Similarity in milk microbiota in replicates

In this study DNA from 44 bovine milk samples were extracted twice and the V3-V4 region of the 16S rRNA gene was sequenced in two separate runs. The same bioinformatics pipeline was used and results from the two data sets were compared. Results show a significant difference in species richness between the two sequencing runs although Shannon and Simpson diversity was the same. Multivariate analyses of all samples demonstrate that sequencing run was a driver for variation. Direct comparison of similarity between samples and sequencing run showed an average similarity of 42-45% depending on if binary or abundance-based similarity indices were used.