The intestinal microbiota is a community of microorganisms inhabiting the human intestines, potentially influencing both physiological and pathophysiological processes in the human body. Existing evidence suggests that nutrients can influence the modulation of the gut microbiota. However, there is still limited evidence regarding the effects of vitamin and mineral supplementation on the human gut microbiota through epigenetic modification. It is plausible that maintaining an adequate dietary intake of vitamin D, iron, fibre, zinc and magnesium may have a beneficial effect on alleviating inflammation in the body, reducing oxidative stress, and improving the condition of the intestinal microbiota through various epigenetic mechanisms. Moreover, epigenetics involves alterations in the phenotype of a cell without changing its fundamental DNA sequence. It appears that the modulation of the microbiota by various nutrients may lead to epigenetic regulation. The correlations between microbiota and epigenetics are potentially interdependent. Therefore, the primary objective of this review is to identify the complex relationships between diet, gut microbiota, and epigenetic regulation. These interactions could play a crucial role in systemic health.

Deregulation of microRNAs (miRNAs) has been implicated in the development of inflammatory bowel disease (IBD). Specific miRNAs are differentially expressed in patients with IBD compared to healthy individuals. Regulation of their expression can modulate the inflammatory response, the composition of the intestinal microbiota, and intestinal barrier function. miRNAs can regulate the immune and inflammatory response via multiple mechanisms, from Th1/Th17 regulation and ferroptosis to modulation of NLRP3 (NOD-like receptor family, pyrin domain-containing 3) and control of the NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) pathway. The use of miRNAs as biomarkers and therapeutic targets may help monitor IBD treatment and support the development of new, more individualized therapies that minimize common side effects.

Nigella sativa L. (family Ranunculaceae), also known as black cumin, has been used in cuisine around the world for many years. Due to its health-promoting properties, it can be used not only in the food industry but also in medicine. The main bioactive compound contained in the black cumin extract is thymoquinone (TQ), which has a special therapeutic role. The results of research in recent years confirmed its hypoglycemic, hypolipemic, and hepatoprotective effects, among others. In addition, the results of laboratory tests also indicate its immunomodulatory and anticancer effects, although there is still a lack of data on the mechanisms of how they are involved in the fight against cancer. Including this plant material in one’s diet can be both an element of prophylaxis and therapy supporting the treatment process, including pharmacological treatment. However, attention should be paid to its potential interactions with drugs used in the treatment of chronic diseases.

Inflammatory bowel diseases (IBDs) are a group of chronic diseases characterized by recurring periods of exacerbation and remission. Fibrosis of the intestine is one of the most common complications of IBD. Based on current analyses, it is evident that genetic factors and mechanisms, as well as epigenetic factors, play a role in the induction and progression of intestinal fibrosis in IBD. Key genetic factors and mechanisms that appear to be significant include NOD2, TGF-β, TLRs, Il23R, and ATG16L1. Deoxyribonucleic acid (DNA) methylation, histone modification, and ribonucleic acid (RNA) interference are the primary epigenetic mechanisms. Genetic and epigenetic mechanisms, which seem to be important in the pathophysiology and progression of IBD, may potentially be used in targeted therapy in the future. Therefore, the aim of this study was to gather and discuss selected mechanisms and genetic factors, as well as epigenetic factors.

Obesity, type 2 diabetes mellitus (T2DM) and steatohepatitis associated with metabolic dysfunction (MASLD) are on the rise and pose serious health challenges worldwide. In recent years, researchers have gained a better understanding of the important role of the gut microbiota in the development and progression of these diseases. Intestinal dysbiosis can contribute to the occurrence of increased intestinal permeability, inflammation and reduced numbers of commensal bacteria. In obesity, these changes contribute to chronic low-grade inflammation and deregulated metabolism. In MASLD, gut microbiota dysbiosis can promote liver fibrosis and impair bile acid metabolism, while in T2DM, they are associated with impaired glycemic control and insulin resistance. Regular physical activity has a positive effect on the composition of the gut microbiota, increasing its diversity, modulating its metabolic functions, strengthening the intestinal barrier and reducing inflammation. These findings suggest that exercise and microbiota-targeted interventions may play an important role in the prevention and treatment of metabolic diseases.

Inflammatory bowel disease (IBD) represents a growing public health challenge worldwide, and its prevalence is increasing year by year. A growing body of evidence suggests that diet plays a key role in shaping the gut microbiota, whose dysbiosis is a significant component of IBD pathogenesis. In response to the limitations of traditional, one-size-fits-all dietary recommendations, the concept of precision nutrition is emerging, which involves tailoring nutrition to a patient’s clinical, biological, and genetic characteristics. Of particular importance in this context is nutrigenomics, the science that studies the impact of dietary components on gene expression and the modulation of immune processes. Dietary components, such as polyphenols and certain vitamins, may influence gene expression and immune pathways. However, direct evidence that specific nutrients directly regulate genes associated with inflammatory bowel disease in humans remains limited. Nutrigenomic mechanisms reveal complex relationships between diet, gut microbiota, and genetic predispositions in IBD, encompassing transcriptome regulation, metabolomic changes, and epigenetic processes. A personalized nutritional approach, based on regular assessment of clinical and biological parameters and the close integration of dietary therapy with comprehensive treatment, appears to be a promising direction for the further development of IBD therapy.