Analysis of milk microbial profiles using 16s rRNA gene sequencing in milk somatic cells and fat (original) (raw)

Recent work using 16s rRNA sequencing has led to the understanding that milk microbiota is complex, harboring great multifunctional diversity. An important question is if milk in the mammary gland is sterile and bacteria come from the external environment or if there are endogenous bacteria present in milk. In the present study, we performed a preliminary metagenome analysis of bovine milk by sequencing the V1-V2 hypervariable regions of 16S rRNA gene. Milk samples were collected from the same cow at 3 different stages of lactation (15, 90, 120 dim), with and without using a cannula. Microbial DNA was extracted from two tissues, somatic cells and fat. Our findings showed: 1) The microbiota structure of the two tissues was completely different (adonis R 2 = 0.68, p-value=0.001). Fat samples present a uniform profile composed of three highly abundant bacterial genera: Janthinobacterium, Acinetobacter and Pseudomonas. Microbiota from somatic cells presents significantly higher diversity and more variability in the taxonomic profile. 2) Most of the taxonomic divergences among lactation days were found in fat samples obtained with no cannula. 3) Comparing milk fat samples from mastitic and healthy quarters, taxonomic profiles of healthy quarters were more homogeneous then affected quarters. This observation could be linked to the so called, Anna Karenina Principle, that states that dysbiotic samples vary more in microbial community composition than healthy samples (Zaneveld et al. Nat. Micro 2017). The focus of this study was to develop the sampling and analytical methodology to assess milk microbiota in somatic cells and fat tissues. Although a larger number of samples are needed to support some of our observations, we feel examining milk microbiota in these two tissues will prove to be scientifically insightful.

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