Diverse spore-forming bacterial populations in US organic raw milk are driven by climate region

Spore-forming bacteria pose significant challenges to the dairy industry, as they are present at high levels in the natural environment and can cause finished product spoilage. To improve organic raw milk quality and minimize spoilage caused by spore-forming bacteria, we used a farm-to-table approach, by assessing the levels and diversity of various spore types through longitudinal studies of United States (US) organic dairy supplies, including (1) raw milk from 100 organic dairy farms, (2) raw milk intended for organic cheese production from 5 processing plants, (3) pasteurized milk from 5 processing plants, and (iv) dairy powders from 2 processing plants. Based on a total of 4,194 isolates characterized by either rpoB or 16S rRNA gene sequencing, Bacillus spp. dominated the aerobic spore-formers isolated from farm raw milk, pasteurized milk, and powders. Nonmetric multidimensional scaling revealed that aerobic spore-former populations in organic farm raw milk differ significantly between climate zones at genus, species, and allelic type levels. The anaerobic/facultative anaerobic spore-formers isolated from farm and cheese raw milk samples represented the orders Clostridiales and Bacillales. Evaluation of the gas produced by anaerobic/facultative anaerobic spore-forming bacteria isolates showed that gas production varied significantly between Clostridiales clades, and 1 Bacillales clade produced gas amounts that were not significantly different from most Clostridiales clades. Overall, our data indicate (1) a substantial diversity of aerobic and anaerobic spore-formers in US organic dairy supplies with predominant genera and species similar between organic and conventional dairy supplies as previously described; (2) both anaerobic and facultative anaerobic spore-formers found in organic raw milk produce gas; and (3) climate may affect aerobic spore-former diversity in farm raw milk.