequencing?

DNA extraction is the first step in whole‑genome shotgun metagenomic sequencing and determines how well the DNA from every organism in a sample is recovered; poor extraction can miss rare microbes or degrade DNA, leading to incomplete data. The technique must lyse a wide range of cell types—bacteria, archaea, fungi, and viruses—without preferentially breaking some cells, because bias in extraction skews the apparent community composition. High‑quality, intact DNA also reduces the amount of sequencing needed to cover each genome, saving time and money. For example, using bead‑beating with enzymatic lysis can recover both tough bacterial spores and delicate viral genomes, whereas a mild protocol might miss the spores and over‑represent viruses. Therefore, choosing an extraction method that is gentle, thorough, and unbiased is essential for accurate, representative metagenomic analysis.