ArticleNature communications2024
Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's 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 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Molecular Mechanisms Underlying the Higher Prevalence of Anemia in Crohn's Disease Compared with Ulcerative Colitis: A Systematic Review.International journal of molecular sciences · 2026Pooled it
- Protease-serpin-microbiome interactions in inflammatory bowel disease: toward integrated biomarkers of gut health.Gut microbes · 2026Review
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.Cell reports. Medicine · 2026Article
- Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.Gut pathogens · 2026Article
- Review
- Review
- Coal Dust Nanoparticles Induce Colitis-Like Lesions in Rats via Gut Microbiota Dysbiosis and P53/SCO2/SLC7A11-Mediated Epithelial Ferroptosis.Digestive diseases and sciences · 2026Article
- Unraveling Effects and Pharmacological Mechanisms of Phellodendrine on Inflammatory Bowel Disease.Biomolecules · 2026Article
- Gut microbiota in health and disease.Molecular biomedicine · 2026Review
- Fusobacterium varium Exacerbates Neutrophil-driven Intestinal Inflammation Associated with Succinate-SUCNR1-NF-κB Signaling.Inflammation · 2026Article
- Deciphering the Implications ofPathogens (Basel, Switzerland) · 2026Review
- Gut microbiota alterations and signatures across subthreshold depression and major depressive disorders in adolescents.Journal of translational medicine · 2026Article
- The Structure-Decoding-Conversion-Effect Paradigm of Natural Polysaccharides for Gut Microbiota Remodeling in Ulcerative Colitis.Nutrients · 2026Review
- Article
- Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.Nature medicine · 2026Article
- Microecological Interventions against Antibiotic-Induced Dysbiosis and Related Resistome Expansion.Journal of microbiology and biotechnology · 2026Review
- Gut Microbiota Remodeling Mediates the Therapeutic Effects of a Plant-Based Medicine on DSS-Induced Ulcerative Colitis in Mice via the Butyrate-SVCT1-Vitamin C Axis.International journal of molecular sciences · 2026Article
- Cross-kingdom microbial interactions in the gut during inflammatory bowel disease.Journal of translational medicine · 2026Review
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Silk-based biomimetic nanocomposite for precision eradication of Helicobacter pylori and gut microbiome preservation.Journal of nanobiotechnology · 2026Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.
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