The microbiota programs DNA methylation to control intestinal homeostasis and inflammation

Ansari, Ihab; Raddatz, Günter; Gutekunst, Julian; Ridnik, Meshi; Cohen, Daphne; Abu-Remaileh, Monther; Tuganbaev, Timur; Shapiro, Hagit; Pikarsky, Eli; Elinav, Eran; Lyko, Frank; Bergman, Yehudit

doi:10.1038/s41564-019-0659-3

Cited by 106 publications

(77 citation statements)

References 67 publications

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“…The authors also found a high enrichment of binding sites for FoxA, Eklf and AP1 transcription factors in corresponding hypomethylated low-methylated regions. Those factors were previously linked to gut homeostasis and the inflammatory response [2]. These findings subscribe to the concept of a microbiota-dependent epigenetic landscape in the gut, based on previous genome-wide histone modification analyses showing that commensal bacteria regulate chromatin organization in intestinal immune cell subpopulations [4].…”

supporting

confidence: 82%

“…In a recent publication in Nature Microbiology, Ansari et al (2020) identified gut microbiota as a critical mediator of the intestinal inflammatory response through epigenetic programming [2]. In this study, the authors use an elegant germ-free (GF) and germ-containing (GC) murine model to contrast the differing DNA methylation signatures resulting from the presence or absence of microbiota.…”

mentioning

confidence: 99%

“…Colorectal cancer (CRC) is one of the most lethal and prevalent cancers globally, likely owing to the complexity of the colonic environment [1]. The human gut microbiota includes trillions of microorganisms playing a fundamental role in regulating the interactions of intestinal epithelial cells with environmental drivers [2]. Important changes in the constitution and metabolome of the microbiota were observed in CRC patients.…”

mentioning

confidence: 99%

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Intestinal Microbiota Influences DNA Methylome and Susceptibility to Colorectal Cancer

Zouggar

Haebe

Benoit

2020

Genes

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In a recent publication, Ansari et al. identified gut microbiota as a critical mediator of the intestinal inflammatory response through epigenetic programming of host intestinal epithelium. Exposure to the microbiota induces Ten-Eleven-Translocation (TET)-dependent hypomethylation of genomic elements regulating genes associated with inflammatory response and colorectal cancer. Here, we discuss the impact of such a discovery on the understanding of how the intestinal microbiota may contribute to epigenetic reprogramming and influence the onset of colorectal tumorigenesis. Finally, we examine the prospect of TET inhibition strategies as a therapeutic and/or preventive approach for colorectal cancer in patients afflicted by inflammatory bowel disease.

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supporting

confidence: 82%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Intestinal Microbiota Influences DNA Methylome and Susceptibility to Colorectal Cancer

Zouggar

Haebe

Benoit

2020

Genes

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“…These data seem to be supported also by the evidence in a large pediatric IBD population, where specific epigenetic variations in the intestinal epithelium might influence the progression of the disease and might gain prognostic value as biomarkers for the disease [76]. Microbiota influences the activation of some genes associated with hypomethylated active regulatory regions, thus inducing the expression of genes associated with colitis and IBD [77].…”

Section: Ibd Genetics and Epigeneticsmentioning

confidence: 70%

Nutrition, IBD and Gut Microbiota: A Review

et al. 2020

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Inflammatory bowel disease (IBD) is a chronic relapsing–remitting systemic disease of the gastrointestinal tract, characterized by an inflammatory process that requires lifelong treatment. The underlying causes of IBD are still unclear, as this heterogeneous disorder results from a complex interplay between genetic variability, the host immune system and environmental factors. The current knowledge recognizes diet as a risk factor for the development of IBD and attributes a substantial pathogenic role to the intestinal dysbiosis inducing an aberrant mucosal immune response in genetically predisposed individuals. This review focused on the clinical evidence available that considers the impact of some nutrients on IBD onset and the role of different diets in the management of IBD and their effects on the gut microbiota composition. The effects of the Specific Carbohydrate Diet, low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet, gluten free diet, anti-inflammatory diet and Mediterranean diet are investigated with regard to their impact on microbiota and on the evolution of the disease. At present, no clear indications toward a specific diet are available but the assessment of dysbiosis prior to the recommendation of a specific diet should become a standard clinical approach in order to achieve a personalized therapy.

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“…Another level of complexity is introduced when the presence of other bacterial species, such as the components of the microbiota, are considered. Recent advances in microbiome research have shown that the gut microbiota can influence intestinal homeostasis and immunity by modulating host epitranscriptomic [133] and epigenetic modifications [134][135][136]. Lm is known to produce bacteriocins that kill other bacteria to promote its own infection, therefore, it may also be able to affect the transcriptional profile of its host by targeting specific members of the host gut microbiome [137,138].…”

Section: Discussionmentioning

confidence: 99%

Pathogenic Biohacking: Induction, Modulation and Subversion of Host Transcriptional Responses by Listeria monocytogenes

Eldridge

Cossart

Hamon

2020

Toxins

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During infection, the foodborne bacterial pathogen Listeria monocytogenes dynamically influences the gene expression profile of host cells. Infection-induced transcriptional changes are a typical feature of the host-response to bacteria and contribute to the activation of protective genes such as inflammatory cytokines. However, by using specialized virulence factors, bacterial pathogens can target signaling pathways, transcription factors, and epigenetic mechanisms to alter host gene expression, thereby reprogramming the response to infection. Therefore, the transcriptional profile that is established in the host is delicately balanced between antibacterial responses and pathogenesis, where any change in host gene expression might significantly influence the outcome of infection. In this review, we discuss the known transcriptional and epigenetic processes that are engaged during Listeria monocytogenes infection, the virulence factors that can remodel them, and the impact these processes have on the outcome of infection.

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The microbiota programs DNA methylation to control intestinal homeostasis and inflammation

Cited by 106 publications

References 67 publications

Intestinal Microbiota Influences DNA Methylome and Susceptibility to Colorectal Cancer

Intestinal Microbiota Influences DNA Methylome and Susceptibility to Colorectal Cancer

Nutrition, IBD and Gut Microbiota: A Review

Pathogenic Biohacking: Induction, Modulation and Subversion of Host Transcriptional Responses by Listeria monocytogenes

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