Peer-reviewedCC BY 4.0Genome Biology
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.
Related
- Uncovering spatially resolved functional genomics with CRISPR screen sequencing
- Library strategies differentially shape microbial, functional, and host signals in clinical metagenomic sequencing
- From microbiomes to predictive ecosystems: challenges and opportunities in artificial intelligence-based approaches
- Microbiome Continuum: Connecting Environmental, Host-Associated and Engineered Microbiomes Through One Health and Artificial Intelligence.
- Global Analysis of Public Cheese Microbiomes Reveals Widespread Bacterial Taxa and Geographic Community Structure
BibTeX
@article{escobarzepeda2026biosiftr,
title = {{BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes}},
author = {Alejandra Escobar-Zepeda and Matti O. Ruuskanen and Martin Beracochea and Jennifer Lu and Dattatray Mongad and Lorna Richardson and Robert D. Finn and Leo Lahti},
journal = {Genome Biology},
year = {2026},
month = oct,
doi = {10.1186/s13059-026-04303-8},
url = {https://link.springer.com/article/10.1186/s13059-026-04303-8},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes
AU - Alejandra Escobar-Zepeda
AU - Matti O. Ruuskanen
AU - Martin Beracochea
AU - Jennifer Lu
AU - Dattatray Mongad
AU - Lorna Richardson
AU - Robert D. Finn
AU - Leo Lahti
PY - 2026
DA - 2026/10/21
JO - Genome Biology
DO - 10.1186/s13059-026-04303-8
UR - https://link.springer.com/article/10.1186/s13059-026-04303-8
AB - 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.
SN - 1474-760X
ER -