Research Topic

Plant Role in Human Gene Expression and Gut Microbiome Regulation

About this Research Topic

A diet rich in fruits and vegetables significantly contributes to the maintenance of human health and aging. Numerous factors can be involved. For many years, scientists believed that these beneficial effects were only due to the antioxidant properties of polyphenols or other similar nutrients present in almost all fruits or vegetables typically used in the human diet. Nowadays, thanks to the advent of omics studies and the application of bioinformatics and computational biology approaches, it is recognized worldwide that plant nutrients can affect the level of expression of human genes and gut microbiome regulation. The molecular mechanisms through which these effects are propagated in humans is still poorly understood, but the number of publications in the field is growing at an exponential rate. The types of approaches used are multidisciplinary and can span from gene- and nutrient-specific investigations to large-scale analyses at the genomic, transcriptomic, epigenomic, and microbiome level.

The impact of ingested RNA from vegetable food sources on gene expression in nematodes and insects is something that has been known for a long time. More recently, a similar phenomenon has also been reported in human and other mammals. This discovery brought on what has been called the “xenomiR hypothesis,” which give rise to a new research field in nutrition based on the concept that plant miRNAs can target and regulate the expression of animal genes. Altogether, these findings have generated both excitement and controversy, with a critical debate as to whether the plant-derived miRNAs detected in animal samples represent contamination during experiments or bona fide xenomiRs. Different published studies have provided evidence that plant-derived miRNAs could survive the digestive system, be absorbed and transferred into the blood, circulate through the body, regulate animal gene expression as endogenous RNAs, and induce different phenotypes. On the other side, accumulating evidence demonstrates that miRNAs can be transferred to neighboring or distant cells via secreted endoplasmic vesicles (EVs), such as exosomes, and act as a modulator of cell function. Notably, the diet has a considerable effect on the composition of the human gut microbiota that in turn has an essential role in maintaining host physiology and its health condition. In this context, a recent study showed that plant-derived exosome-like nanoparticles (ELNs) are adsorbed by the gut microbiota and contain RNAs that alter microbiome composition and host physiology.

The present Research Topic focuses on studies and methodological approaches that can shed light on the molecular mechanisms and biological processes of a possible cross-kingdom genetic interaction between plant RNA and human genes or the microbiome. It will also feature perspectives of the potential impact of these findings on the improvement of nutrition for human health, effects on the gut microbiome, and the therapeutic potential of these RNAs in the medical field.

This Research Topic includes, but is not limited to, the following aspects:
· Nutrigenomics, epigenomics, transcriptomics, and microbiome studies investigating a potential cross-kingdom genetic interaction between bioavailable plant nutrients and human gene expression or gut microbiome regulation
· Bioinformatics, computational biology, and machine learning models and applications that can aid big data analysis and research in this field


Keywords: plant ncRNAs, gut microbiome, gene expression, nutrition, nutrigenetics, plant miRNAs


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.

A diet rich in fruits and vegetables significantly contributes to the maintenance of human health and aging. Numerous factors can be involved. For many years, scientists believed that these beneficial effects were only due to the antioxidant properties of polyphenols or other similar nutrients present in almost all fruits or vegetables typically used in the human diet. Nowadays, thanks to the advent of omics studies and the application of bioinformatics and computational biology approaches, it is recognized worldwide that plant nutrients can affect the level of expression of human genes and gut microbiome regulation. The molecular mechanisms through which these effects are propagated in humans is still poorly understood, but the number of publications in the field is growing at an exponential rate. The types of approaches used are multidisciplinary and can span from gene- and nutrient-specific investigations to large-scale analyses at the genomic, transcriptomic, epigenomic, and microbiome level.

The impact of ingested RNA from vegetable food sources on gene expression in nematodes and insects is something that has been known for a long time. More recently, a similar phenomenon has also been reported in human and other mammals. This discovery brought on what has been called the “xenomiR hypothesis,” which give rise to a new research field in nutrition based on the concept that plant miRNAs can target and regulate the expression of animal genes. Altogether, these findings have generated both excitement and controversy, with a critical debate as to whether the plant-derived miRNAs detected in animal samples represent contamination during experiments or bona fide xenomiRs. Different published studies have provided evidence that plant-derived miRNAs could survive the digestive system, be absorbed and transferred into the blood, circulate through the body, regulate animal gene expression as endogenous RNAs, and induce different phenotypes. On the other side, accumulating evidence demonstrates that miRNAs can be transferred to neighboring or distant cells via secreted endoplasmic vesicles (EVs), such as exosomes, and act as a modulator of cell function. Notably, the diet has a considerable effect on the composition of the human gut microbiota that in turn has an essential role in maintaining host physiology and its health condition. In this context, a recent study showed that plant-derived exosome-like nanoparticles (ELNs) are adsorbed by the gut microbiota and contain RNAs that alter microbiome composition and host physiology.

The present Research Topic focuses on studies and methodological approaches that can shed light on the molecular mechanisms and biological processes of a possible cross-kingdom genetic interaction between plant RNA and human genes or the microbiome. It will also feature perspectives of the potential impact of these findings on the improvement of nutrition for human health, effects on the gut microbiome, and the therapeutic potential of these RNAs in the medical field.

This Research Topic includes, but is not limited to, the following aspects:
· Nutrigenomics, epigenomics, transcriptomics, and microbiome studies investigating a potential cross-kingdom genetic interaction between bioavailable plant nutrients and human gene expression or gut microbiome regulation
· Bioinformatics, computational biology, and machine learning models and applications that can aid big data analysis and research in this field


Keywords: plant ncRNAs, gut microbiome, gene expression, nutrition, nutrigenetics, plant miRNAs


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.

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Submission Deadlines

24 July 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

24 July 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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