Meta Analysis of Paired Short-read 16S V4, Full-length 16S, and Shotgun Metagenomic Profiling

This study evaluates the concordance between amplicon and shotgun sequencing approaches for microbiome profiling. The dataset comprises a total of 54 samples derived from human fecal material and defined mock communities. To assess taxonomic resolution and technical biases, we generated matched data for each sample using three distinct sequencing strategies: (1) Short-read 16S rRNA gene sequencing targeting the V4 region (n=18); (2) Full-length 16S rRNA gene sequencing (n=18); and (3) Shotgun metagenomic sequencing (n=18). These data support the development of bioinformatic frameworks for harmonizing taxonomic assignments across variable-region amplicon, long-read amplicon, and shotgun metagenomic platforms.