Microbial profile of short-beaked echidna: feces with Eimeria echidnae
To identify the eukaryotes present in the diagnostic specimen, we used a community profiling based amplification 454 sequencing approach of conserved eukaryotic SSU rDNA. Extraction of genomic DNA from fecal (150 mg) sample was performed using a FastDNA spin kit for soil (MP Biomedicals, Australia) according to the manufacturer’s instructions assisted by the FastPrep-24 homogeniser (MP Biomedicals, Australia). The gDNA was submitted to the diversity profiling service at the Australian Genomic Research Facility, Australia. The SSU rDNA assay applied was based on primer pair Euk1A (5’-CTGGTTGATCCTGCCAG-3’) and Euk516 (5’-CCAGACTTGCCCTCC-3’), amplifying approximately 500-550 bp of the 5’-end of the eukaryotic SSU rDNA. The barcoded PCR amplicon was pooled and sequenced on the 454 GS‐FLX platform.