Isolating Bacterial DNA from Goat Milk and Its Products: Comparative Analysis

Despite its high demand in molecular diagnostics, the bacterial DNA extraction from dairy products remains an understudied area. The effectiveness of different DNA extraction methods for detecting microorganisms in food matrices needs a comprehensive comparative analysis. The article introduces a comparative analysis of bacterial DNA extraction methods from goat milk and its products. The research included samples of raw, pasteurized, and powdered goat milk, as well as a goat milk yogurt and a goat milk cheese. The nucleic acid tests relied on five commercially available kits based on 1) a silica sorbent (DNA-Sorb-S-M), 2) salt precipitation of nucleic acids (DNA-Extran-2), 3) spin columns with a silica filter (K-Sorb), 4) magnetic particles (GMO-MagnoSorb), 5) a combination of phenol-chloroform extraction and silica sorbent (Sorb-GMO-B). The concentration and purity of DNA preparations were analyzed using standard fluo- and spectrometric methods. The isolated total DNA was used as a template for amplification of bacterial 16S rRNA gene fragments. All kits were able to isolate bacterial DNA from all samples but goat milk powder, where the lack of amplification could be due to some technological production features or DNA degradation during extraction. The best results belonged to the method that combined phenol-chloroform extraction and silicon sorbent, especially for complex matrices. The method with silica sorbent without organic solvents was second in efficiency. The analysis of the yield and purity of bacterial DNA showed that some methods were less effective with milk matrices. The method of phenol-chloroform extraction with adsorption on a silicon sorbent proved to be the most productive and universal method for extracting DNA from goat milk and its products. However, other protocols could be calibrated for specific viscosity, density, bacterial cell count, complex protein profile, exopolysaccharide/fat matrices of microbial encapsulation, etc.