Milk preservation and amplicon sequencing

For large-scale epidemiological studies on factors affecting the quality of dairy milk, immediate analysis of fresh milk collected over large or remote areas is often impossible. More often than not, effective preservatives are necessary to stabilize milk microbiota and enable, when required, the recovery of microorganisms by culture-based techniques. For culture-independent approaches involving 16S rRNA gene sequencing, the choice of hypervariable region may have considerable impact on research outcomes. We comprehensively analysed microbial changes occurring during the cold storage of fresh and preserved raw milk. Our study revealed unreliable results after amplicon sequencing of the V3-V4 and V6-V8 regions and identifies the combination of azidiol and dimethyl sulfoxide as a suitable preservative. Given the importance of sampling procedures in analysing ecological data, a better knowledge of the responses of milk microbial species to other preservatives will help develop more efficient study designs and improve reproducibility in dairy microbiome research.