Figure legends:
Figure 1 . Simpson and Shannon alpha diversity of different cow’s milk samples.
Figure 2. Principle coordinates analysis (PCoA) based on Bray-Curtis dissimilarity of different cow’s milk samples.
Figure 3. Composite bar graph of lactic acid producing bacteria and pathogens with potential relevance to human health.
Online supporting information :
Figure S1. Bar plot of relative abundance of bacteria in the different cow’s milk samples at phylum level, excluding low abundance taxa.
Figure S2. Bar plot of relative abundance of organisms in the different cow’s milk samples at genus level, excluding low abundance taxa.
Figure S3 . Log2-transformed counts of taxa significantly different in terms of relative abundance or frequency between fermented versus unfermented samples. Taxa are merged at the lowest available taxonomic level and samples were clustered using complete linkage clustering of the Bray-Curtis dissimilarity matrix. Taxa were deemed significantly different (in terms of abundance and/or absence/presence) between fermented versus unfermented samples if they exhibited a fold change (beta coefficient) of ≥ 1.5 and had an adjusted p-value of ≤ 0.05 and if at least one of the two groups compared had ≥ 60% of samples with the given ASV/taxon, or, if the result of Fisher’s exact test was significant (after multiple-testing correction by the Benjamini-Hochberg method), using the R package metagenomeSeq.