Figure 1.

Experimental set‐up for one volunteer for one time point measurement. This set‐up was performed for all three volunteers, each at two different time points. Selection of best assay each round was based on Nanodrop and Qubit quantification and quality assessment and quantification by means of qPCR for Escherichia coli, Bifidobacterium spp. and all bacterial species. Procedure was carried out twice on two different days in duplicate. n: Number of faecal samples used; PK: proteinase K pre‐treatment; M: mutanolysin pre‐treatment; B: bead beating pre‐treatment; RNase: RNase treatment followed by a DNA purification step; EM: semi‐automated NucliSens easyMag; QIA: QIAamp DNA Stool Mini kit; PL: PureLink Microbiome DNA Purification kit; PF: QIAamp PowerFecal DNA kit; PM: RNeasy PowerMicrobiome kit; light grey: mechanical lysis; dark grey: combination of mechanical and enzymatic lysis; light blue: no enzymatic or mechanical lysis; dark blue: enzymatic lysis. [Colour figure can be viewed at wileyonlinelibrary.com]