DNA extraction methodology can substantially influence human breast milk microbiome analysis

We assessed the performance of five common approaches used for bacterial DNA extraction from breast milk samples. These included four based on commercial kits (QIAgen PowerLyzer PowerSoil DNA Isolation, Sigma Aldrich GenElute Bacterial Genomic DNA Kit, QIAamp DNA Stool Mini Kit, and QIAamp DNA Stool Mini Kit with bead beating) as well as a phenol-chloroform based extraction method. All of these approaches were applied to both a mock breast milk sample, in which a defined bacterial community was added to filer-sterilised breast milk, and to aliquots of four human breast milk samples. The performance and reproducibility of each method were assessed based on DNA yield and purity, and bacterial community composition.