Fig. 5

Removal of contaminants identified by decontam reduces technical variation in dilution series of S. bongori. A dilution series of 0, 1, 2, 3, 4, and 5 ten-fold dilutions of a pure culture of Salmonella bongori was subjected to a amplicon sequencing of the 16S rRNA gene at three sequencing centers and b shotgun sequencing using three different DNA extraction kits. Contaminants were identified by the decontam frequency method with a classification threshold of P* = 0.0 (no contaminants identified), P* = 0.1 (default), and P* = 0.5 (aggressive identification). After contaminant removal, pairwise between-sample Bray-Curtis dissimilarities were calculated, and an MDS ordination was performed. The two dimensions explaining the greatest variation in the data are shown