The gut enterotype describes the dominant microbial community structures present in the human gastrointestinal tract, characterized by specific combinations of prevalent bacterial genera. This microbial composition is not static; it undergoes changes throughout an individual’s life span, influenced by various factors including the quality of diet (especially long-term dietary habits) environmental conditions, age, physiological state, and certain pharmacological interventions (23).

In the field of microbiome research, three primary enterotypes have been characterized. The first enterotype, dominated by bacteria of the genus Bacteroides, is predominantly observed in individuals who adhere to diets high in animal proteins and fats. This enterotype is associated with a pro-inflammatory profile and an elevated risk of metabolic syndrome and other cardiometabolic disorders. The second enterotype is characterized by a predominance of Prevotella, which is commonly observed in populations consuming high amounts of complex carbohydrates and dietary fiber. This enterotype has been associated with anti-inflammatory effects and a metabolically protective phenotype. The third enterotype is dominated by Ruminococcus; however, its functional characterization remains less defined and necessitates further scientific investigation to elucidate its biological contributions. Preliminary findings suggest a link to mucin degradation and carbohydrate metabolism (24–26).

Table 1 provides an overview of the major bacterial phyla and genera of the gut microbiota and their predominant functions, while Figure 1 illustrates the interaction between plant-based dietary components, key microbial taxa, and their main metabolic effects.

The gut microbiota is integral to numerous metabolic and nutritional processes that facilitate digestion. It plays a key role in the fermentation of indigestible components, enhances nutrient absorption, and is involved in the synthesis of various metabolites, referred to as postbiotics, including short-chain fatty acids (SCFAs) and phytoestrogens (40). Moreover, the gut microbiota plays a critical protective role by promoting mucus production in intestinal epithelial cells, thereby forming a barrier against pathogenic microorganisms and environmental toxins. In addition, it supports gastrointestinal maturation, maintains intestinal mucosal integrity, ensures appropriate enzymatic activity, and contributes to host immune defense by regulating local immune responses. This multifaceted role underscores the importance of the gut microbiota in both metabolic function and immune regulation (41, 42).

Postbiotics are bacterial metabolites produced or secreted by intestinal microbiota, as well as molecules released during bacterial lysis. These compounds are recognized as bioactive substances with potential health benefits for the host, as they can enhance immunomodulatory, immunostimulatory, neuroregulatory, and antimicrobial functions (43). The category of postbiotics encompasses a diverse array of compounds, including short-chain fatty acids (SCFAs) such as butyrate, acetate, and propionate, as well as phytoestrogens, organic acids, enzymes, extracellular polysaccharides, gamma-aminobutyric acid (GABA), vitamins, and ribosomal peptides, among others (44).

These substances exhibit mechanisms akin to probiotics by having the capacity to modify intestinal pH and suppress the proliferation of pathogenic microorganisms, thereby contributing to intestinal homeostasis. Moreover, postbiotics can exert their effects independently of live microbial cells, enabling direct modulation and stimulation of the host’s immune response (45). As detailed in Table 2, postbiotics possess a range of beneficial properties, including anti-inflammatory, intestinal barrier-strengthening, immunomodulatory, anti-adhesive, antihypertensive, antiproliferative, antiviral, hypocholesterolemic, and antioxidant activities. Collectively, these bacterial metabolites are regarded as crucial factors in promoting health due to their ability to modulate physiological processes and support the prevention or alleviation of various pathologies (46).

The bacterial diversity within the gut microbiome is effectively characterized by the Prevotella: Bacteroides ratio, which serves as a sensitive indicator of dietary patterns. Empirical research demonstrates that individuals whose diets are abundant in dietary fiber, complex carbohydrates, and resistant starch tend to exhibit a higher prevalence of Prevotella. This microbial profile is associated with beneficial metabolic functions. In contrast, individuals who consume diets rich in animal protein and saturated fat typically show a predominance of Bacteroides, which correlates with diminished microbial diversity and less favorable metabolic profiles (1, 65).

In this context, Plant-based diets are associated with the enhancement of various beneficial gut microbiota, including genera such as Lactobacillus, Ruminococcus, Eubacterium rectale, Roseburia, Bifidobacterium, Veillonella, Lachnospira, Rikenellaceae, as well as members of the phylum Verrucomicrobia. These microorganisms play critical roles in the degradation of dietary fiber, the production of postbiotic metabolites, particularly short-chain fatty acids, and the modulation of immune responses. Consequently, they contribute significantly to the prevention and management of cardiovascular, metabolic, immune, and neurodegenerative diseases (30, 66).

Early studies established that diet is a major determinant of gut microbial structure, giving rise to predominant enterotypes characterized by Prevotella, Bacteroides, and Ruminococcus. Comparative analyses of fecal microbiota across mammalian species and herbivores provided foundational evidence demonstrating that dietary patterns exert a strong influence on intestinal microbial composition. In these studies, the dietary habits of omnivorous mammals closely resembled those of humans consuming mixed diets, whereas herbivorous feeding patterns showed similarities to plant-based dietary regimens in humans (67). These observations laid the groundwork for understanding how diet quality and composition modulate enterotype distribution.

Subsequent research has shown that increased consumption of animal proteins and fats, particularly when combined with long-term inadequate fiber intake, favors the proliferation of Bacteroides. This genus exhibits high tolerance to bile salts, conferring a competitive advantage under high-fat dietary conditions and concomitantly reducing the abundance of microorganisms specialized in fermenting complex carbohydrates. In contrast, regular and sustained consumption of plant-based foods, including vegetables, fruits, whole grains, and fiber-rich legumes, has been consistently associated with increased abundance, diversity, and prevalence of Prevotella and Ruminococcus. These taxa play a key role in polysaccharide degradation and the production of metabolites that support host metabolic and intestinal health (68).

More recent dietary intervention studies have further refined these associations by identifying specific microbial responses to distinct carbohydrate sources. Diets enriched in non-digestible carbohydrates derived from whole grains and wheat bran have been linked to increased abundance of Bifidobacterium and Lactobacillus, genera characterized by predominantly saccharolytic metabolism and protective effects on intestinal barrier integrity through inhibition of pathogenic bacteria. Additionally, intake of resistant starch, such as that present in whole barley, promotes the growth of lactic acid bacteria including Eubacterium rectale and Roseburia. Conversely, other members of the phylum Firmicutes, such as Clostridium and Enterococcus, tend to be less prevalent in gut microbiota shaped by plant-based dietary patterns (1).

Low nutritional bioavailability is a characteristic feature of foods that maintain intact cell walls, possess large particulate structures, and/or have not undergone thermal or mechanical treatments that enhance nutrient release, as is often the case with various raw plant-based foods. The consumption of products with lower bioavailability, such as fresh and minimally processed vegetables, yields systemic benefits. This is attributed to a greater proportion of their constituents reaching the distal regions of the gastrointestinal tract in an intact form, where they function as fermentable substrates for gut microbiota. This process promotes the production of beneficial bacterial metabolites and supports the maintenance of a diverse and stable microbial community. Conversely, a diet rich in ultra-processed foods significantly diminishes the availability of nutrients to the intestinal ecosystem, potentially altering the composition, metabolism, and functionality of the microbiota (8, 81). The composition of gut microbiota plays a crucial role in host health, with dietary nutritional characteristics significantly influencing the regulation, maintenance, and proliferation of beneficial microorganisms. A diet abundant in plant-based foods enhances the microbial synthesis of vitamins and promotes the production of neurotransmitters such as GABA, dopamine, and norepinephrine. Furthermore, it facilitates the generation of metabolites involved in energy homeostasis, intestinal motility, and immunomodulation. This dietary pattern also contributes to the integrity of the intestinal barrier, thereby reducing permeability associated with inflammatory processes, inadequate nutrient absorption, and gastrointestinal disorders, such as Crohn’s disease. Consequently, a plant-based diet is linked to a reduced incidence of various diseases, including cardiovascular, neurodegenerative, immunological, endocrine, and metabolic disorders, including diabetes mellitus (82).

Research has demonstrated that only 5–10% of dietary phytochemicals are absorbed in the small intestine, while approximately 90–95% are transported to the colon, where they undergo transformation by the bacterial communities within the microbiota (19). These microbial transformations yield metabolites with significant biological activity, which may exert beneficial systemic effects on the host, including cardioprotective properties and modulation of glucose metabolism. The regular consumption of plant-based foods increases the availability of polyphenols, compounds that are associated with the prevention of metabolic disorders such as obesity and type 2 diabetes mellitus, both of which are characteristic of metabolic syndrome. Furthermore, a variety of phytochemicals have the capacity to modulate gut microbial composition. For example, phenolic compounds present in tea have been shown to inhibit the growth and adhesion of Clostridium spp., E. coli, and Salmonella typhimurium (98, 99).

Flavonoids have been linked to favorable alterations in the Bacteroidetes to Firmicutes ratio, as well as a reduction in Proteobacteria at the phylum level. These changes may confer benefits for individuals with metabolic syndrome and enhance fecal microbial diversity. Furthermore, flavonoids have been shown to impact glucose metabolism and amino acid fermentation, potentially offering protective effects against obesity. Increased serum levels of carotenoids are associated with a reduced risk of chronic diseases and a microbiome that is healthier from both functional and metabolic perspectives. Similarly, glucosinolates present in cruciferous vegetables may facilitate the inoculation and reinoculation of specific bacterial populations, promoting a rise in the proportion of Bacteroidetes by up to 8 percent according to some studies in relation to Firmicutes (100, 101).

Finally, allicin, a prominent phytochemical found in garlic, exhibits significant anti-inflammatory properties and plays an important role in regulating cardiovascular health indicators, including blood pressure, arterial stiffness, and vascular function. Additionally, garlic consumption has been associated with an increased abundance of beneficial gut microbiota, specifically Lactobacillus and Clostridium spp., which are recognized for their positive effects on metabolic and cardiovascular health (102).

Table 3 presents a comprehensive overview of the effects of various micronutrients (including vitamins and minerals) and phytochemicals on gut microbiota. It outlines their influence on beneficial microorganisms, such as Bifidobacterium, Prevotella, Lactobacillus, and Faecalibacterium prausnitzii, alongside potentially pathogenic bacteria, including Bacteroides fragilis, Salmonella Typhimurium, and Campylobacter jejuni. These relationships are further illustrated in Figures 2, 3, which provide a schematic representation of the interactions between micronutrients, phytochemicals, and gut microbial taxa. This synthesis underscores the role of micronutrients and bioactive compounds derived from plant-based foods in modulating key physiological processes, including inflammation, oxidative stress, intestinal barrier integrity, and microbial composition. These factors collectively contribute to the maintenance of host health.

A vegetarian diet is defined by the exclusion of specific foods and products derived from animals, either completely or partially. This dietary pattern encompasses several categories based on the inclusion of certain food items. One category is the ovo-lacto vegetarian diet, which allows for the consumption of both dairy products and eggs. Another variation is the ovo vegetarian diet, wherein individuals consume eggs but exclude dairy products. Conversely, the lacto vegetarian diet permits the intake of dairy products while excluding eggs. Additionally, there is the semi-vegetarian approach, which allows for the consumption of red meat, poultry, and fish no more than once a week. Finally, the pescatarian diet includes fish, as well as dairy products and eggs (105).

The adoption of a vegetarian diet has significant implications for the composition of gut microbiota, resulting in marked changes in the abundance of microorganisms at the genus, species, and strain levels. This dietary pattern is increasingly recognized as a viable nutritional intervention strategy, with the potential to regulate gut health and offer protection against inflammatory processes. Research indicates a greater abundance of certain bacterial genera, such as Prevotella, Clostridium, Lactobacillus, Ruminococcus, Eubacterium rectale, and Faecalibacterium prausnitzii among individuals following vegetarian diets, coupled with a reduced presence of Bacteroides and Bifidobacterium when compared to those adhering to omnivorous diets (105).

Furthermore, the recognition of vegetarianism as a healthy dietary approach is supported by emerging evidence of its physiological benefits. Vegetarians typically exhibit a lower body mass index, decreased serum cholesterol concentrations, lower prevalence rates of diabetes, and reduced blood pressure levels. A higher intake of plant-based foods, characterized by increased dietary fiber and antioxidants, has also been associated with a diminished risk of cardiometabolic conditions and other chronic diseases (106). This evidence underscores the potential of vegetarian diets to contribute positively to overall health outcomes.

The vegan diet is characterized by the exclusion of animal fats and proteins, which alters the amino acid profile and increases the intake of dietary fiber. These changes are associated with significant modifications in the gut microbiota, particularly via an increase in Prevotella, a microbial genus often linked to plant-based dietary patterns (107).

Vegan diets are associated with numerous health benefits, primarily due to their high concentrations of fiber, folic acid, vitamins C and E, potassium, magnesium, and a diverse array of phytochemicals. Furthermore, they typically contain a higher proportion of unsaturated fats compared to non-vegan diets. However, if not carefully planned, a vegan diet may lead to deficiencies in essential nutrients such as protein, iron, and vitamin B₁₂. Despite these potential limitations, recent studies indicate that the adoption of a vegan diet may facilitate improvements in metabolic syndrome, reduce the risk of cardiovascular disease, and provide clinical benefits in managing inflammatory conditions, including rheumatoid arthritis (108).

The Mediterranean diet is characterized by a high consumption of plant-based foods, including fruits, vegetables, legumes, whole grains, nuts, and extra virgin olive oil. It also promotes moderate intake of fish, lean meats, and dairy products, while restricting consumption of red and processed meats. This dietary pattern is associated with numerous health benefits, particularly in relation to cardiovascular health, metabolic function, and inflammation reduction, all of which contribute to an enhanced quality of life (109).

Emerging research indicates that adherence to a Mediterranean diet has a beneficial impact on gut microbiota. Specifically, it increases the abundance of short-chain fatty acid (SCFA)-producing bacteria, primarily Faecalibacterium prausnitzii, Roseburia spp., and Bifidobacterium spp. (110). These bacteria metabolize dietary fiber and polyphenols to produce butyrate and other SCFAs, which are essential for reinforcing the intestinal barrier and diminishing inflammatory markers. The presence of these microorganisms within a balanced gut microbiome plays a crucial role in improving lipid and glucose metabolism as well as modulating immune responses. Furthermore, a healthy microbiota is linked to a reduced incidence of chronic degenerative diseases, particularly those associated with cardiovascular health and metabolic syndrome (111).

The flexitarian diet, commonly referred to as the semi-vegetarian diet, emphasizes the predominant consumption of plant-based foods while permitting the occasional intake of animal products, such as lean meats, fish, seafood, eggs, and dairy (112). Current scientific reviews indicate that this dietary approach has a favorable impact on gut microbiota, attributable to its high dietary fiber content and the diversity of plant-based foods included.

Research demonstrates that the flexitarian diet fosters the proliferation of beneficial bacterial populations, akin to those observed in strictly vegetarian diets. Notably, there is an increased prevalence of Bacteroidetes, which are implicated in the fermentation of polysaccharides, as well as specific bacterial groups such as Prevotella, Ruminococcus, and Roseburia, which produce SCFAs (113). This distinct microbial composition is directly associated with elevated SCFA production, which confers various health benefits, including enhanced regulation of the immune system, diminished systemic inflammation, and improved cardiometabolic health. Furthermore, the inherent flexibility of the flexitarian diet facilitates long-term adherence and encourages a gradual transition toward healthier eating patterns. This characteristic may contribute to its effectiveness in promoting sustainable dietary change (114).

The whole food plant-based (WFPB) diet is characterized by a focus on the intake of natural and minimally processed plant-based foods, including fruits, vegetables, legumes, whole grains, seeds, and nuts. This dietary framework restricts or eliminates animal products and ultra-processed foods to the greatest extent possible. Research indicates that the WFPB diet promotes a beneficial microbial profile conducive to intestinal health. By favoring the growth of bacteria such as Prevotella and Bacteroides, this diet enhances the metabolism of complex polysaccharides and the production of health-promoting metabolites. Furthermore, it creates an optimal environment for the development of butyrate-producing bacteria, including Faecalibacterium, Eubacterium rectale, and Roseburia (115).

These microbial communities play a critical role in maintaining the integrity of the intestinal mucosa, decreasing intestinal permeability, modulating inflammatory responses, and supporting metabolic health. Consequently, adherence to a WFPB diet is associated with a more anti-inflammatory microbiome, greater microbial diversity, and a reduction in cardiometabolic risk markers (116).

In comparing the dietary patterns previously discussed, it is evident that specific microorganisms confer substantial health benefits, including the reduction of systemic inflammation and the enhancement of cardiometabolic regulation. In particular, microorganisms associated with fiber fermentation and the production of short-chain fatty acids, specifically Ruminococcus spp., Eubacterium spp., Faecalibacterium prausnitzii, Roseburia, Prevotella, and Bifidobacterium spp., exhibit increased abundance with higher consumption of plant-based foods (117).

The composition and relative abundance of specific gut bacteria can vary significantly based on an individual’s dietary profile maintained over an extended period. For instance, research indicates that a whole-food, plant-based diet is associated with a microbiota that exhibits increased production of short-chain fatty acids compared to a flexitarian diet. Conversely, the Mediterranean diet, characterized by its high intake of foods rich in healthy fats and polyphenols, enhances specific metabolic pathways that are instrumental in modulating immune responses and regulating lipid metabolism (111, 113, 115).

Diets characterized by a higher intake of animal-based foods are associated with the proliferation of bacteria involved in protein fermentation, as well as an increase in metabolites that contribute to inflammation and elevate cardiometabolic risk (118).

Apparent inconsistencies across studies, such as variable reports on Bifidobacterium abundance in individuals following vegan diets, likely reflect differences in the specific composition of plant-based diets, including fiber type and intake, degree of food processing, geographic and cultural context, duration of dietary adherence, and methodological approaches used to assess the gut microbiota.