two-week microbiome (ZWoMi)

Human microbiome data are commonly obtained by sequencing amplicons of the 16S rRNA gene using DNA isolated from fecal samples. Microbial composition of stool samples varies spatially within each sample and temporally between one sample and the other. It is important to know the extent of these variations to determine the imporance of homogenization and multiple sampling (including samples from different timepoints). We collected stool samples from 6 healthy adult volunteers on 10 days in a 2-week perion and determined the microbial composition by sequencing amplicons of variable region V4 of the 16S rRNA gene. In addition multiple aliquots were takes from a subset of stool samples before homogenization to determine spatial variation. All samples were also subjected to flow cytometry based cell counting to determine the total bacterial load (following the protocol by Vandeputte et al., doi: 10.1038/nature24460). As an alternative method, another subset of sample aliquots was spiked with a mix of two known bacterial species (Alicyclobacillus acidophilus and Rhizobium radiobacter) to normalize microbial counts (following the protocol by Stämmler et al, doi: 10.1186/s40168-016-0175-0).