Microbiome.jl is a Julia package to facilitate analysis of microbial community data. BiobakeryUtils.jl is built on top of Microbiome.jl, and provides utilities for working with a suite of command line tools (the bioBakery) that are widely used for converting raw metagenomic sequencing data into tables of taxon and gene function counts. Together, these packages provide an effective way to link microbial community data with the power of Julia’s numerical, statistical, and plotting libraries.