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

ABSTRACT 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, specifically those 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 ). IMPORTANCE The “CNPS.cycle” R package offers significant environmental implications by simplifying the analysis of shotgun metagenomic data related to biogeochemical cycles. Its automated workflow identifies key genes and microbes involved in carbon, nitrogen, phosphorus, and sulfur cycling, enhancing our understanding of microbial contributions to ecosystem functions. This tool enables researchers to explore microbial-mediated nutrient cycling more efficiently, supporting informed decisions in environmental management and climate change mitigation. By providing accessible, high-quality outputs, “CNPS.cycle” facilitates data-driven insights into the interplay between microbes and global biogeochemical processes.