Core microbiome identification

Question

[vikasmh111]

I have classified the organisms in my metagenomic shotgun sequencing data using metaphlan3. With metaphlan3 output, can I identify the core microbiome?

Or is there a way I can convert metaphlan3 output to phyloseq input format and use Core microbiome R package?

[cpad0112]

import metaphlan3 data into phyloseq: https://github.com/wipperman/wipperman/blob/master/R/microbiota.R and What are the input files for lwaldron / metaphlanToPhyloseq.R ?.