Time series cluster analysis reveals individual assignment of microbiota in captive tiger (Panthera tigris) and wildebeest (Connochaetes taurinus)

Our objective was to characterize species specific and individual specific abundance patterns in the fecal microbiota of herbivores and carnivores, represented by wildebeests and tigers. We collected 95 fecal samples of 11 animal individuals and analyzed those with Illumina MiSeq sequencing of the V3V4 region of the 16SrRNA gene. In order to identify individual variations, we applied two different agglomerative hierarchical clustering algorithms a community detection algorithm and Wards linkage with and without prior dynamic time warping. Our results showed that both, species-specific as well as individual specific clustering is possible, but considerably more reliable results were achieved using dynamic time warping. Furthermore, the individual microbiota in both species was characterized by a combination of daily occurring core bacteria as well as individual dependent and more fluctuating bacterial families.