{
  "abstract": "Multi-omics approaches have revolutionized our understanding of microbial communities by enabling simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic data. The systematic integration and analysis of these deep datasets help decipher the functional roles of microbiomes, providing critical insights into microbial activities, interactions, and dynamics across diverse environments. Biological complexity makes multi-omics analysis of a single, isolated organism demanding but highly informative, yet this complexity increases further when samples comprise hundreds to thousands of individual species. As microbiome research continues to expand into clinical, environmental, and engineered systems, standardized workflows, benchmarked datasets, and community-driven initiatives are essential to ensure reproducibility, standardization and interpretability. Establishing and disseminating best practices for experimental design, data processing, and integrative analyses will be critical for maximizing comparability and scientific rigor across studies. This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence (AI) advances comparable to those of AlphaFold in the field of microbiome science.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
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  "author_total": 45,
  "authors": [
    {
      "name": "Tim van den Bossche"
    },
    {
      "name": "Eunice Adeline Lazau"
    },
    {
      "name": "Velma Aho"
    },
    {
      "name": "J. Alfredo Blakeley-Ruiz"
    },
    {
      "name": "Maximilian Wolf"
    },
    {
      "name": "Benoit Josef Kunath"
    },
    {
      "name": "Luis Valentin-Alvarado"
    },
    {
      "name": "Patrick Hellwig"
    },
    {
      "name": "Pieter Verschaffelt"
    },
    {
      "name": "Andrew Rajczewski"
    },
    {
      "name": "Jannie. Henderickx"
    },
    {
      "name": "Tomi Suomi"
    },
    {
      "name": "Feng Xian"
    },
    {
      "name": "Shruti Shah"
    },
    {
      "name": "Lennart Martens"
    },
    {
      "name": "Dirk Benndorf"
    },
    {
      "name": "Samir Damare"
    },
    {
      "name": "Bastiaan Willem Haak"
    },
    {
      "name": "Sven-Bastiaan Haange"
    },
    {
      "name": "Paul Piehowski"
    },
    {
      "name": "Anne Kupczok"
    },
    {
      "name": "Daniel Figeys"
    },
    {
      "name": "Bart Mesuere"
    },
    {
      "name": "Magnus Palmblad"
    },
    {
      "name": "Robert Hettich"
    },
    {
      "name": "Laura Elo"
    },
    {
      "name": "Juan Antonio Vizcaíno"
    },
    {
      "name": "Neha Garg"
    },
    {
      "name": "Zhong Wang"
    },
    {
      "name": "Muzaffer Arıkan"
    },
    {
      "name": "Lee Ann Mccue"
    },
    {
      "name": "Timothy Griffin"
    },
    {
      "name": "Laure-Alix Clerbaux"
    },
    {
      "name": "Robert Heyer"
    },
    {
      "name": "Marnix Medema"
    },
    {
      "name": "Sabine Matallana-Surget"
    },
    {
      "name": "David Gomez-Varela"
    },
    {
      "name": "Thilo Muth"
    },
    {
      "name": "Bree Tillett"
    },
    {
      "name": "Jean Armengaud"
    },
    {
      "name": "Robert Finn"
    },
    {
      "name": "Paul Wilmes"
    },
    {
      "name": "J. Gregory Caporaso"
    },
    {
      "name": "Lucia Grenga"
    },
    {
      "name": "Pratik Dilip Jagtap"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d39jhzq0d05v9.bib",
  "cited_by": 1,
  "doi": "10.1038/s41467-026-77539-4",
  "fulltext_url": null,
  "id": "d39jhzq0d05v9",
  "issns": [
    "2041-1723",
    "2041-1723"
  ],
  "landing_url": "https://hal.science/hal-05768814v1",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "hal",
      "0.sdv"
    ],
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7211944669",
  "pdf_url": "https://www.nature.com/articles/s41467-026-77539-4.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-08",
  "publisher": "Nature Publishing Group",
  "ris": "https://research.draconitic.com/paper/d39jhzq0d05v9.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:43Z",
      "native_id": "hal-05768814",
      "source": "hal",
      "url": "https://hal.science/hal-05768814v1"
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  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Integrating multi-omics technologies to decipher microbiome functions",
  "title_text": "Integrating multi-omics technologies to decipher microbiome functions",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:43Z",
  "url": "https://research.draconitic.com/paper/d39jhzq0d05v9",
  "venue": "Nature Communications",
  "versions": []
}