Fig. 2

The microbiota profiles of retail milk over room temperature incubations. a NMDS of retail milk samples based on Bray-Curtis (k = 3; stress = 0.15; linear fit, R² = 0.76; non-metric fit, R² = 0.96). All 902 samples, after excluding low sequencing read milks (Raw = 270; Vat = 108; HTST = 347; UHT = 177), were included in this analysis. b Alpha diversity as measured by Shannon index in retail milk over RT incubation. c Alpha diversity as measured by Faith’s phylogenetic diversity (PD) in retail milk over RT incubation. d Bar plot depicting the relative abundance of bacterial families over time; bacterial families which has a relative abundance less than 1% were grouped into “Others”. ^★★P < 0.01, and ^★★★P < 0.001 for comparison with start point (0 h) in HTST milk