Fig. 2

Analysis of mock community HM-783D. The expected relative abundances of genera in the mock community sample is presented next to that observed in the sequencing output across the three setups. The Escherichia genus consisted of ASVs classified to family level (Enterobacteriaceae); ASV ffc36e27c82042664a16bcd4d380b286 dominated Setup 1 targeting the 16S rRNA gene V3 V4 region and ASV d46e2205f0c6ecf67b51f83d111c509c dominated Setups 2 and 3 targeting the V4 region. Using the NCBI blastn tool we were able to confirm that these ASVs belonged to the Escherichia coli genus. Bioinformatics processing steps were limited to DADA2, VSEARCH, taxonomy assignment and removal of features not classified at minimum to phylum level. Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region)