Fig. 2

Effect of DNA method on each step of typical bioinformatics analysis pipeline. The left and right columns show organisation by per method and per sample basis, respectively. In terms of the total useful reads that are mapped to OTU, QIAG kit performed better than the other two methods as roughly 50 % of the reads were mapped to OTUs during the construction stage (see Additional file 2 : Table S1 for actual read numbers and Additional file 1 : Figure S1 summary statistics). In terms of quality trimming, QIAG lost more reads than the other two methods. ED, AB, IM correspond to the three faecal sample and VSL to the proprietary probiotic capsule ID respectively