ArticleNature communications2024
Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 59 citations in OpenAlex.
- Investigating the shared genetic architecture between inflammatory bowel disease and pancreatitis: a genome-wide cross-trait analysis.Molecular genetics and genomics : MGG · 2026Pooled it
- Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn's disease: an open-label pilot study.Nature communications · 2026Trial
- Evidence for a Modulatory Effect of a 12-Week Pomegranate Juice Intervention on the Transcriptional Response in Inflammatory Bowel Disease Patients Reducing Fecal Calprotectin Levels: Findings From a Proof-of-Principle Study.Molecular nutrition & food research · 2025Trial
- A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.Gut microbes · 2026Article
- Next-generation natural killer cell therapy: bench to bedside and beyond.Signal transduction and targeted therapy · 2026Review
- Gut-on-Chip Models for Host-Microbiome Studies: A Systematic Review.Microorganisms · 2026Review
- Multi-level aggregation analysis of microbiome composition and host gene expression reveals associations with systemic and local immunity.Microbiology spectrum · 2026Article
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- Alterations of the host-lung microbiome metasystem in systemic inflammatory response syndrome is associated with secondary pneumonia.Cell reports. Medicine · 2026Article
- Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tracing NADCell reports · 2026Article
- Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine.bioRxiv : the preprint server for biology · 2026Article
- Gut Microbiota: A Potential Role in Modulating Carcinogenesis and Response to Anti-Cancer Therapies.Cancer reports (Hoboken, N.J.) · 2026Review
- Review
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- Cross-ethnic evaluation of gut microbial signatures reveal increased colonization with oral pathobionts in the north Indian inflammatory bowel disease cohort.Intestinal research · 2026Article
- A simplified synthetic microbial community enhances resistance of crucian carp (Synthetic and systems biotechnology · 2026Article
- DUOX2-Driven Oxidative Stress Alters the Gut Redox Niche and Promotes Microbial Dysbiosis in Crohn's Disease.Antioxidants (Basel, Switzerland) · 2026Article
- Manganese oxide nanozyme-loaded CO-releasing halloysite nanotubes for remodeling colonic immune, microbiota, and intestinal barrier homeostasis with concurrent pain relief in ulcerative colitis.Bioactive materials · 2026Article
- Mucosa-associated bacteria and metabolites in inflammatory bowel disease: from inside to insight.NPJ biofilms and microbiomes · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 1 institution in 2 countries.
Funding
Abstract
Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal biopsies (645 derived from 335 patients with IBD and 52 from 16 non-IBD controls). Mucosal gene expression patterns in IBD are mainly determined by tissue location and inflammation, whereas the mucosal microbiota composition shows a high degree of individual specificity. Analysis of transcript-bacteria interactions identifies six distinct groups of inflammation-related pathways that are associated with intestinal microbiota (adjusted P < 0.05). An increased abundance of Bifidobacterium is associated with higher expression of genes involved in fatty acid metabolism, while Bacteroides correlates with increased metallothionein signaling. In patients with fibrostenosis, a transcriptional network dominated by immunoregulatory genes is associated with Lachnoclostridium bacteria in non-stenotic tissue (adjusted P < 0.05), while being absent in CD without fibrostenosis. In patients using TNF-α-antagonists, a transcriptional network dominated by fatty acid metabolism genes is linked to Ruminococcaceae (adjusted P < 0.05). Mucosal microbiota composition correlates with enrichment of intestinal epithelial cells, macrophages, and NK-cells. Overall, these data demonstrate the presence of context-specific mucosal host-microbe interactions in IBD, revealing significantly altered inflammation-associated gene-taxa modules, particularly in patients with fibrostenotic CD and patients using TNF-α-antagonists. This study provides compelling insights into host-microbe interactions that may guide microbiota-directed precision medicine and fuels the rationale for microbiota-targeted therapeutics as a strategy to alter disease course in IBD.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.