RFW captures species-level metagenomic functions by integrating genome annotation information.

Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.