{"doi":"10.1016/j.cell.2021.05.002","title":"A global metagenomic map of urban microbiomes and antimicrobial resistance","abstract":"We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.","journal":"Cell","year":2021,"id":145502,"datarank":5.127978603077704,"base_score":5.968707559985366,"endowment":5.968707559985366,"self_citation_contribution":0.895306133997805,"citation_network_contribution":4.2326724690798985,"self_endowment_contribution":0.895306133997805,"citer_contribution":4.2326724690798985,"corpus_percentile":95.87684690956912,"corpus_rank":534,"citation_count":390,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9425,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":75.0,"fair_percentile":95.6282482421278,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":28467,"name":"Daniela Bezdan","orcid":"0000-0002-1203-8239","position":1,"is_corresponding":false},{"id":619413,"name":"Evan E. Afshin","orcid":null,"position":2,"is_corresponding":false},{"id":617758,"name":"Sofia Ahsanuddin","orcid":"0000-0003-3379-6802","position":3,"is_corresponding":false},{"id":550381,"name":"Chandrima Bhattacharya","orcid":"0000-0003-2991-8491","position":4,"is_corresponding":false},{"id":231221,"name":"Daniel Butler","orcid":"0000-0002-3687-8419","position":5,"is_corresponding":false},{"id":66077,"name":"Kern Rei Chng","orcid":"0000-0003-2746-9880","position":6,"is_corresponding":false},{"id":619414,"name":"Daisy Donnellan","orcid":null,"position":7,"is_corresponding":false},{"id":617759,"name":"Jochen Hecht","orcid":"0000-0002-6996-5279","position":8,"is_corresponding":false},{"id":617760,"name":"Katelyn Jackson","orcid":"0000-0003-1167-5196","position":9,"is_corresponding":false},{"id":619415,"name":"Katerina Kuchin","orcid":null,"position":10,"is_corresponding":false},{"id":617761,"name":"Mikhail Karasikov","orcid":"0000-0001-6200-5972","position":11,"is_corresponding":false},{"id":619416,"name":"Abigail Lyons","orcid":null,"position":12,"is_corresponding":false},{"id":617762,"name":"Lauren Mak","orcid":"0000-0002-2414-7838","position":13,"is_corresponding":false},{"id":550383,"name":"Dmitry Meleshko","orcid":"0000-0002-7398-9820","position":14,"is_corresponding":false},{"id":617763,"name":"Harun Mustafa","orcid":"0000-0002-2125-6086","position":15,"is_corresponding":false},{"id":617764,"name":"Beth Mutai","orcid":"0000-0002-7396-3903","position":16,"is_corresponding":false},{"id":617765,"name":"Russell Y. Neches","orcid":"0000-0002-2055-8381","position":17,"is_corresponding":false},{"id":66066,"name":"Amanda Hui Qi Ng","orcid":"0009-0008-1604-9876","position":18,"is_corresponding":false},{"id":619417,"name":"Olga Nikolayeva","orcid":null,"position":19,"is_corresponding":false},{"id":619418,"name":"Tatyana Nikolayeva","orcid":null,"position":20,"is_corresponding":false},{"id":617766,"name":"Eileen Png","orcid":"0000-0001-5586-6395","position":21,"is_corresponding":false},{"id":550379,"name":"Krista Ryon","orcid":"0000-0001-9440-2729","position":22,"is_corresponding":false},{"id":617767,"name":"Jorge L. Sánchez","orcid":"0000-0001-9645-0302","position":23,"is_corresponding":false},{"id":619419,"name":"Heba Shaaban","orcid":null,"position":24,"is_corresponding":false},{"id":318598,"name":"Maria A. Sierra","orcid":"0000-0003-4115-034X","position":25,"is_corresponding":false},{"id":619420,"name":"Dominique Thomas","orcid":null,"position":26,"is_corresponding":false},{"id":619421,"name":"Ben Young","orcid":null,"position":27,"is_corresponding":false},{"id":7478,"name":"Omar O. Abudayyeh","orcid":"0000-0002-7979-3220","position":28,"is_corresponding":false},{"id":619422,"name":"Josue Alicea","orcid":null,"position":29,"is_corresponding":false},{"id":617768,"name":"Malay Bhattacharyya","orcid":"0000-0001-7781-1264","position":30,"is_corresponding":false},{"id":20926,"name":"Ran Blekhman","orcid":"0000-0003-3218-613X","position":31,"is_corresponding":false},{"id":415279,"name":"Eduardo Castro‐Nallar","orcid":"0000-0003-4384-8661","position":32,"is_corresponding":false},{"id":619423,"name":"A Cañas","orcid":null,"position":33,"is_corresponding":false},{"id":617769,"name":"Aspassia D. Chatziefthimiou","orcid":"0000-0002-6557-2427","position":34,"is_corresponding":false},{"id":619424,"name":"Robert W. Crawford","orcid":null,"position":35,"is_corresponding":false},{"id":617770,"name":"Francesca De Filippis","orcid":"0000-0002-3474-2884","position":36,"is_corresponding":false},{"id":320407,"name":"Youping Deng","orcid":"0000-0002-5951-8213","position":37,"is_corresponding":false},{"id":617771,"name":"Christelle Desnues","orcid":"0000-0002-2178-0355","position":38,"is_corresponding":false},{"id":85845,"name":"Emmanuel Dias-Neto","orcid":"0000-0001-5670-8559","position":39,"is_corresponding":false},{"id":373425,"name":"Marius Dybwad","orcid":"0000-0002-0521-9955","position":40,"is_corresponding":false},{"id":261791,"name":"Eran Elhaik","orcid":"0000-0003-4795-1084","position":41,"is_corresponding":false},{"id":615085,"name":"Danilo Ercolini","orcid":"0000-0003-3061-9560","position":42,"is_corresponding":false},{"id":617772,"name":"Alina Frolova","orcid":"0000-0001-5469-7366","position":43,"is_corresponding":false},{"id":619425,"name":"Dennis Gankin","orcid":null,"position":44,"is_corresponding":false},{"id":7479,"name":"Jonathan S. Gootenberg","orcid":"0000-0003-2757-2175","position":45,"is_corresponding":false},{"id":617773,"name":"Alexandra B. Graf","orcid":"0000-0002-2738-3270","position":46,"is_corresponding":false},{"id":617774,"name":"David C. Green","orcid":"0000-0002-0695-4660","position":47,"is_corresponding":false},{"id":35202,"name":" Iman Hajirasouliha ","orcid":"0000-0002-0600-3371","position":48,"is_corresponding":false},{"id":37840,"name":"Jaden J. A. Hastings","orcid":"0000-0003-1459-3364","position":49,"is_corresponding":false},{"id":617775,"name":"Mark Hernandez","orcid":"0000-0001-8598-1343","position":50,"is_corresponding":false},{"id":617776,"name":"Gregorio Iraola","orcid":"0000-0002-6516-3404","position":51,"is_corresponding":false},{"id":617777,"name":"Soojin Jang","orcid":"0000-0002-2921-7196","position":52,"is_corresponding":false},{"id":228578,"name":"André Kahles","orcid":"0000-0002-3411-0692","position":53,"is_corresponding":false},{"id":441846,"name":"Frank J. Kelly","orcid":"0000-0003-2558-8392","position":54,"is_corresponding":false},{"id":619426,"name":"Kaymisha Knights","orcid":null,"position":55,"is_corresponding":false},{"id":19851,"name":"Nikos C. Kyrpides","orcid":"0000-0002-6131-0462","position":56,"is_corresponding":false},{"id":457050,"name":"Paweł P. Łabaj","orcid":"0000-0002-4994-0234","position":57,"is_corresponding":false},{"id":617778,"name":"Patrick K. H. Lee","orcid":"0000-0003-0911-5317","position":58,"is_corresponding":false},{"id":617779,"name":"Marcus H. Y. Leung","orcid":"0000-0002-6342-8181","position":59,"is_corresponding":false},{"id":617780,"name":"Per O. Ljungdahl","orcid":"0000-0002-6625-3540","position":60,"is_corresponding":false},{"id":619427,"name":"Gabriella Mason-Buck","orcid":null,"position":61,"is_corresponding":false},{"id":617781,"name":"Ken McGrath","orcid":"0000-0002-5958-1079","position":62,"is_corresponding":false},{"id":227777,"name":"Cem Meydan","orcid":"0000-0002-0663-6216","position":63,"is_corresponding":false},{"id":238447,"name":"Emmanuel F. Mongodin","orcid":"0000-0003-3833-7437","position":64,"is_corresponding":false},{"id":398100,"name":"Milton Ozório Moraes","orcid":"0000-0003-2653-0037","position":65,"is_corresponding":false},{"id":453030,"name":"Niranjan Nagarajan","orcid":"0000-0003-0850-5604","position":66,"is_corresponding":false},{"id":617782,"name":"Marina Nieto‐Caballero","orcid":"0000-0002-7755-2490","position":67,"is_corresponding":false},{"id":1835,"name":"Houtan Noushmehr","orcid":"0000-0003-4051-8114","position":68,"is_corresponding":false},{"id":617783,"name":"Manuela Oliveira","orcid":"0000-0001-5785-7521","position":69,"is_corresponding":false},{"id":13890,"name":"Stephan Ossowski","orcid":"0000-0002-7416-9568","position":70,"is_corresponding":false},{"id":617784,"name":"Olayinka Osuolale","orcid":"0000-0001-6525-8502","position":71,"is_corresponding":false},{"id":617785,"name":"Orhan Özcan","orcid":"0000-0002-6574-2465","position":72,"is_corresponding":false},{"id":302177,"name":"David Páez-Espino","orcid":"0000-0002-2939-5398","position":73,"is_corresponding":false},{"id":617786,"name":"Nicolás Rascovan","orcid":"0000-0002-2129-5878","position":74,"is_corresponding":false},{"id":617787,"name":"Hugues Richard","orcid":"0000-0001-7776-1340","position":75,"is_corresponding":false},{"id":301859,"name":"Gunnar Rätsch","orcid":"0000-0001-5486-8532","position":76,"is_corresponding":false},{"id":19861,"name":"Lynn M. Schriml","orcid":"0000-0001-8910-9851","position":77,"is_corresponding":false},{"id":617788,"name":"Torsten Semmler","orcid":"0000-0002-2225-7267","position":78,"is_corresponding":false},{"id":617789,"name":"Osman Uğur Sezerman","orcid":"0000-0003-0905-6783","position":79,"is_corresponding":false},{"id":457044,"name":"Leming Shi","orcid":"0000-0002-2981-4150","position":80,"is_corresponding":false},{"id":617790,"name":"Tieliu Shi","orcid":"0000-0001-5592-2836","position":81,"is_corresponding":false},{"id":617791,"name":"Rania Siam","orcid":"0000-0002-2879-6368","position":82,"is_corresponding":false},{"id":619428,"name":"Le Huu Song","orcid":null,"position":83,"is_corresponding":false},{"id":617792,"name":"Haruo Suzuki","orcid":"0000-0003-1447-6109","position":84,"is_corresponding":false},{"id":617793,"name":"Denise Syndercombe Court","orcid":"0000-0003-2348-6915","position":85,"is_corresponding":false},{"id":33230,"name":"Scott Tighe","orcid":"0000-0002-3988-0741","position":86,"is_corresponding":false},{"id":619429,"name":"Xinzhao Tong","orcid":null,"position":87,"is_corresponding":false},{"id":617794,"name":"Klas I. Udekwu","orcid":"0000-0002-8434-0744","position":88,"is_corresponding":false},{"id":295564,"name":"Juan A. Ugalde","orcid":"0000-0001-6638-0817","position":89,"is_corresponding":false},{"id":619430,"name":"Brandon Valentine","orcid":null,"position":90,"is_corresponding":false},{"id":617795,"name":"Dimitar Vassilev","orcid":"0000-0002-2478-7528","position":91,"is_corresponding":false},{"id":617796,"name":"Elena Vayndorf","orcid":"0000-0001-9416-3350","position":92,"is_corresponding":false},{"id":74512,"name":"Thirumalaisamy P. Velavan","orcid":"0000-0002-9809-9883","position":93,"is_corresponding":false},{"id":71438,"name":"Jun Wu","orcid":"0000-0002-3381-2561","position":94,"is_corresponding":false},{"id":617797,"name":"María Mercedes Zambrano","orcid":"0000-0002-0796-4473","position":95,"is_corresponding":false},{"id":617798,"name":"Jifeng Zhu","orcid":"0000-0001-9825-6941","position":96,"is_corresponding":false},{"id":617799,"name":"Sibo Zhu","orcid":"0000-0003-4800-8987","position":97,"is_corresponding":false},{"id":36370,"name":"Christopher E. Mason","orcid":"0000-0002-1850-1642","position":98,"is_corresponding":false},{"id":619431,"name":"Natasha Abdullah","orcid":null,"position":99,"is_corresponding":false},{"id":363450,"name":"David Danko","orcid":"0000-0002-1456-9498","position":0,"is_corresponding":true}],"reference_count":95,"raw_metadata":null,"created_at":"2026-07-18T23:42:12.871665Z","pmid":"34043940","pmcid":"PMC8238498","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":83.3333,"fair_a":62.5,"fair_i":100.0,"fair_r":41.6667,"fair_zscore":1.6051,"fair_rationale":{"fair_score":75.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","grounded":true,"rationale":"The paper provides a BioProject accession (PRJNA732392), which is a persistent identifier scheme.","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":1.0,"verdict":"yes","evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","grounded":true,"rationale":"The SRA (Sequence Read Archive) is named as the repository holding the data.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Accessions and data access All data from this study including data tables that resulted from analyses may be found at https://pngb.io/metasub-2021 . Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","grounded":true,"rationale":"The statement points to a repository record (SRA) with an accession number.","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years","grounded":true,"rationale":"The dataset's size and scope are described in running prose only; no itemised inventory of files or variables is given. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","grounded":true,"rationale":"The dataset identifier appears only in the body text, not as a reference-list entry.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","grounded":true,"rationale":"The text gives a route to the data in a public repository with no stated precondition.","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","grounded":true,"rationale":"The paper describes where the data are deposited but does not apply an explicit access-level label like 'open access'. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are environmental metagenomic samples and not sensitive; no gatekeeper is named.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence states how long the data will remain available or when they become accessible.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":100.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"This pipeline includes all steps from extracting data from raw sequence FASTQ files to producing refined results like taxonomic and functional profiles.","grounded":true,"rationale":"The paper names FASTQ, an open community-standard format, for the raw sequence data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"We mapped reads to known antibiotic resistance genes, using the MegaRES ontology and alignment software.","grounded":true,"rationale":"The paper applies the MegaRES ontology, a community-standard vocabulary for antimicrobial resistance. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"Deposited data NCBI/RefSeq Microbial ca. March 2017 NCBI https://www.ncbi.nlm.nih.gov/refseq/","grounded":true,"rationale":"The Key Resources Table lists external databases with URLs, providing identifiers for resources other than the study's own dataset. [majority verdict 'yes' (3/5 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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No reuse license is stated for the data; the CC BY license applies only to the article.","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":1.0,"verdict":"yes","evidence":"Each sample was sequenced with 5–7 million 125bp paired-end reads using Illumina NGS sequencers","grounded":true,"rationale":"The paper names the specific sequencing platform (Illumina NGS) used to produce the data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No README, data dictionary, codebook, or variable-definition table is named for the data. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given to pin a specific snapshot of the data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"https://github.com/MetaSUB/main_paper_figures","grounded":true,"rationale":"The paper provides a GitHub repository URL for the code used to generate figures and analyses. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"the NIH (R01AI151059, R25EB020393, R21AI129851, R35GM138152, U01DA053941)","grounded":true,"rationale":"The paper lists specific NIH award numbers, providing grant identifiers.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"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. '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 reuse license is stated for the data; the CC BY license applies only to the article.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","why":"The dataset identifier appears only in the body text, not as a reference-list entry.","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is given to pin a specific snapshot of the data. [majority verdict 'no' (4/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years","why":"The dataset's size and scope are described in running prose only; no itemised inventory of files or variables is given. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Additionally, raw sequencing reads are uploaded to the SRA and may be found under the accession SRA ID: PRJNA732392.","why":"The paper describes where the data are deposited but does not apply an explicit access-level label like 'open access'. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No README, data dictionary, codebook, or variable-definition table is named for the data. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are environmental metagenomic samples and not sensitive; no gatekeeper is named.","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 will remain available or when they become accessible.","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. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link."],"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":"2026-07-20T10:49:29.691336Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}