The human gastrointestinal (GI) tract is home to a complex and dynamic ecosystem of microorganisms including bacteria, viruses (viromes), fungi (mycobiome), and archaea (archaeome), where host genetics, epigenetics, and microbiome-derived metabolites interact to maintain GI homeostasis and overall health. Recent research has illuminated the pivotal roles of genetic, epigenetic, and epi-transcriptomic factors in this process. These mechanisms orchestrate host-microbiome-derived metabolite interactions, influencing both normal physiological functions and the pathogenesis of GI disorders. Furthermore, studies have revealed that the interplay between the host and its microbiome is not solely dependent on genetic factors but is also significantly influenced by epigenetic and epi-transcriptomic modifications, including methylation, acetylation, etc., which can alter gene expression without changing the DNA sequence, thereby modulating host-microbiome interactions in the development and differentiation of healthy and diseased states. In the context of the GI tract, the microbiome’s metabolites have emerged as key players influencing host epigenetics by using integrated transcriptomic and epi-transcriptomic approaches with microbiome metabolites. Therefore, understanding these mechanisms is crucial as they orchestrate host-microbiome interactions, influencing both normal physiological functions and the pathogenesis of GI disorders including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), hepatocellular carcinoma (HCC), and other related conditions.
Despite significant progress, the exact epigenetic mechanisms by which the microbiome influences host physiology and contributes to GI disorders remain poorly understood. The challenge lies in comprehensively mapping these complex interactions and understanding how they can be targeted for therapeutic benefit. The objective of this research topic is to elucidate these epigenetic pathways and identify novel biomarkers and therapeutic targets. Achieving this requires integrating recent advances in high-throughput sequencing, epigenome editing, and computational biology to dissect the host-microbiome epigenetic interface.
This issue seeks to present pioneering research on how genetic, epigenetic, and epi-transcriptomic factors, and microbiome metabolites collectively influence GI health. We invite original research articles, reviews, and perspectives that cover, but are not limited to, the following topics:
• Genetic Influences on Microbiome Composition and Function: Analyzing how host genetic variations affect microbiome diversity, stability, and metabolic outputs, and their subsequent impact on GI health.
• Epigenetic Regulation of Host-Microbiome Interactions: Exploring the roles of DNA methylation, histone modifications, and chromatin remodeling in controlling genes involved in host-microbiome dynamics.
• Epi-Transcriptomic Modulation: Investigating RNA modifications, such as methylation and editing, and their impact on gene expression profiles related to microbiome interactions and GI stability.
• Microbiome Metabolites in GI Homeostasis: Understanding how microbiome-derived metabolites (e.g., short-chain fatty acids, bile acids, neurotransmitters) influence host cellular processes, immune responses, and metabolic functions.
• Integrative Approaches to GI Homeostasis: Utilizing multi-omics techniques to uncover the synergies between genetic, epigenetic, and epi-transcriptomic factors, and microbiome metabolites in maintaining GI equilibrium and identifying biomarkers for GI diseases.
• Pathophysiological Implications: Addressing how disruptions in these regulatory networks contribute to GI disorders such as IBD, CRC, HCC, and metabolic syndromes.
Keywords:
human GI tract, gut microbiome, host genetics, host epigenetics, epi-transcriptomics, GI homeostasis, microbiome-derived metabolites, DNA methylation, histone acetylation
Important Note:
All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
The human gastrointestinal (GI) tract is home to a complex and dynamic ecosystem of microorganisms including bacteria, viruses (viromes), fungi (mycobiome), and archaea (archaeome), where host genetics, epigenetics, and microbiome-derived metabolites interact to maintain GI homeostasis and overall health. Recent research has illuminated the pivotal roles of genetic, epigenetic, and epi-transcriptomic factors in this process. These mechanisms orchestrate host-microbiome-derived metabolite interactions, influencing both normal physiological functions and the pathogenesis of GI disorders. Furthermore, studies have revealed that the interplay between the host and its microbiome is not solely dependent on genetic factors but is also significantly influenced by epigenetic and epi-transcriptomic modifications, including methylation, acetylation, etc., which can alter gene expression without changing the DNA sequence, thereby modulating host-microbiome interactions in the development and differentiation of healthy and diseased states. In the context of the GI tract, the microbiome’s metabolites have emerged as key players influencing host epigenetics by using integrated transcriptomic and epi-transcriptomic approaches with microbiome metabolites. Therefore, understanding these mechanisms is crucial as they orchestrate host-microbiome interactions, influencing both normal physiological functions and the pathogenesis of GI disorders including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), hepatocellular carcinoma (HCC), and other related conditions.
Despite significant progress, the exact epigenetic mechanisms by which the microbiome influences host physiology and contributes to GI disorders remain poorly understood. The challenge lies in comprehensively mapping these complex interactions and understanding how they can be targeted for therapeutic benefit. The objective of this research topic is to elucidate these epigenetic pathways and identify novel biomarkers and therapeutic targets. Achieving this requires integrating recent advances in high-throughput sequencing, epigenome editing, and computational biology to dissect the host-microbiome epigenetic interface.
This issue seeks to present pioneering research on how genetic, epigenetic, and epi-transcriptomic factors, and microbiome metabolites collectively influence GI health. We invite original research articles, reviews, and perspectives that cover, but are not limited to, the following topics:
• Genetic Influences on Microbiome Composition and Function: Analyzing how host genetic variations affect microbiome diversity, stability, and metabolic outputs, and their subsequent impact on GI health.
• Epigenetic Regulation of Host-Microbiome Interactions: Exploring the roles of DNA methylation, histone modifications, and chromatin remodeling in controlling genes involved in host-microbiome dynamics.
• Epi-Transcriptomic Modulation: Investigating RNA modifications, such as methylation and editing, and their impact on gene expression profiles related to microbiome interactions and GI stability.
• Microbiome Metabolites in GI Homeostasis: Understanding how microbiome-derived metabolites (e.g., short-chain fatty acids, bile acids, neurotransmitters) influence host cellular processes, immune responses, and metabolic functions.
• Integrative Approaches to GI Homeostasis: Utilizing multi-omics techniques to uncover the synergies between genetic, epigenetic, and epi-transcriptomic factors, and microbiome metabolites in maintaining GI equilibrium and identifying biomarkers for GI diseases.
• Pathophysiological Implications: Addressing how disruptions in these regulatory networks contribute to GI disorders such as IBD, CRC, HCC, and metabolic syndromes.
Keywords:
human GI tract, gut microbiome, host genetics, host epigenetics, epi-transcriptomics, GI homeostasis, microbiome-derived metabolites, DNA methylation, histone acetylation
Important Note:
All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.