Characterization of bacterial community of raw milk from dairy cows during subacute ruminal acidosis challenge by high-throughput sequencing.

Abstract

Four cannulated primiparous Holstein dairy cows (84 ± 25 DIM) were used in a 2 × 2 crossover experimental design. The two diets contained 40% (low-concentrate diet, or control diet, LC) and 70% (high-concentrate diet, or SARA induction diet, HC) concentrate feeds respectively. Milk samples were collected on days 17, 18 and 19 of each experimental period. DNA was extracted from each milk sample, and pyrosequencing was applied to analyse the milk microbial community. Regardless of diet, the bacterial community of milk was dominated by Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes. HC feeding showed a higher proportion of some mastitis-causing pathogen bacteria, such as Stenotrophomonas maltophilia, Streptococcus parauberis and Brevundimonas diminuta, as well as of psychrotrophic bacteria, such as Pseudomonas, Brevundimonas, Sphingobacterium, Alcaligenes, Enterobacter and Lactobacillus. However, the diversity of the milk bacterial microbiota (ACE, Chao, and Shannon index) was not affected by HC feeding. To the best of our knowledge, this is the first report on the use of pyrosequencing for evaluating the impacts of nutrition on changes in the composition of milk microbiota. These findings indicate that HC feeding may increase the risk of dairy cows suffering from mastitis, decrease the organoleptic quality of raw milk and dairy products, and limit the shelf life of processed fluid milk.