{
  "abstract": "Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.",
  "abstract_shown": true,
  "affiliations": [
    "University of California San Diego"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 20,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "M. O. Din"
    },
    {
      "name": "C. Brennan"
    },
    {
      "name": "J. Zhao"
    },
    {
      "name": "R. Oles"
    },
    {
      "name": "L. Patel"
    },
    {
      "name": "A. Birmingham"
    },
    {
      "name": "D. M. Sevilir"
    },
    {
      "name": "L. Hansen"
    },
    {
      "name": "G. M. Wright"
    },
    {
      "name": "M. Ambre"
    },
    {
      "name": "M. Tomita"
    },
    {
      "name": "T. Boyer"
    },
    {
      "name": "A. Gonzalez"
    },
    {
      "name": "G. Ackermann"
    },
    {
      "name": "D. McDonald"
    },
    {
      "name": "S. Kralicek"
    },
    {
      "name": "G. Hecht"
    },
    {
      "name": "J. Hasty"
    },
    {
      "name": "L. Smarr"
    },
    {
      "name": "R. Knight"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/c37xax7pgvq35.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.28.754546",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.28.754546v1.full",
  "id": "c37xax7pgvq35",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.28.754546v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ],
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7214928097",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.28.754546v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-28",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/c37xax7pgvq35.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:17Z",
      "native_id": "10.64898/2026.09.28.754546",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.28.754546v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics",
  "title_text": "Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:17Z",
  "url": "https://research.draconitic.com/paper/c37xax7pgvq35",
  "venue": "bioRxiv",
  "versions": []
}