ArticleGut microbes
Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence.
Article in Gut microbes. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- Is the microbiome the answer to inflammatory bowel disease: systematic review.Langenbeck's archives of surgery · 2025Pooled it
- Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.Gut microbes · 2026Article
- An atlas of colonization factors in the human gut microbiome reveals ecological strategies and inflammatory bowel disease signatures.Nature communications · 2026Article
- Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.Cell reports. Medicine · 2026Article
- Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease.Gut microbes · 2025Review
- Intestinal Microbiota and Fecal Transplantation in Patients with Inflammatory Bowel Disease andJournal of clinical medicine · 2025Review
- Artificial intelligence in inflammatory bowel disease.Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association · 2025Review
- Revolutionizing gastroenterology and hepatology with artificial intelligence: From precision diagnosis to equitable healthcare through interdisciplinary practice.World journal of gastroenterology · 2025Review
- Current methods in explainable artificial intelligence and future prospects for integrative physiology.Pflugers Archiv : European journal of physiology · 2025Review
- Artificial intelligence use for precision medicine in inflammatory bowel disease: a systematic review.American journal of translational research · 2025Review
- Inflammation, Gut Microbiota, and Metabolomic Shifts in Colorectal Cancer: Insights from Human and Mouse Models.International journal of molecular sciences · 2024Article
- Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.Nature protocols · 2024Review
- Fecal microbiota and metabolites in the pathogenesis and precision medicine for inflammatory bowel disease.Precision clinical medicine · 2024Review
- Establishment and evaluation of on-chip intestinal barrier biosystems based on microfluidic techniques.Materials today. Bio · 2024Review
- Hyperbaric oxygen therapy ameliorates intestinal and systematic inflammation by modulating dysbiosis of the gut microbiota in Crohn's disease.Journal of translational medicine · 2024Article
- Identification of Marker Genes in Infectious Diseases from ScRNA-seq Data Using Interpretable Machine Learning.International journal of molecular sciences · 2024Article
- Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis.Communications biology · 2024Article
- Characteristics of gut microbiome in patients with pediatric solid tumor.Frontiers in pediatrics · 2024Article
- Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.Gut microbes · 2023Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. We collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. Microbial alterations in CD patients were assessed at multidimensional levels including species, gene, and SNV level, and then diagnostic models were constructed using artificial intelligence algorithm. A total of 227 species, 1047 microbial genes, and 21,877 microbial SNVs were identified that differed between CD and controls. The species, gene, and SNV models achieved an average AUC of 0.97, 0.95, and 0.77, respectively. Notably, the gene model exhibited superior diagnostic capability, achieving an average AUC of 0.89 and 0.91 for internal and external validations, respectively. Moreover, the gene model was specific for CD against other microbiome-related diseases. Furthermore, we found that phosphotransferase system (PTS) contributed substantially to the diagnostic capability of the gene model. The outstanding performance of PTS was mainly explained by genes celB and manY, which demonstrated high predictabilities for CD with metagenomic datasets and was validated in an independent cohort by qRT-PCR analysis. Our global metagenomic analysis unravels the multidimensional alterations of the microbial communities in CD and identifies microbial genes as robust diagnostic biomarkers across geographically and culturally distinct cohorts.
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