16S rDNA high-throughput sequencing and MALDI-TOF MS are complementary when studying psychrotrophic bacterial diversity of raw cows' milk

Refrigeration of raw milk favours the growth of psychrotrophic bacteria (psychrotrophs) that can produce spoilage enzymes, which may deteriorate final dairy products. The psychrotrophs from raw milk across four seasons were identified using culture-dependent and culture-independent approaches. Both 16S rDNA high-throughput sequencing (HTS) and MALDI-TOF MS showed the Pseudomonas genus to predominate; however, predominant species differed between the two identification methods. There was no geographical trend in microbiota, but a seasonal variation was evident. The use of HTS and MALDI-TOF MS was complementary in describing the psychrotrophic bacterial diversity of raw milk and provides an understanding of the raw milk microflora that may influence milk quality. This is the first report to compare data obtained from 16S rDNA high-throughput sequencing and MALDI-TOF analysis to assess the psychrotrophic microbial quality of refrigerated raw milk in New Zealand.