Microbiota dynamics and bacterial pathogen survival during milk kefir fermentation and storage

This study identified and investigated the relative abundance of bacterial and fungal (predominantly yeast) species in the milk kefir grains, during a typical fermentation (25◦C for 48 h) and subsequent chilled storage (4◦Cfor up to 30d) using Nanopore sequencing (16S and ITS amplicon). Challenge studies were also undertaken toexamine the behaviour of Listeria monocytogenes, Salmonella Senftenberg, Escherichia coli O157:H7, Staphylococcusaureus as well as non-toxigenic mesophilic and psychrophilic Clostridium spp. (Clostridium sporogenes and Clos-tridium gasigenes, respectively). Lactobacillus and Lactococcus were the predominant bacterial genera with relativeabundance of 91% and 2% in milk kefir grains, 32% and 63.7% after 24 h of the fermentation, 87% and 2% after48 h, respectively. Other bacteria detected included Lentilactobacillus, Leuconostoc, Acetobacter, Asaia and Ento-mobacter. The most abundant fungal genus in the milk kefir grains was the yeast, Brettanomyces (90%), consistingsolely of the species Brettanomyces anomalus, which remained dominant at 24 h (80.7%), 14d (71.7%) and 21d(75.6%). Zygotorulaspora florentina was most abundant immediately after adding the grains to the milk (42.8%)and after 7d (33.9%). Other significant yeast genera detected included Kazachstania (mainly K. unispora) andGrigorovia (mainly G. humatica). In the challenge studies, the L. monocytogenes population increased by 1.3 log10cfu ml