{
  "abstract": "Integrating multi-omics data is essential for microbiome research, as microbial communities are shaped by and respond to interdependent processes, including taxonomic composition, metabolite production and utilization, and gene expression. However, accurately capturing ecosystem-wide patterns across these modalities is statistically challenging due to differences in scale, sparsity, and compositionality. While a growing number of multi-omics methods have emerged, they differ in their mathematical objectives and modeling assumptions, which in turn shape how biological patterns are represented and interpreted. This underscores the need for tools that explicitly account for the statistical properties of microbial ecosystems. Here, we present Joint Robust Principal Component Analysis (Joint-RPCA), a method designed with these statistical properties in mind and broadly applicable to multi-omics settings with similar challenges. Built on the OptSpace matrix completion framework, Joint-RPCA assumes an underlying shared low-rank structured component across modalities to identify shared variation and cross-modal associations from matched samples. Within this setting and under these statistical assumptions, Joint-RPCA showed stronger performance than the benchmarked general-purpose methods in phenotype separation and feature association tasks, achieving up to sixfold improvement in classification accuracy and over 100-fold faster runtimes. Applied to real-world datasets, including the Integrative Human Microbiome Project (iHMP), mammalian gut microbiomes, and decomposition studies, Joint-RPCA reveals replicable and interpretable multi-omic patterns, offering a scalable and domain-aware solution for systems-level microbiome analysis. Joint-RPCA is available in both Python (https://github.com/biocore/gemelli) and R (https://bioconductor.org/packages/mia).",
  "abstract_shown": true,
  "affiliations": [
    "Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY USA",
    "Leaven Foods, San Diego, CA USA",
    "Department of Pediatrics, University of California San Diego, La Jolla, CA USA",
    "Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA USA",
    "Department of Animal Sciences, Colorado State University, Fort Collins, CO USA",
    "Department of Microbiology, University of Tennessee, Knoxville, TN USA",
    "Department of Computing, FI-20014 University of Turku, Turku, Finland",
    "Department of Public Health, Finnish Institute for Health and Welfare, Helsinki, Finland",
    "Department of Internal Medicine, Turku University Hospital and University of Turku, Turku, Finland",
    "Institute for Molecular Medicine Finland, FIMM- HiLIFE, Helsinki, Finland",
    "Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada",
    "National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel",
    "Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel",
    "Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva, Israel",
    "Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA",
    "Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA",
    "Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA USA",
    "Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA USA",
    "Department of Bioengineering, University of California San Diego, San Diego, La Jolla, CA USA",
    "Department of Microbiology, New York University Grossman School of Medicine, New York, NY USA",
    "Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY USA",
    "Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY USA"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 22,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Bianca Cordazzo Vargas",
      "orcid": "0009-0001-9562-593X"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Cameron Martino",
      "orcid": "0000-0001-9334-1258"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Amanda Hazel Dilmore"
    },
    {
      "affs": [
        4
      ],
      "name": "Jessica L Metcalf"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Zachary M Burcham",
      "orcid": "0000-0003-1600-9643"
    },
    {
      "affs": [
        6
      ],
      "name": "Leo Lahti",
      "orcid": "0000-0001-5537-637X"
    },
    {
      "affs": [
        6
      ],
      "name": "Aituar Bektanov",
      "orcid": "0009-0005-5609-5525"
    },
    {
      "affs": [
        6
      ],
      "name": "Tuomas Borman"
    },
    {
      "affs": [
        7
      ],
      "name": "Veikko Salomaa",
      "orcid": "0000-0001-7563-5324"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Teemu Niiranen",
      "orcid": "0000-0002-7394-7487"
    },
    {
      "affs": [
        6,
        7,
        9
      ],
      "name": "Aki S Havulinna"
    },
    {
      "affs": [
        10
      ],
      "name": "Rachel Gregor",
      "orcid": "0000-0003-4071-9573"
    },
    {
      "affs": [
        11,
        12
      ],
      "name": "Stav Eyal"
    },
    {
      "affs": [
        11,
        13
      ],
      "name": "Michael M Meijler",
      "orcid": "0000-0001-7095-1467"
    },
    {
      "affs": [
        11,
        12
      ],
      "name": "Itzhak Mizrahi",
      "orcid": "0000-0001-6636-8818"
    },
    {
      "affs": [
        14
      ],
      "name": "Se Jin Song"
    },
    {
      "affs": [
        14
      ],
      "name": "Andrew Bartko"
    },
    {
      "affs": [
        2,
        14,
        15,
        16
      ],
      "name": "Pieter C Dorrestein"
    },
    {
      "affs": [
        2,
        17
      ],
      "name": "James T Morton",
      "orcid": "0000-0003-3189-2681"
    },
    {
      "affs": [
        2
      ],
      "name": "Daniel McDonald"
    },
    {
      "affs": [
        2,
        15,
        17,
        18
      ],
      "name": "Rob Knight"
    },
    {
      "affs": [
        0,
        19,
        20,
        21
      ],
      "name": "Liat Shenhav",
      "orcid": "0000-0003-1708-6050"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3gd4kp62eb445.bib",
  "cited_by": 0,
  "doi": "10.1038/s44320-026-00236-3",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13728224/",
  "id": "3gd4kp62eb445",
  "issns": [
    "1744-4292"
  ],
  "landing_url": "https://doi.org/10.1038/s44320-026-00236-3",
  "language": "en",
  "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": [
    [
      "heading",
      "Method"
    ],
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7203600515",
  "pdf_url": "https://link.springer.com/content/pdf/10.1038/s44320-026-00236-3.pdf",
  "pmcid": "PMC13728224",
  "pmid": "42608579",
  "published": "2026-08-18",
  "publisher": "Nature Publishing Group",
  "ris": "https://research.draconitic.com/paper/3gd4kp62eb445.ris",
  "sources": [
    {
      "first_seen": "2026-11-06T12:23:57Z",
      "native_id": "PMC13728224",
      "source": "pmc",
      "url": "https://doi.org/10.1038/s44320-026-00236-3"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Joint-RPCA: domain-aware multi-omics integration for systems microbiology",
  "title_text": "Joint-RPCA: domain-aware multi-omics integration for systems microbiology",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T12:21:15Z",
  "url": "https://research.draconitic.com/paper/3gd4kp62eb445",
  "venue": "Molecular Systems Biology",
  "versions": []
}