Intestinal biome sequencing of carnivores

Intestinal eukaryotes are investigated for their role as pathogens but remain hard to assess comprehensively. Comprehensive bacterial microbiomes are routinely characterised in intestines of humans, domestic and wild animals using sequencing of amplification products from PCRs obtained with (more or less) universally binding primers. For eukaryotes comprehensive amplification remains challenging due to the unclear status of evolutionary conservation of primer binding sites even in the small ribosomal subunit (SSU) rRNA gene.We here used 48 PCR reactions targeting different regions of the SSU gene, resulting in 44 different amplicons for the eukaryotic 18S SSU and four for the bacterial 16S SSU. We used a microfluidics amplification system which allows efficient handling and amplification in parallel reactions. We assess the capabilities of this system using a carefully replicated and controlled experimental design and assess the bacterial and eukaryotic intestinal biome of two carnivore species: the spotted hyena and the grey wolf.