Comparative metagenomic profiling of canine gut microbial community using different sample preparation methodes
Dogs can be used as a model in human gut microbiome investigations, however the technique of sample preparation or type of DNA-isolation may influence the outcomes of any metagenomics survey. That is way it is important to standardize the whole workflow from the sample collection through the downstream bioinformatics applications.   In this study 4 different commonly used stool DNA-isolation kits were compared to analyze the same dog stool sample (ID=Toto) in quadruplicates. The microbial metagenome was sequenced by, Illumina Shot-gun and Illumina amplicon sequencing methods using the V1-V3, and V1-V2 and also V3-V4 16S rRNA regions, and long-read nanopore and PacBio using V1-V9 16S rRNA regions. Microbial community mix (Zymo) was used as base of standardization.  Based on the uploaded .fastq files a whole-diversity metagenomics microbiome analysis can be conducted, providing a useful insight into the experimental design not only of dog's microbiota, but the survey of human microbial community samples as well.