Fig. 1

Schematic diagram of the geneshot tool for gene-level metagenomic analysis of microbiome experiments. a Description of the data flow through geneshot, with the coordinated execution of multiple constituent bioinformatic processes in order to analyze the experimental data on the basis of protein-coding genes encoded by microbes present in each physical specimen. De novo assembly is performed independently for each biological specimen, and the resulting protein-coding sequences are aggregated across all assemblies prior to deduplication. Alignment of WGS reads to the deduplicated gene catalog is performed independently for each specimen, and the resulting abundance data is aggregated across all specimens in order to compute pairwise gene co-abundance values. b Summary of the geneshot analysis to identify microbes associated with ICI response from published WGS datasets, indicating the number of biological features identified at each step