Abstract

The human gastrointestinal tract harbors a complex and diverse community of microorganisms, collectively referred to as the gut microbiota. This ecosystem, composed of bacteria, archaea, viruses, and fungi, plays a critical role in host health by contributing to digestion, nutrient absorption, immune function, and metabolic regulation. In recent years, research has increasingly highlighted the link between gut microbiota composition and metabolic disorders such as obesity, type 2 diabetes mellitus (T2DM), dyslipidemia, metabolic syndrome, and non-alcoholic fatty liver disease (NAFLD). Dysbiosi, which is an imbalance in the microbial community, has been implicated in the pathogenesis and progression of these conditions. Dietary interventions aimed at modulating the gut microbiota have emerged as promising strategies for managing and potentially reversing metabolic disorders. This systematic review evaluates the current evidence on the effects of various dietary interventions such as the Mediterranean diet, ketogenic diet, low-fat vegan diet, low-carbohydrate diet, and supplementation with probiotics, prebiotics, and synbiotics on gut microbiota composition and key metabolic indicators in adults with metabolic disorders. Following PRISMA guidelines and the PICO framework, fifteen randomized controlled trials and crossover studies published between 2010 and 2025 were reviewed. These studies involved 1669 adult participants diagnosed with metabolic disorders and assessed changes in microbiota composition alongside metabolic outcomes including body weight, insulin sensitivity, blood glucose, lipid profiles, and inflammatory biomarkers. Findings across the studies demonstrated that dietary interventions frequently resulted in positive shifts in gut microbial communities. In particular, increased abundance of beneficial taxa such as Bifidobacterium, Faecalibacterium prausnitzii, and Akkermansia muciniphila was often associated with improved metabolic outcomes. These bacteria are known to produce short-chain fatty acids (SCFAs), especially butyrate, which support gut barrier function, reduce inflammation, enhance insulin sensitivity, and regulate lipid metabolism. Several studies reported significant reductions in body weight, visceral fat, and BMI, as well as improvements in fasting glucose, HbA1c, cholesterol levels, and inflammatory cytokines following dietary intervention. However, the review also identified variability in individual responses and outcomes across studies. Factors such as baseline gut microbiota composition, genetic predisposition, type and duration of dietary intervention, and adherence influenced results. Not all studies reported statistically significant improvements, and some control groups also experienced metabolic benefits, limiting the observed differences.

Keywords

Gastrointestinal Tract Harbors, Microorganism, Ecosystem

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1. Introduction

The human gastrointestinal tract harbors a diverse array of microorganisms, collectively referred to as the gut microbiota [1]. This community includes bacteria, fungi, viruses, and other microbes residing in the gastrointestinal tract. These organisms form a complex ecosystem that plays a crucial role in maintaining homeostasis, facilitating food digestion, promoting nutrient absorption, supporting immune function, and regulating various metabolic processes [2] [3].

The gut microbiota contributes to host metabolism through multiple biochemical pathways. For example, gut microbes are involved in the breakdown of bile acids, biosynthesis of essential vitamins such as vitamins K and B12, and fermentation of dietary polysaccharides—particularly those in dietary fibers that humans cannot digest—into short-chain fatty acids (SCFAs), including butyrate, propionate, and acetate [4]. These SCFAs serve as an energy source for intestinal epithelial cells and exert beneficial effects such as modulating inflammation, regulating appetite, and influencing glucose and lipid metabolism [4]. Consequently, the composition of the gut microbiota has been recognized as a critical determinant of metabolic health, with mounting evidence linking dysbiosis to various metabolic disorders.

Metabolic disorders, characterized by disturbances in normal metabolic processes, often involve systemic dysfunction in the metabolism of glucose, lipids, and other substrates. Common examples include type 2 diabetes mellitus (T2DM), obesity, dyslipidemia, non-alcoholic fatty liver disease (NAFLD), and metabolic syndrome. Diet plays a central role in the etiology, progression, and management of these conditions. Nutritional interventions are widely utilized as therapeutic strategies [5]. For instance, excessive caloric intake contributes to obesity, while high-glycemic diets can elevate blood glucose levels, increase insulin demand, and promote insulin resistance. Similarly, diets rich in saturated and trans fats are associated with dyslipidemia, and the growing prevalence of metabolic syndrome has been linked to poor dietary habits [6]-[8].

Dietary interventions serve as an effective approach for the management and prevention of metabolic disorders by aiming to regulate body weight, blood glucose, lipid profiles, and inflammatory status. Caloric restriction has proven effective in managing obesity [9], while low-glycemic index diets aid in stabilizing blood glucose and insulin levels in T2DM [5]. Reducing the intake of saturated and trans fats can also improve lipid profiles. Such interventions may involve altering the nutrient composition of the diet, using supplements, or modulating the gut microbiota to produce favorable metabolic outcomes. Common strategies include the administration of probiotics, prebiotics, synbiotics, high-protein diets, vegan diets, low-fat diets, and low-carbohydrate diets.

Assessing metabolic health indicators is essential for monitoring disease progression and evaluating responses to dietary or pharmacologic interventions. These indicators include anthropometric measures (e.g., weight, body composition, body mass index [BMI]), biochemical markers (e.g., fasting blood glucose, glycated hemoglobin [HbA1c], lipid profiles including LDL, HDL, and triglycerides), and inflammatory biomarkers (e.g., interleukin-6 [IL-6], interleukin-8 [IL-8]). Monitoring these metrics allows clinicians and researchers to evaluate the effectiveness of interventions. Several studies have explored how dietary modifications targeting the gut microbiome affect metabolic outcomes in conditions such as obesity, T2DM, and NAFLD [10].

Over time, research has expanded the understanding of the role of gut microbiota in human health. Early studies in the 20th century identified gut microbes but lacked insights into their functional significance due to technological limitations. Recent advances, such as high-throughput sequencing and metagenomics, have elucidated the diversity and metabolic functions of the gut microbial ecosystem [11]. Some studies have reported associations between gut microbiota dysbiosis and metabolic disorders. For example, Turnbaugh et al. (2006) found differences in gut microbial composition between obese and lean individuals [12]. Ridaura et al. demonstrated that fecal microbiota transplantation from obese mice could induce obesity in germ-free mice, implicating microbiota in the pathogenesis of obesity [13]. Other studies have explored the mechanisms through which the microbiota influences metabolism, further emphasizing its potential as a therapeutic target [14].

Multiple dietary approaches have been investigated for their ability to modulate the gut microbiota and improve metabolic health. Probiotics—live microorganisms such as Lactobacillus spp. and Bifidobacterium spp., administered in adequate amounts—have been shown to enhance insulin sensitivity, reduce inflammation in T2DM, and improve lipid metabolism [15]. Prebiotics, such as inulin, stimulate the growth and activity of beneficial gut microbes, thereby increasing SCFA production [16] [17]. Synbiotics, which combine probiotics and prebiotics, have also been studied, although results are mixed; for example, Kazanawa et al. reported no significant changes in glycemic control following 24 weeks of synbiotic supplementation [18] [19].

The Mediterranean diet—rich in fruits, vegetables, whole grains, nuts, and olive oil—has been shown to enhance gut microbial diversity and improve glucose metabolism. Galie et al. observed increased insulin sensitivity following dietary intervention with the Mediterranean diet [20]-[22]. Similarly, ketogenic and low-carbohydrate diets have been associated with alterations in gut microbiota and improved metabolic outcomes. Deledda et al. reported enhanced insulin sensitivity and glycemic control following the introduction of a ketogenic diet [23] [24].

Recent studies have also considered individual variability in baseline gut microbiota composition and host genetics, which may influence responses to dietary interventions. For example, Zhang et al. (2021) found that individuals with higher baseline levels of Bacteroides experienced greater weight loss [25]. Comparative studies, such as randomized crossover trials, have examined the differential effects of dietary interventions; Deledda et al. reported greater weight loss with a ketogenic diet than with a Mediterranean diet [23].

Given the increasing global prevalence of T2DM and obesity, there is an urgent need for sustainable and effective interventions. Dietary strategies offer a promising non-pharmacologic approach that could reduce reliance on medication, lower healthcare costs, and enhance quality of life. Some studies suggest that these interventions may be tailored to individual needs based on microbiota profiles. However, translating these findings into clinical practice requires comprehensive and systematically synthesized evidence, which is currently lacking. Variability in study design, population characteristics, dietary interventions, and outcome measures has contributed to the heterogeneity of existing data.

These gaps in the literature limit the development of robust clinical guidelines. This systematic review seeks to address these gaps by critically appraising recent evidence on dietary interventions targeting the gut microbiome and their effects on metabolic health indicators in adults with metabolic disorders. Specifically, the objectives are to:

• Identify the effects of dietary interventions on gut microbiota composition and diversity.

• Assess the impact of each intervention on metabolic indicators such as body weight, glycemic control, lipid profiles, and inflammatory biomarkers.

• Compare the microbiota and metabolic effects of different dietary interventions in similar populations.

This review will enhance the understanding of the interactions among diet, gut microbiota, and metabolism, and inform clinical decision-making in the management of metabolic disorders. It will also provide recommendations based on the strengths and limitations of current research, thereby guiding future investigations and supporting evidence-based practice.

2. Methodology

This study followed the PRISMA guidelines, and the PICO framework was used to formulate the research question and study selection [26] [27]. The population (P) refers to adults with metabolic disorders, the intervention (I) includes dietary interventions that aim to modulate gut microbiota, such as the use of probiotics, specific diets and so on, the comparison (C) is a standard/conventional diet, and the outcomes (O) being assessed are metabolic health indicators. The purpose of this study is to address this research question: In adults with metabolic disorders (P), how does modulation of gut microbiota through dietary interventions (I) compared to a standard diet (C) affect metabolic health indicators (O)?

2.1. Inclusion and Exclusion Criteria

Original peer-reviewed studies on this topic were selected (Randomized controlled trials (RCTs), cohort studies, clinical trials). Studies investigating dietary interventions modulating gut microbiota were included (probiotics, prebiotics, fiber supplementation, Mediterranean diet, ketogenic diet). Studies that measure metabolic health indicators such as insulin sensitivity, blood glucose levels, lipid profiles, BMI, weight loss, and inflammation were included.

Studies on non-human populations (animal studies), and studies without a standard diet control group or clear metabolic health indicators. Studies published outside the 2010-2025 timeframe, non-peer-reviewed articles, and dissertations were not included. Studies not published in English or not available in full-text format were also excluded.

Animal studies were excluded in order to ensure that the findings of this review are applicable to human health due to various interspecies differences in gut microbiome composition, diet, and metabolism (See Table 1).

2.2. Search Strategy

A search was conducted in PubMed Google Scholar, and Cochrane library and the following search terms were used:

Table 1. Inclusion and exclusion criteria.

• “dietary intervention” OR “probiotics” OR “prebiotics” OR “dietary fiber” OR “Mediterranean diet” OR “ketogenic diet”

• “gut microbiota” OR “gut microbiome” OR “microbiome”

• “metabolic health” OR “insulin sensitivity” OR “glucose metabolism” OR “lipid metabolism” OR “BMI” OR “weight loss” OR “inflammatory markers”

• “metabolic disorders” OR “obesity” OR “type 2 diabetes” OR “dyslipidemia”

• “clinical trial” OR “randomized controlled trial”

• “adult”

Boolean operators “AND” and “OR” were used to combine the keywords into strings for advanced searches and the studies were filtered for publication in English and published within the last 15 years (2010-2025).

2.3. Study Selection and Screening

The initial search on PubMed, Google Scholar and Cochrane Library retrieved a total of 22,399 articles. The titles and abstracts of these articles were screened, and 22,328 were excluded for failing to meet the inclusion criteria. The remaining 71 articles were uploaded into Rayyan software for duplicate detection and were reviewed in full text [28]. Studies were included and excluded based on the inclusion and exclusion criteria.

Four individuals carried out the full-text screening and differences resolved through discussion. Data from the included studies were extracted into a data extraction matrix (See Table 2) that included study characteristics (authors, publication year, study design), Population (sample size, characteristics, metabolic disorder diagnosed), Intervention details (type of dietary intervention, duration), Outcome measures, Key findings and a Critical Appraisal of the findings. A CASP checklist (See Appendix) was also used to assess the quality of the studies [29].

2.4. Ethical Considerations

As this study involved a review of existing literature, no ethical approval was required. All data used in the review were from publicly available, peer-reviewed sources. The studies that involved primary data collection received ethical approval to be conducted and obtained informed consent from participants, the confidentiality of participants was maintained.

3. Results

3.1. Study Characteristics

The studies selected for this review were published between 2019 and 2024, 15 in total- 13 randomized control trials and 2 crossover trials. They all studied the effects of dietary interventions that modulate gut microbiota on metabolic outcomes. The individual sample sizes ranged from (n = 11) in the study by Deledda et al. in 2022 [23], to (n = 362) in the study by Muralidharan et al. in 2022 [30] and a total of 1669 participants across all studies. The populations studied included Adults with metabolic disorders such as Obesity, Type 2 Diabetes Mellitus, Gestational Diabetes, Dyslipidemia, Metabolic syndrome and Non-alcoholic fatty liver disease. Most of the studies had a balanced gender distribution but 2 of the studies used an all-female population [31] [32].

The studies were conducted in various locations, 5 studies were conducted in Europe (Belgium, Spain, Italy and Greece), 7 studies were conducted in Asian countries such as Japan, China, Malaysia and Israel and 3 of the studies were conducted in the United States of America. The different dietary interventions included low-fat vegan diet, ketogenic diet, mediterranean diet, avocado-enriched hypocaloric diet, synbiotics, probiotics and prebiotics, and all studies had control groups.

Figure 1. Prisma flowchart.

The search results presented in Figure 1 above (the PRISMA flow chart) show the summary of the papers used in the study. The databases provided a total of Twenty two thousand three hundred and ninety five (22,399) research papers, of which only fifteen met the inclusion criteria for this systematic review (See Appendix).

3.2. Changes in Gut Microbiota

Differences in the composition of gut microbiota were observed with most dietary interventions. Kahleová et al. (2020) reported an increase in the abundance of Faecalibacterium prausnitzii following the introduction of a low-fat vegan diet. Similarly, Hiel et al., in a study on inulin supplementation in obese individuals, observed an increase in Bifidobacterium, which was associated with improvements in metabolic health [33]. Chooi et al. reported an increase in Bifidobacterium adolescentis resulting from C-15 (pentadecanoic acid) supplementation, and Kanazawa et al. also reported favorable changes in the abundance of Bifidobacterium adolescentis and Bifidobacterium pseudocatenulatum in their intervention group [31]. Another study by Hassain et al. (2022) also documented an increase in Bifidobacterium adolescentis following a dietary intervention [32].

Zikou et al. (2023) reported the effects of a probiotic supplement on gut microbiota, showing an increase in the genera Akkermansia, Megamonas, and Flavonifractor, while Shigella showed a significant decrease in relative abundance in the intervention group [34]. An intervention by Deledda et al. (2022) involving a ketogenic diet demonstrated a shift in the gut microbiome, with a significant increase in beneficial microbial taxa such as members of the phylum Verrucomicrobiota—including Verrucomicrobiae, Verrucomicrobiales, Akkermansiaceae, and Akkermansia—as well as Christensenellaceae, Eubacterium spp., and a reduction in microbial taxa previously associated with obesity, such as Firmicutes and Actinobacteriota [23].

In the BE-GONE trial, which utilized beans as a prebiotic, an increase in the abundance of Bifidobacterium adolescentis, Eubacterium rectale, and Eubacterium spp. was reported after the intervention, accompanied by reductions in pro-inflammatory markers [35].

In 2021, Zhang et al. investigated the effects of a low-carbohydrate diet and observed an increase in butyrate-producing bacteria such as Ruminococcaceae and Porphyromonadaceae [25]. Rinott et al. reported that the Green-Mediterranean diet led to an increase in Prevotella and a decrease in Bifidobacterium spp. [21]. Sergeev et al., in a placebo-controlled study on a synbiotic intervention, reported an increase at the genus level in Ruminococcus, Bifidobacterium, Sutterella, Tyzzerella, Eisenbergiella, Eubacterium, Eggerthella, Methanobrevibacter, Lachnospiraceae, Edwardsiella, Lactobacillus, Allobaculum, Enterococcus, Hydrogenoanaerobacterium, Coprococcus, and Butyricimonas. Conversely, the relative abundance of Ruminococcaceae, Prevotella, Gardnerella, Turicibacter, and Megasphaera was lower in the synbiotic group compared to the placebo group [36].

3.3. Effect on Body Composition and Weight

Some studies reported no significant differences in weight or body composition following dietary interventions. For example, Henning et al. (2019) found that an avocado-based hypocaloric diet resulted in significant weight loss; however, weight loss was also observed in the control group, and no statistically significant differences were noted between the groups [37]. Similarly, Sergeev et al. reported no significant changes in body composition or body fat percentage following their intervention [36].

Conversely, several studies reported positive changes, including reductions in body weight and composition, as a result of dietary interventions. In a randomized controlled trial conducted by Kahleová et al. (2020), a low-fat vegan diet led to a significant reduction in body weight, fat mass, and visceral fat volume (treatment effect: −5.9 kg, −3.9 kg, and −240 cm³, respectively) [33]. Hiel et al. also reported greater weight loss and a reduction in body mass index (BMI) following inulin supplementation [17]. Similarly, Deledda et al. (2022) documented reductions in body weight and BMI after the introduction of ketogenic and Mediterranean diets [23]. In another study, Muralidharan et al. (2021) found that adherence to a Mediterranean diet combined with physical activity resulted in greater weight loss (−4.2 kg) [30]. Zhang et al. (2021) also observed significant weight loss following a low-carbohydrate dietary intervention [25].

3.4. Effect on Insulin Sensitivity and Glucose Control

Some studies reported improvements in blood glucose control and insulin sensitivity following dietary interventions. For example, Galié et al. observed an improvement in HOMA-IR, a measure of insulin sensitivity, after an intervention with the Mediterranean diet [22]. Hasain et al. and Zikou et al. reported that probiotic supplementation significantly reduced fasting blood glucose and glycated hemoglobin (HbA1c) levels in study participants [32]-[34]. Deledda et al. (2022) also found that a ketogenic diet led to improvements in insulin sensitivity and glucose control [23].

However, Kanazawa et al. (2021) reported no significant differences in glycemic control between the two groups at 24 weeks. Notably, the symbiotic group exhibited significantly higher fasting blood glucose and HbA1c levels at 12 weeks compared to the control group [19].

3.5. Lipid Profile and Other Biomarkers

Positive changes in lipid profiles were reported in several studies. For example, Galié et al. reported a reduction in total cholesterol and an improvement in HDL cholesterol levels following a Mediterranean dietary intervention, while Zikou et al. observed reductions in LDL cholesterol and triglycerides with probiotic supplementation [22] [34]. Chooi et al. (2024) also reported a reduction in LDL cholesterol as a result of C15 (pentadecanoic acid) supplementation [31]. Similarly, Hasain et al. observed a decrease in mean total cholesterol levels following probiotic supplementation [32]. Henning et al. reported a reduction in serum hepatic growth factor following the introduction of an avocado-based hypocaloric diet [37].

Some studies also assessed the effects of these interventions on inflammatory biomarkers. Hasain et al. (2022) reported higher levels of interleukin-6 (IL-6) and interleukin-8 (IL-8) in the control group, while Kanazawa et al. noted no significant differences in IL-6 levels between groups [132]. The BE-GONE trial by Zhang et al. (2023) reported an increase in fibroblast growth factor 19 (FGF-19), while levels of interleukin-10 receptor alpha (IL10RA) and other cytokines—including tumor necrosis factor-related activation-induced cytokine (TRANCE), T-cell surface glycoprotein CD8 alpha chain (CD8A), programmed cell death 1 ligand 1 (PD-L1), C-X-C motif chemokine ligand 1 (CXCL1), and urokinase-type plasminogen activator (uPA)—decreased in response to an 8-week bean-based dietary intervention [35].

3.6. Comparison of Dietary Interventions

A comparison of the Mediterranean diet and ketogenic diet by Deledda et al. (2022) reported greater weight loss in the ketogenic diet group than in the Mediterranean diet group, although both diets led to an increase in beneficial gut microbiota, such as Akkermansia [23]. Galié et al. also compared the Mediterranean diet to nut supplementation and reported a general increase in circulating plasma amino acids; specifically, phenylalanine, histidine, cystathionine, and threonine levels were higher in the Mediterranean diet group, while cysteine was higher in the nut supplementation group. Additionally, they reported higher succinate levels and increased testosterone in the Mediterranean diet group, whereas androsterone sulfate levels were elevated in the nut supplementation group [22].

4. Discussion

Certain gut microbial taxa may be responsible for the positive metabolic changes observed following dietary interventions. Bifidobacterium, Akkermansia, and Faecalibacterium were reported in several of the studies reviewed. These studies documented increases in these microbial groups, accompanied by improvements in metabolic indicators. For instance, Hiel et al. (2020) found that inulin supplementation increased Bifidobacterium abundance, which was associated with enhanced weight loss and insulin sensitivity. Several other studies similarly reported an increase in Bifidobacterium [17]. Zikou et al. and Deledda et al. observed increased levels of Akkermansia following their respective interventions, along with improvements in weight loss and glycemic control [34]. Kahleova et al. reported that Faecalibacterium prausnitzii increased among participants following a vegan diet intervention, with corresponding weight reduction [33].

Short-chain fatty acids (SCFAs), which are produced by these bacterial taxa, serve as energy sources for gastrointestinal cells and perform various metabolic functions, including appetite regulation, inflammation reduction, improved insulin sensitivity, and maintenance of intestinal barrier integrity [4]. These effects may underlie the metabolic benefits observed with increased abundance of these taxa. However, not all studies reported a consistent relationship between increased abundance of these organisms and improved metabolic parameters. For example, Zhang et al. (2021) suggested that baseline gut microbiota composition influenced individual responses to dietary interventions; participants with higher baseline levels of Bacteroides experienced more pronounced weight loss [25]. Furthermore, sample sizes in many of these studies were small, and the duration of interventions relatively short. A subsequent study by Zhang et al. (2023) found no significant improvement in insulin resistance in some participants, despite increased Faecalibacterium prausnitzii abundance [35].

Although Bifidobacterium, Akkermansia, and Faecalibacterium are important gut taxa implicated in metabolic benefits from dietary interventions, findings suggest that their increase alone does not universally lead to clinical improvements. Other factors, such as host genetics and baseline microbiota composition, may also play significant roles.

Dietary interventions targeting the gut microbiome have shown potential to promote weight loss and improve body composition in adults with metabolic disorders. Several studies reported significant reductions in body weight and other anthropometric measurements. For example, Kahleova et al. (2020) observed weight and fat mass reduction following a low-fat vegan diet. Similarly, Hiel et al. reported weight loss and BMI reduction with inulin supplementation [33]. Zhang et al. (2021) noted weight loss among participants on a low-carbohydrate diet, while Deledda et al. reported similar outcomes with ketogenic and Mediterranean diets [25]. Muralidharan et al. found that combining a Mediterranean diet with physical activity further enhanced weight loss [30]. However, not all studies demonstrated statistically significant differences; Henning et al. and Sergeev et al. observed no significant differences between intervention and control groups [36] [37].

Several mechanisms have been proposed to explain these effects, including increased SCFA production by gut microbiota. Butyrate, for example, may regulate appetite by promoting satiety and improve energy expenditure and fat metabolism [4]. Contradictory results in some studies may be attributed to short intervention durations or to control diets that also conferred metabolic benefits—for instance, a hypocaloric diet (Henning et al.) and a low-carbohydrate high-protein diet (Sergeev et al.) [36] [37]. Nevertheless, dietary modifications targeting the gut microbiota remain a promising strategy for achieving weight loss and improving body composition in individuals with metabolic disorders.

Dietary interventions may also enhance glycemic control in individuals with type 2 diabetes mellitus (T2DM) by modulating the gut microbiome and increasing insulin sensitivity. Galie et al. linked increased SCFA-producing bacteria, induced by adherence to a Mediterranean diet, to improved insulin sensitivity (measured by HOMA-IR), HbA1c, and fasting blood glucose levels [22]. Deledda et al. similarly reported improved insulin sensitivity and glycemic regulation following a ketogenic diet intervention [23]. Zikou et al. and Hasain et al. observed reductions in fasting blood glucose and HbA1c after probiotic supplementation [32] [34]. In contrast, Kanazawa et al. (2021) found no significant differences in glycemic control following synbiotic supplementation at 24 weeks [19].

It is postulated that these improvements arise from reduced gut permeability and systemic inflammation, mediated by SCFAs [38]. However, confounding factors, such as the use of hypoglycemic agents like metformin, which also influence gut microbiota composition, may affect responses to dietary interventions. Despite individual variability, the evidence supports the efficacy of microbiota-targeting dietary interventions in improving glycemic control in T2DM patients [34].

Lipid metabolism also appears to benefit from dietary interventions that alter the gut microbiota. Several studies reported favorable changes in lipid profiles. For example, Zikou et al. and Hasain et al. observed reductions in LDL cholesterol and triglycerides following probiotic supplementation. Chooi et al. reported lowered LDL cholesterol with C15 supplementation, and Galie et al. noted reductions in total cholesterol and improvements in HDL cholesterol after adherence to a Mediterranean diet [31] [32] [34].

SCFAs are known to influence bile acid metabolism and lipid synthesis. Butyrate, in particular, plays a critical role in regulating lipid storage and synthesis pathways [39]. SCFAs also activate GPR43 receptors, which regulate cholesterol metabolism and triglyceride storage in tissues [40]. Thus, dietary interventions that enhance SCFA production via gut microbiota modulation may contribute to improved lipid metabolism.

Furthermore, some dietary interventions reduce systemic inflammation by lowering levels of inflammatory biomarkers in individuals with metabolic disorders. Several studies reported decreases in pro-inflammatory cytokines following intervention. For instance, Hasain et al. found higher levels of interleukin-6 and interleukin-8 in the control group compared to the intervention group, whereas Kanazawa et al. found no significant differences in interleukin-6 levels [32]. The anti-inflammatory effects are believed to be mediated by SCFAs, which act as signaling molecules that activate receptors promoting the release of anti-inflammatory cytokines and suppressing pro-inflammatory mediators. SCFA-producing bacteria may also modulate immune responses through T-cell regulation [41]. Thus, the anti-inflammatory benefits of dietary interventions targeting the gut microbiota are likely mediated by microbial metabolites such as SCFAs.

The effectiveness of dietary interventions in modulating the gut microbiome and improving metabolic outcomes varies depending on the specific dietary approach. The studies included in this review utilized various diets, including vegan, ketogenic, low-carbohydrate, and Mediterranean diets, as well as probiotic and synbiotic supplementation, each demonstrating differing degrees of impact on metabolic parameters. For instance, one study comparing ketogenic and Mediterranean diets found greater weight loss in the ketogenic group [23]. Galie et al. also reported distinct metabolomic profiles when comparing Mediterranean diets to nut supplementation, with differences in plasma amino acid and hormone levels [22].

These differences may be attributed to variations in macronutrient composition, fiber content, and bioactive compounds, which influence gut microbial communities in unique ways. Ketogenic diets, typically low in fermentable fiber, promote the growth of specific bacteria [42], whereas Mediterranean diets, rich in fiber and polyphenols, support the proliferation of SCFA-producing taxa [43]. These findings suggest that dietary interventions should be individualized based on the patient’s needs and baseline gut microbiota composition to optimize metabolic outcomes, as further supported by evidence from Lauw et al., who demonstrated that synbiotic supplementation tailored to dietary patterns improved metabolic parameters and modulated gut microbiota in overweight individuals [44].

5. Conclusions

This systematic review synthesizes current evidence on the impact of dietary interventions that modulate the gut microbiota on metabolic health indicators in adults with metabolic disorders. The findings affirm the significant role of gut microbiota in influencing metabolic outcomes such as body weight, glycemic control, lipid profiles, and inflammation. Across a diverse range of dietary approaches—including Mediterranean, vegan, ketogenic, low-carbohydrate diets, as well as probiotic, prebiotic, and synbiotic supplementation—there is a consistent association between beneficial shifts in gut microbial composition and improvements in metabolic health.

Notably, certain bacterial taxa such as Bifidobacterium, Faecalibacterium pra-usnitzii, and Akkermansia muciniphila were frequently associated with favorable changes in metabolic indicators. Their presence often coincided with enhanced short-chain fatty acid (SCFA) production, which in turn contributed to reduced systemic inflammation, improved insulin sensitivity, and better lipid metabolism. However, the review also highlights the complexity of the gut microbiome’s interaction with diet; not all interventions led to statistically significant improvements, and individual variability in response—potentially due to baseline microbiota composition and host genetics—was evident.

Weight reduction and improvements in body composition were consistently observed in several studies, especially those involving vegan, ketogenic, and Mediterranean diets. These effects appear to be mediated through both caloric restriction and microbial shifts. Similarly, interventions improved glycemic control in individuals with type 2 diabetes, as reflected by reductions in HbA1c and fasting glucose levels. Lipid profiles also showed notable improvements, particularly reductions in LDL cholesterol and triglycerides, as well as increases in HDL cholesterol in some cases.

Despite promising results, the heterogeneity in study design, intervention duration, sample size, and participant characteristics presents challenges in generalizing these findings. Additionally, confounding factors such as medication use and dietary adherence further complicate the interpretation of outcomes. While the reviewed studies support the therapeutic potential of targeting gut microbiota through diet, robust, long-term randomized controlled trials with standardized methodologies are needed to establish causality and inform clinical guidelines.

In conclusion, modulating the gut microbiota through tailored dietary interventions represents a promising, non-pharmacological strategy for managing metabolic disorders. Integrating microbiome profiling into personalized nutrition plans may enhance intervention efficacy and optimize health outcomes. Future research should prioritize longitudinal designs, mechanistic studies, and the development of individualized treatment frameworks to fully harness the gut microbiota’s therapeutic potential.

Conflicts of Interest

The authors declare no conflicts of interest.

Appendix: Casp Checklist

Paper for appraisal and reference: Effect of modulation of gut microbiota through dietary interventions on metabolic health indicators

Conflicts of Interest

The authors declare no conflicts of interest.

References