Microbiota profiling of cows milk with and without traditional fermentation

There were several ~80 taxa (merged at lowest available taxonomic annotation) that were differentially abundant or differentially absent/present (|FC| >= 1.5 %; presence >= 60% in at least one group; FDR . <= 0.05) when comparing fermented (N=5) vs. unfermented (N=4) milk. Lactococcus and Leuconostoc species were present at higher levels in the the fermented products as expected. The majority of hits were however actually ones that were (strangely?) uniformly present in the unfermented milk (3 of urban and 1 of rural origin). It could be that the urban samples were all collected from the same site which may explain the otherwise odd level of similarity (the elution buffer negative control did not however have any detectable amplicons based on the CPGR's report). One urban sample was clearly infected with Salmonella enterica which was the dominant organism in this sample.