I am analyzing the taxonomic profiling of my shotgun data. Which are 100bp paired-end reads from Illumina Hiseq. Now I am using Metaphlan2 to do the metagenomics profiling. However, the profiling result is far away from Illumina 16S miseq results. Since I have also been using Illumina 16S Miseq to test the taxonomy of my samples for several years. I have two the control samples and treatment samples. In Metaphlan2 results, it gave me around 30% archaea and 70% bacteria for control samples, while Miseq 16S reads tell me that only around 15% archaea and 85% bacteria for control samples. For treatment, shotgun profiling told me 60% archaea and 40% bacteria, while Miseq gave me 20% archaea and 80% bacteria. For my experience, this kind of sample could not achieve that much archaea abundance than bacteria. Furthermore, some(not all) bacteria and archaea composition are different between Miseq result and Metaphlan2 result.
Why is the result so different? Are there any suggestions why the two method result differs so much?
I am confused.