Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2

The characterization of complex microbial communities is a pressing need in the field of microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we introduce Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights into metagenomic samples. To benchmark its performance, we simulated human and mouse gut microbiota samples and compared Meteor2 against established tools for TFSP. Meteor2 demonstrated strong performance in these benchmarks, particularly excelling in sensitivity in detecting low-coverage species while maintaining high specificity in TFSP. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, showcasing its ability to deliver an extensive and actionable metagenomic analysis. These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.