<b>Cross-Comparison of Gut Metagenomic Profiling Strategies</b>

Advances in sequencing and bioinformatics have expanded metagenomic research, but consistent methodologies are essential. We evaluated DNA extraction methods, library preparation techniques, sequencing platforms, and computational tools using dog stool and synthetic samples. Our tool, minitax, standardizes results across platforms. The Zymo Quick-DNA HMW MagBead Kit, Illumina DNA Prep, and minitax were found to be the most effective. However, multiple methods are required to ensure reliable results.All supplementary data are available on Figshare.