Thank you for this nice question. Microbiome study is being conducted using two metagenomic approaches; the targeted or 16S rRNA approach and Shotgun/whole metagenome sequencing (WMS) approach. The first one is more widely in applications but has some inherent drawbacks. The later one (WMS) is the best one in terms of microbiome coverage and their genomic functional potentials prediction. In analyzing the data from these two techniques of microbiome study, the available bioinformatics tools also varied. For 16S rRNA microbiome data, QIIME, MOTHUR, IDSeq, Galaxy etc. can be used. However, shotgun/WMS microbiome data analysis is a bit cumbersome, you can prefer PathoScope 2.0, MG-RAST, IDSeq for taxonomic identification, and VFDB, Bacmet and ResFinder form functional genomic profiling.