Is there a core microbiome in bovine milk samples from healthy quarters with somatic cell counts of less than 200,000 cells/mL?

Abstract Text: Recent analysis has shown that healthy bovine milk contains a commensal bacterial community. Rigorous data are not available on the bacterial community structure in bovine milk, thus it is unknown whether there is a ‘core’ microbiome within healthy bovine milk. Quarter milk samples were collected from 9 Holstein cows that had at least two low SCC quarters (<200,000 cells/mL). Characterization of the microbial community was performed by culture independent 454 pyrosequencing of amplicons from the V1-V3 region of the 16S rRNA gene to determine relative abundance. Cows were selected only if milk from at least two quarters was below 200,000 SCC. The relative abundance data show that most healthy quarters have bacterial communities that include Clostridium spp. (5-75% relative abundance), Pelomonas spp. (10-35% relative abundance), Duganella spp. (<5% relative abundance), Turicibacter spp. (0-10% relative abundance), and Sporacetigenium spp. (0-45% relative abundance), with all samples having a large influence from unclassified bacterial spp (5-55% relative abundance). The Shannon and Chao diversity indices of the bacterial communities between cows were not different (P>0.1) suggesting similar distribution of community membership. Analysis by PCoA using the Bray dissimilarity matrix showed strong clustering based on the relative abundance of Clostridium spp., which was a major contributor in all healthy quarter samples. No clustering based on SCC was apparent among the samples. Clustering of healthy quarters within cow was also not discernable suggesting a high variation in the bacterial community even between quarters of the same cow. These results propose a highly variable bacterial community exists in bovine milk even between healthy quarters within a cow. Though there appears to be no obvious ‘core’ set of bacterial members, the variation present could account for similar functional roles within quarter milk bacterial community. This work was supported by the Idaho Agricultural Experiment Station, NIH grants P20 RR15587 and P20 RR016454 and the Institute for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.

Keywords: Milk, bacteria, microbiome