{"doi":"10.1093/nar/gkab786","title":"gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites","abstract":"gutMGene (http://bio-annotation.cn/gutmgene), a manually curated database, aims at providing a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice. Metagenomic sequencing of fecal samples has identified 3.3 × 106 non-redundant microbial genes from up to 1500 different species. One of the contributions of gut microbiota to host biology is the circulating pool of bacterially derived small-molecule metabolites. It has been estimated that 10% of metabolites found in mammalian blood are derived from the gut microbiota, where they can produce systemic effects on the host through activating or inhibiting gene expression. The current version of gutMGene documents 1331 curated relationships between 332 gut microbes, 207 microbial metabolites and 223 genes in humans, and 2349 curated relationships between 209 gut microbes, 149 microbial metabolites and 544 genes in mice. Each entry in the gutMGene contains detailed information on a relationship between gut microbe, microbial metabolite and target gene, a brief description of the relationship, experiment technology and platform, literature reference and so on. gutMGene provides a user-friendly interface to browse and retrieve each entry using gut microbes, disorders and intervention measures. It also offers the option to download all the entries and submit new experimentally validated associations.","journal":"Nucleic Acids Research","year":2021,"id":1287,"datarank":4.000022082908504,"base_score":5.153291594497779,"endowment":5.153291594497779,"self_citation_contribution":0.772993739174667,"citation_network_contribution":3.2270283437338363,"self_endowment_contribution":0.772993739174667,"citer_contribution":3.2270283437338363,"corpus_percentile":94.45346948247854,"corpus_rank":718,"citation_count":172,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9538,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-09-09","fair_score":41.6667,"fair_percentile":54.173035768878016,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":16292,"name":"Changlu Qi","orcid":null,"position":1,"is_corresponding":false},{"id":16293,"name":"Haixiu Yang","orcid":"0000-0002-7161-1656","position":2,"is_corresponding":false},{"id":16294,"name":"Minke Lu","orcid":null,"position":3,"is_corresponding":false},{"id":16295,"name":"Yiting Cai","orcid":"0000-0001-6295-6989","position":4,"is_corresponding":false},{"id":16296,"name":"Tongze Fu","orcid":null,"position":5,"is_corresponding":false},{"id":16297,"name":"Jialiang Ren","orcid":null,"position":6,"is_corresponding":false},{"id":16298,"name":"Qu Jin","orcid":null,"position":7,"is_corresponding":false},{"id":16299,"name":"Xue Zhang","orcid":"0009-0004-0249-0581","position":8,"is_corresponding":false},{"id":16291,"name":"Liang Cheng","orcid":"0000-0002-6665-6710","position":0,"is_corresponding":true}],"reference_count":25,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"34500458","pmcid":"PMC8728193","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by-nc","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":61.1111,"fair_a":75.0,"fair_i":20.0,"fair_r":25.0,"fair_zscore":0.2857,"fair_rationale":{"fair_score":41.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"http://bio-annotation.cn/gutmgene","grounded":true,"rationale":"The only identifier given is a URL, not a persistent identifier scheme like DOI, Handle, ARK, or repository accession.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"This database is freely available at http://bio-annotation.cn/gutmgene .","grounded":true,"rationale":"The data are hosted on a lab website (bio-annotation.cn), not a named data repository. 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[majority verdict 'no' (3/4 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":25.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is explicitly stated for the data; the CC BY-NC license applies to the article only.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"all the associations between gut microbes, microbial metabolites and genes were manually extracted from previously published studies","grounded":true,"rationale":"The production of the data is described generically (manual curation) without naming specific instruments or software versions. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No license is explicitly stated for the data; the CC BY-NC license applies to the article only.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"http://bio-annotation.cn/gutmgene","why":"The only identifier given is a URL, not a persistent identifier scheme like DOI, Handle, ARK, or repository accession.","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. 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[majority verdict 'no' (3/4 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence states how long the data persist or when it becomes available beyond the current availability. [majority verdict 'no' (3/4 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 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Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:57:49.922806Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}