Assessment of bacterial diversity in bovine bulk tank milk samples from Brazil

This research aimed to analyze and compare bacterial diversity in bulk tank milk (BTM) samples from five Brazilian regions using 16 S rRNA gene sequencing, while correlating this diversity with Somatic Cell Count (SCC) values. A total of 57 samples from Santa Catarina, São Paulo, Minas Gerais, Goiás, Maranhão, Pará, and Tocantins were sequenced through Next Generation Sequencing (NGS). The analysis revealed one kingdom, four phyla, six classes, 14 orders, 28 families, and 43 genera, with Moraxellaceae (22.3%), Streptococcaceae (14.1%), Acetobacteraceae (13.8%), Pseudomonadaceae (11.0%), and Enterococcaceae (9.0%) as the main families, and Acinetobacter (22.3%), Pseudomonas (11.7%), and Acetobacter (8.1%) as the main genera. Alpha diversity differed significantly in Maranhão and Pará compared to Goiás (set as baseline for comparing alpha diversity across regions), as indicated by Fisher, Chao1, and ACE indices (p < 0.05). In terms of beta diversity, significant differences (p < 0.001) were found among the states, highlighting the heterogeneity of these communities inside the country. While high and low SCC groups showed no significant differences in alpha diversity (p > 0.05), beta diversity did exhibit significant variation (p < 0.001). Tracking the bacterial diversity and SCC found in BTM samples using advanced molecular technologies allowed us to understand microbial diversity for future strategy development, consequently improving the quality and safety of the milk produced on Brazilian farms.