Gut microbiota signatures in inflammatory bowel disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38041519", "kind": "science-record", "revision": 3, "content_hash": "sha256:65078f9acb5e83decd4268eee3e90493bffe8adfff4ab396bf48ec095a369192", "created_at": "2026-11-01T19:02:58Z", "updated_at": "2026-11-01T22:10:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gut microbiota signatures in inflammatory bowel disease.", "doi": "10.1002/ueg2.12485", "pmid": "38041519", "authors": ["Marie Vibeke Vestergaard", "Kristine H Allin", "Carsten Eriksen", "Oliwia Zakerska-Banaszak", "Ramesh P Arasaradnam", "Mohammad T Alam", "Karsten Kristiansen", "Susanne Brix", "Tine Jess"], "journal": "United European gastroenterology journal", "year": 2024, "abstract": "BACKGROUND: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence.\nOBJECTIVES: Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients.\nMETHODS: We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms.\nRESULTS: Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found.\nCONCLUSIONS: Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.", "claims": [{"id": "claim-method", "statement": "We employed a zero‐inflated negative binomial (ZINB) model 62 (“zeroinfl”, pscl‐package version: 1.5.5) to model raw microbiota data without any normalization and transformation. ANCOM‐BC 63 (“ancombc”, ANCOMBC‐package version: 1.4.0) and MaAsLin2 64 (“Maaslin2”, Maaslin2‐package version: 1.8.0) were selected based on a recommendation from Nearing et al.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38041519", "locator": "sections[7] \"Statistical analysis of individual genera versus disease status\" paragraph 2", "quote": "We employed a zero‐inflated negative binomial (ZINB) model 62 (“zeroinfl”, pscl‐package version: 1.5.5) to model raw microbiota data without any normalization and transformation. ANCOM‐BC 63 (“ancombc”, ANCOMBC‐package version: 1.4.0) and MaAsLin2 64 (“Maaslin2”, Maaslin2‐package version: 1.8.0) were selected based on a recommendation from Nearing et al."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in this study are already publicly available at the BioProject database of the National Center for Biotechnology Information. All source codes used in this study are available at GitHub: https://github.com/marievibeke/16S_IBD_project.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38041519", "locator": "sections[20] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "All data used in this study are already publicly available at the BioProject database of the National Center for Biotechnology Information. All source codes used in this study are available at GitHub: https://github.com/marievibeke/16S_IBD_project."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38041519", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38041519"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38041519", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/ueg2.12485", "sha256": "sha256:2fc92ad963874350cc5f82d4a5ed83096a497f43e49eb9092aa0ddacfb2a8f54", "bytes": 46963, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/ueg2.12485", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10859715", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "family": null, "specific": null, "label": "zero‐inflated negative binomial (ZINB), ANCOM‐BC, and MaAsLin2", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We employed a zero‐inflated negative binomial (ZINB) model 62 (“zeroinfl”, pscl‐package version: 1.5.5) to model raw microbiota data without any normalization and transformation. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["All data used in this study are already publicly available at the BioProject database of the National Center for Biotechnology Information. 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