{
  "abstract": "The intestinal microbiota is considered as a true organ, playing major roles for its host. Dysbiosis has been shown in a number of diseases including inflammatory bowel diseases, metabolic disorders but also neurological disorders. However, little is known about the underlying mechanisms. In the present review, we attempted to summarize the different methods developed and used to study microbiota-host interactions and their limitations. Among the factors limiting our current understanding of the mechanisms of interaction between the gut microbiota and host cells, the difficulty of culturing most commensal bacteria and the complexity of the culture medium are of particular importance. The development of metagenomic approaches has been a decisive step towards understanding the functions of the intestinal microbiota. We have therefore developed a high-throughput functional metagenomic approach to overcome these limitations and identify bacterial genes and compounds regulating key signalling pathways or effector genes in mammalian immune, intestinal or liver cells. Genomic and metagenomic libraries were constructed by cloning large DNA fragments into a fosmid vector and using E. coli as the host. A highthroughput screening platform was established, enabling the identification of clones modulating pathways and genes in mammalian cells. Although the host is a gram-negative bacterium, it was possible to identify genes derived from the 3 main phyla present in the gut, namely Bacillota, Bacteroidota and Actinomycetota. This functional metagenomic strategy allowed to characterize new genes from commensal bacteria and effector molecules that have an impact on the host's cellular functions, with a potential influence on mammalian health.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "name": "Maxime Naour"
    },
    {
      "name": "Chaima Ezzine"
    },
    {
      "name": "Catherine Michel"
    },
    {
      "name": "Elliot Mathieu"
    },
    {
      "name": "Véronique Lejard"
    },
    {
      "name": "Gwenola Le Dréan"
    },
    {
      "name": "Jean-Marc Lelièvre"
    },
    {
      "name": "Nicolas Lapaque"
    },
    {
      "name": "Joël Doré"
    },
    {
      "name": "Hervé M Blottière"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/a5t9wr7p7pbbm.bib",
  "cited_by": 0,
  "doi": "10.1016/j.anscip.2025.07.002",
  "fulltext_url": null,
  "id": "a5t9wr7p7pbbm",
  "issns": [
    "2772-283X"
  ],
  "landing_url": "https://hal.inrae.fr/hal-05783203v1",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "hal",
      "0.sdv"
    ],
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W4413425178",
  "pdf_url": "https://hal.inrae.fr/hal-05783203/document",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-07",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/a5t9wr7p7pbbm.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:50Z",
      "native_id": "hal-05783203",
      "source": "hal",
      "url": "https://hal.inrae.fr/hal-05783203v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "1. An update on current methods for studying microbiome-host interactions in health and diseases",
  "title_text": "1. An update on current methods for studying microbiome-host interactions in health and diseases",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:50Z",
  "url": "https://research.draconitic.com/paper/a5t9wr7p7pbbm",
  "venue": "Animal. Science proceedings",
  "versions": []
}