{"doi":"10.1186/s13099-024-00606-y","title":"Identification of enterotype and its predictive value for patients with colorectal cancer","abstract":"<h4>Background</h4>Gut microbiota dysbiosis involved in the pathogenesis of colorectal cancer (CRC). The characteristics of enterotypes in CRC development have not been determined.<h4>Objective</h4>To characterize the gut microbiota of healthy, adenoma, and CRC subjects based on enterotype.<h4>Methods</h4>The 16 S rRNA sequencing data from 315 newly sequenced individuals and three previously published datasets were collected, providing total data for 367 healthy, 320 adenomas, and 415 CRC subjects. Enterotypes were analyzed for all samples, and differences in microbiota composition across subjects with different disease states in each enterotype were determined. The predictive values of a random forest classifier based on enterotype in distinguishing healthy, adenoma, and CRC subjects were evaluated and validated.<h4>Results</h4>Subjects were classified into one of three enterotypes, namely, Bacteroide- (BA_E), Blautia- (BL_E), and Streptococcus- (S_E) dominated clusters. The taxonomic profiles of these three enterotypes differed among the healthy, adenoma, and CRC cohorts. BA_E group was enriched with Bacteroides and Blautia; BL_E group was enriched by Blautia and Coprococcus; S_E was enriched by Streptococcus and Ruminococcus. Relative abundances of these genera varying among the three human cohorts. In training and validation sets, the S_E cluster showed better performance in distinguishing among CRC patients, adenoma patients, and healthy controls, as well as between CRC and non-CRC individuals, than the other two clusters.<h4>Conclusion</h4>This study provides the first evidence to indicate that changes in the microbial composition of enterotypes are associated with disease status, thereby highlighting the diagnostic potential of enterotypes in the treatment of adenoma and CRC.","journal":"Gut Pathogens","year":2024,"id":5229,"datarank":0.5664629291404201,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.22107516519131312,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.22107516519131312,"corpus_percentile":52.56305939788446,"corpus_rank":584,"citation_count":11,"citer_count":11,"citers_with_citation_signal":8,"citers_with_endowment":8,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.561,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-02-27","fair_score":47.7083,"fair_percentile":44.415127528583994,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":52541,"name":"Zhuang Jing","orcid":"0000-0002-6910-8824","position":1,"is_corresponding":false},{"id":52542,"name":"Qu Zhanbo","orcid":null,"position":2,"is_corresponding":false},{"id":52543,"name":"Chu Jian","orcid":null,"position":3,"is_corresponding":false},{"id":52544,"name":"Song Yifei","orcid":null,"position":4,"is_corresponding":false},{"id":52545,"name":"Wu Yinhang","orcid":"0000-0001-5227-7413","position":5,"is_corresponding":false},{"id":52546,"name":"Han Shuwen","orcid":null,"position":6,"is_corresponding":false},{"id":52547,"name":"Qingbo Li","orcid":null,"position":7,"is_corresponding":false},{"id":52548,"name":"Jing Zhuang","orcid":null,"position":8,"is_corresponding":false},{"id":52549,"name":"Jian Chu","orcid":null,"position":9,"is_corresponding":false},{"id":52550,"name":"Shuwen Han","orcid":"0000-0001-6180-9565","position":10,"is_corresponding":false},{"id":52540,"name":"Li Qingbo","orcid":null,"position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"38414077","pmcid":"PMC10897996","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":0.2259,"fair_rationale":{"fair_score":47.71,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper provides standard bibliographic metadata (DOI, title, authors) but lacks explicit machine-readable metadata or structured data descriptions beyond the DOI."}]},"A":{"name":"Accessible","score":67.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The data access protocol is clear with NCBI SRA accession numbers for newly generated data, but no code or software access is provided."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"Standard bioinformatics tools (QIIME2, DADA2, Greengenes) and NCBI identifiers are used, but adherence to community metadata standards (e.g., MIxS) is not stated."}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.5,"signal":null,"rationale":"Data are publicly available under CC BY 4.0 license, but the absence of code, detailed software versions, and a reproducible workflow limits reusability."}]}},"suggestions":["Include machine-readable metadata (e.g., JSON-LD) for the paper to enhance findability.","Deposit analysis code in a public repository (e.g., GitHub) with version control and documentation.","Adopt community metadata standards (e.g., MIxS) for describing sequencing data and sample attributes.","Provide detailed software versions, parameters, and a reproducible workflow (e.g., using containers or Snakemake).","Add a formal data citation with persistent identifiers for all datasets used."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:49:47.485190Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}