Fig. 1

Dendrogram illustrating the microbial composition in two babies, pre-weaning. Thirty-eight sequenced samples are shown, derived from DNA extracted using the Fast DNA SPIN Kit for Soil, which contains a bead-beating step, from nine distinct samples from two babies at different time points, amplified with four primer sets (Table 2), and a further single DNA extraction of one sample using the, non-bead-beating, Qiagen QIAamp kit. N-BF indicates samples from the natural birth, solely breast-fed infant. C-MF indicates samples from the C-section birth, mixed-feeding infant. The infant age at time of sampling is shown (in weeks). The dendrogram clearly shows the difference in composition, specifically the lack of bifidobacterial sequences, between the Qiagen kit (marked with QIA and red branches in the figure) and every other sample. Different PCR primer combinations are indicated by branch colouring: yellow—27f-YM primer; green—27f-Mix combination of forward primers; the two shades of blue represent samples processed with the 27f-Bif and Bif164 control primer sets. Adjacent bar charts show the bacterial composition of the sequence data at the family level. Using the 27f-Mix PCR primers increased detection of bifidobacterial sequences compared to using the 27f-YM primer, which has two mismatches to the Bifidobacterium genus