{
  "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.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "name": "Alejandra Escobar-Zepeda"
    },
    {
      "name": "Matti O. Ruuskanen",
      "orcid": "0000-0003-4221-2880"
    },
    {
      "name": "Martin Beracochea"
    },
    {
      "name": "Jennifer Lu"
    },
    {
      "name": "Dattatray Mongad"
    },
    {
      "name": "Lorna Richardson"
    },
    {
      "name": "Robert D. Finn"
    },
    {
      "name": "Leo Lahti"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ce9ezy7z0tvd0.bib",
  "cited_by": 0,
  "doi": "10.1186/s13059-026-04303-8",
  "fulltext_url": null,
  "id": "ce9ezy7z0tvd0",
  "issns": [
    "1474-760X"
  ],
  "landing_url": "https://link.springer.com/article/10.1186/s13059-026-04303-8",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7223007109",
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-21",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/ce9ezy7z0tvd0.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:06Z",
      "native_id": "10.1186/s13059-026-04303-8",
      "source": "crossref",
      "url": "https://link.springer.com/article/10.1186/s13059-026-04303-8"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes",
  "title_text": "BioSIFTR: functional inference from shallow shotgun sequencing using biome-specific genome catalogues benchmarked in gut microbiomes",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:06Z",
  "url": "https://research.draconitic.com/paper/ce9ezy7z0tvd0",
  "venue": "Genome Biology",
  "versions": []
}