ArticleNature microbiology2020
The microbiota programs DNA methylation to control intestinal homeostasis and inflammation.
Article in Nature microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05779904 (DNA Methylation, Microbiome Profile, Nutritional Status, and Developmental Outcomes of Stunted and Non-stunted Children Growing up During Covid-19 Pandemic), which is not on this map. Cited by 120 papers, 2 of them syntheses that pooled it.
What it found
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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.
DNA Methylation, Microbiome Profile, Nutritional Status, and Developmental Outcomes of Stunted and Non-stunted Children Growing up During Covid-19 Pandemic: a Case-control Study
Who cites it
120 citing papers in PubMed, 2 syntheses or guidelines pooled it, 202 citations in OpenAlex.
- Multi-Omics Analyses Reveal Relationships Between Gut Microbiota and Frailty.Brain and behavior · 2025Pooled it
- Inflammation and Stem Cell Stochasticity of HPV-induced Cervical Cancer: Epigenetics based Biomarkers through Microbiome and Metabolome for Personalized Medicine: A Systematic Review.Current medicinal chemistry · 2025Pooled it
- Microbial epigenetic regulation as a multilevel regulatory interface in host-microbe interactions.Gut microbes · 2026Review
- Exclusive enteral nutrition containing transforming growth factor-β improves intestinal barrier function in a colitis mouse model.Journal of pediatric gastroenterology and nutrition · 2026Article
- TET2 as a Context-Dependent Epigenetic Integrator in Clonal Hematopoiesis, Inflammation, Cancer, and Immunotherapy.Cell biochemistry and function · 2026Review
- Resistant starch as a dietary strategy for metabolic and gut health: Implications for Asia-Pacific populations.Asia Pacific journal of clinical nutrition · 2026Review
- TET Enzymes as Epigenetic Integrators in Intestinal Immunity, Inflammation, and Disease.Journal of personalized medicine · 2026Review
- Efficacy, Safety, and Mechanism of the Qi-Lian-Xiao-Pi Prescription (WW-1) for Chronic Atrophic Gastritis After Helicobacter Pylori Eradication: Protocol for a Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial.JMIR research protocols · 2026Article
- Defined bacterial consortium highlights the impact of intestinal bacteria on DNA methylation and tumorigenesis.Genome biology · 2026Article
- The Gut Microbiome in Early Ontogeny: Implications for Brain and Immune System Development.Journal of developmental biology · 2026Review
- Harnessing the microbiome for cancer therapy.Nature reviews. Microbiology · 2026Review
- Fusobacterium nucleatum drives colorectal cancer progression through the circPTBP3/miR-760/PUM1 axis.Oncogene · 2026Article
- Epigenetic Alterations in Microbiome-Host Interactions in Inflammatory and Autoimmune Diseases.International journal of molecular sciences · 2026Review
- Weaning drives microbiome-mediated epigenetic regulation to shape immune memory in mice.Nature microbiology · 2026Article
- Atlas of one-carbon metabolism in conventional and germ-free mice reveals folate as a key determinant of biochemical pathways.Nature metabolism · 2026Article
- TET1 deficiency amplifies macrophage inflammatory signaling associated with Crohn's disease.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Review
- The gut as a central hub for multi-organ crosstalk in aging.Cellular and molecular life sciences : CMLS · 2026Review
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
- tRNA mCell discovery · 2026Article
60 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although much research has been done on the diversity of the gut microbiome, little is known about how it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested to operate at the interface between the microbiota and the intestinal epithelium. We performed whole-genome bisulfite sequencing on conventionally raised and germ-free mice, and discovered that exposure to commensal microbiota induced localized DNA methylation changes at regulatory elements, which are TET2/3-dependent. This culminated in the activation of a set of 'early sentinel' response genes to maintain intestinal homeostasis. Furthermore, we demonstrated that exposure to the microbiota in dextran sodium sulfate-induced acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements, leading to alterations in gene expression programs enriched in colitis- and colon-cancer-associated functions. Finally, by employing genetic interventions, we show that microbiota-induced epigenetic programming is necessary for proper intestinal homeostasis in vivo.
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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.