BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes

Abstract Shallow shotgun sequencing is an accurate microbiome profiling method, but its use for functions is limited. BioSIFTR extrapolates shallow shotgun read mapping to precalculated pangenome functions in 15 MGnify biome-specific catalogues, which span host-associated and environmental microbiomes. We benchmarked BioSIFTR on synthetic communities and on three gut microbiomes — red junglefowl, mouse, and human — using matched deep shotgun and 16S rRNA metabarcoding data, outperforming similar approaches. Further validation will require matched benchmark datasets and is a priority for future work. BioSIFTR is thus a practical method for functional inference from cost-effective shallow shotgun sequencing, currently validated in gut microbiomes.