Development and evaluation of a three-stage ensemble model to identify host-related metadata from fecal microbiota of zoo-housed mammals

In this study, we aim to describe the influence of the three factors diet, digestive system, and host on the microbiota in order to develop a model that is able to characterize host-specific metadata from an unknown fecal sample. While herbivores show positive correlations with a large number of bacterial taxa, we found fewer taxa correlating with carnivores or omnivores. We also detected considerable differences in the microbiota of the ruminant, hindgut fermenting, and simple digestive system. Based on these results, we developed a three-stage logistic ensemble model, that predicts first the diet, second the digestive system, and third the host family from a given microbiota composition of a fecal sample. This model is able to effectively discriminate herbivores, omnivores, and carnivores.