Differences in microbiome variability of carnivores and herbivores. First Submission

hrough the rapid development in third generation sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species or animal groups at the same time in order to obtain a general overview of the microbiome. However, there is still uncertainty on the variability of the microbiome of different animal groups and on whether certain bacteria within a species are subject to greater fluctuations than others. However, this is of interest to conduct studies with few samples per species and thus to be able to compare groups of animals on the basis of a few representatives. In our study, we aim to close this knowledge gap by analyzing multiple samples of species from four mammalian groups: Ruminantia, Perissodactyla, Canoidea and Feloidea with the individuals studied living in different zoos. Studying zoo-housed animals offers the possibility to control for external factors such as nutrition, age and pedigree, because these general conditions are well-known. To assess microbial diversity, multiple fecal samples were characterized by sequencing the V3-V4 region of the 16S rRNA gene using Illumina MiSeq.We found significant differences in the microbial diversity and composition between carnivore and herbivore species. The microbiome of both herbivore groups is more uniform and constant within and between species than that of carnivores. Canoidea as well as Feloidea show a highly diverse microbiome, which is inconsistent within their species. Especially Fusobacteriaceae, which is among the dominant bacterial families within carnivores, shows the greatest deviations within the species. Additionally, some species deviate in their microbial composition from other members of their respective dietary group such as Ursus arctos, Ursus maritimus and Ailurus fulgens. Especially Fusobacteriaceae only occurs in minor proportions within those animals, whereas Erysipelochtrichaceae and Enterobacteriaceae are the dominant inhabitants of the microbiome. In contrast to herbivores, the microbiome of carnivores is highly diverse. This high variability leads to new methodological aspects to consider for microbiome studies. When conducting research on carnivore species, it is necessary to collect and analyze a minimum amount of samples per species and individuals to adjust for this volatility. For herbivores in contrast, it might be sufficient to work with a few samples per species due to their similarity within species and across species boundaries.