The microbiome of bulk tank milk: Characterization and associations with somatic cell count and bacterial count

Numerous studies have evaluated associations between bacterial groups and milk quality parameters. However, to our knowledge, no research has been published that has analyzed associations between the microbiome and quality parameters of bulk tank milk (BTM). Thus, the aims of this study were to identify the core microbiome of BTM and to examine associations between the microbiome and milk quality parameters. Four hundred seventy-two BTM samples from 19 different dairy farms located in New York State were analyzed by next-generation sequencing and quantitative PCR of the 16S rRNA gene to assess the milk microbiome and measure total bacterial load, respectively. Flow cytometry was used to determine bacterial and somatic cell counts. Heatmaps were constructed and simple linear regressions and response screening analysis were performed. To facilitate data analysis and interpretation of the results, we dichotomized the BTM samples into high (HSCC, >200,000) and low somatic cell count (LSCC, ≤200,000) and into high (HSPC, >3.6) and low log₁₀ SPC (LSPC, ≤3.6). Spoilage-causing, spore-forming, and pathogenic bacteria of importance to the dairy industry were identified in the core microbiome. In addition, the taxa Thermoanaerobacterium and 5-7N15 were identified in the core microbiome; to our knowledge, these genera have not been previously identified in milk samples. Several bacterial genera were encountered in significantly higher relative abundances in the HSCC group when compared with the LSCC group, including Corynebacterium, Streptococcus, Lactobacillus, Coxiella, Arthrobacter, and Lactococcus. Additionally, several bacterial taxa were found in significantly higher relative abundances in the HSPC groups versus the LSPC groups: Acinetobacter, Enterobacteriaceae, Corynebacterium, and Streptococcus. In addition, Streptococcus was highly correlated with HSPC, and this genus was the second most abundant bacterial taxon detected in samples classified as HSCC. Bacterial diversity (Shannon index) was negatively correlated with bacterial load, suggesting that the microbiomes of high-bacterial load BTM samples are dominated by smaller groups of bacterial taxa. In conclusion, the associations described corroborated current knowledge about pathogens and spoilage bacteria in relationship to milk quality, and also indicated that other bacterial taxa should be a focus of further investigations.