CNPS.cycle: streamlining shotgun metagenomic data analysis for biogeochemical cycles

Shotgun metagenomic data analysis for investigating biogeochemical cycles in the environment remains challenging, primarily due to the steep learning curve, intensive time investment, and high computational demands, all of which pose significant barriers for many researchers. We present a new R package called “CNPS.cycle,” designed to streamline the interpretation of shotgun metagenomic data related to biogeochemical processes, complete with visually informative outputs. This comprehensive package comprises four distinct analysis modules, focused on carbon, nitrogen, phosphorus, and sulfur cycling. Users can easily utilize the package by uploading annotation result files derived from shotgun metagenomic data, specificallyspecificallythose based on the Kyoto Encyclopedia of Genes and Genomes and the NCBI non-redundant protein sequence database. The package then automates essential steps, including data preprocessing, curation, and differential analysis of biogeochemical cycle-related genes; analysis of microorganisms possessing biogeochemical cycle-related genes at the contig level; β-diversity analysis; and, finally, data visualization. The outcome is a comprehensive analysis revealing differentially abundant genes and functionally significant microbial entities associated with the carbon, nitrogen, phosphorus, and sulfur cycles, presented in the form of tables and high-quality images. This tool will provide profound insights into the relationship between soil microorganisms and elemental chemical cycles, thereby advancing our comprehension of soil ecosystems. For accessibility, the CNPS.cycle package is available on GitHub (https://github.com/yuezhengfu/CNPS.cycle), where detailed instructions on its usage can be found in the project’s GitHub page (https://github.com/yuezhengfu/CNPS.cycle/wiki).