Personalized Nutrition Through the Gut Microbiome in Metabolic Syndrome and Related Comorbidities

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This review article addresses an important and timely topic: the role of the gut microbiome in metabolic syndrome (MetS) and its integration into personalized nutrition strategies. The manuscript is comprehensive, well-structured, and supported by an extensive reference list. It effectively synthesizes mechanistic insights, observational evidence, and intervention studies, while highlighting future directions and implementation challenges.

However, the manuscript would benefit from minor revisions to improve clarity, conciseness, and practical relevance for clinical and research audiences.

 

Firstly, I would like to point out the strengths of the manuscript:

• Relevance: The topic aligns well with current research priorities in personalized nutrition and microbiome science.
• Comprehensive coverage: Includes mechanistic pathways (SCFAs, bile acids, endotoxemia), diet–microbiome interactions, exercise effects, and clinical translation.
• Logical structure: Clear progression from background to mechanisms, interventions, and future directions.
• References: Up-to-date and extensive, reflecting the state of the field.

 

My major suggestions are:

• Abstract: The abstract is dense and highly technical. It should be more concise and clearly state: background and rationale, objective of the review, key findings and novelty and practical implications. Suggested revision: Emphasize the gap in current “one-size-fits-all” dietary guidelines and the potential of microbiome-informed personalization.
• Language and Readability: Several sentences are long and complex, reducing clarity. For example: “Novel evidence suggests that the gut microbiome could play key role in several pathways related to diet-host interactions…” Suggested rewrite: “Emerging evidence indicates that the gut microbiome plays a central role in diet–host interactions, influencing energy harvest, glucose and lipid metabolism, bile acid signaling, and inflammatory pathways.” Frequent passive voice and redundant phrases should be minimized.
• Introduction: While informative, the introduction could better highlight the clinical gap: why microbiome-informed personalization is needed beyond standard guidelines. Add a sentence on clinical relevance (e.g., improved adherence and metabolic outcomes).
• Figures and Tables: The review lacks figures and tables, which could help readability and interest from readers. Consider adding at least a schematic figure illustrating the diet–microbiome–host axis and key mechanistic pathways and a summary table of intervention studies (Mediterranean diet, prebiotics, probiotics, exercise).
• Discussion and Conclusion: Strong synthesis, but could better emphasize practical implications: How can clinicians use microbiome data today? What are the next steps for implementation?

 

Minor suggestions are:

• Ensure consistency in reference formatting (DOI spacing, journal abbreviations).
• Check for minor grammatical issues (e.g., “Nowadays is among the major public health issues” → “It is now a major public health issue”).
• Keywords are appropriate; consider adding “precision nutrition” explicitly.

 

I would like to recommend “Minor revisions”. The manuscript is promising and highly relevant but requires improvements in language clarity, abstract conciseness, and inclusion of visual elements to enhance readability and impact.

Comments on the Quality of English Language

Language and Readability: Several sentences are long and complex, reducing clarity. For example: “Novel evidence suggests that the gut microbiome could play key role in several pathways related to diet-host interactions…” Suggested rewrite: “Emerging evidence indicates that the gut microbiome plays a central role in diet–host interactions, influencing energy harvest, glucose and lipid metabolism, bile acid signaling, and inflammatory pathways.” Frequent passive voice and redundant phrases should be minimized.

Author Response

January 12^th, 2026

Ms. Letty Lei
Assistant Editor

Nutrients

 

Thank you for providing us with the opportunity to submit a revised version of our manuscript entitled “Personalized Nutrition Through the Gut Microbiome in Metabolic Syndrome and Related Comorbidities”. The authors thank the reviewers for their thoughtful comments and suggestions on our manuscript. We have considered all of the comments and incorporated them into the revised manuscript. Changes to the original document are highlighted as track changes, and an itemized point-by-point response to the reviewers’ comments is presented below.

 

COMMENTS FROM REVIEWER #1

 

Comment 1

This review article addresses an important and timely topic: the role of the gut microbiome in metabolic syndrome (MetS) and its integration into personalized nutrition strategies. The manuscript is comprehensive, well-structured, and supported by an extensive reference list. It effectively synthesizes mechanistic insights, observational evidence, and intervention studies, while highlighting future directions and implementation challenges.

However, the manuscript would benefit from minor revisions to improve clarity, conciseness, and practical relevance for clinical and research audiences. Firstly, I would like to point out the strengths of the manuscript:

• Relevance: The topic aligns well with current research priorities in personalized nutrition and microbiome science.
• Comprehensive coverage: Includes mechanistic pathways (SCFAs, bile acids, endotoxemia), diet–microbiome interactions, exercise effects, and clinical translation.
• Logical structure: Clear progression from background to mechanisms, interventions, and future directions.
• References: Up-to-date and extensive, reflecting the state of the field.

 

Response 1: We are most grateful for the Reviewers’ highly valued comments and concerns of our study which have undoubtedly enriched and strengthened the presentation of our research in the manuscript.

 

Comment 2

My major suggestions are:

Abstract: The abstract is dense and highly technical. It should be more concise and clearly state: background and rationale, objective of the review, key findings and novelty and practical implications. Suggested revision: Emphasize the gap in current “one-size-fits-all” dietary guidelines and the potential of microbiome-informed personalization.

 

Response 2: The abstract was modified using your comment and now state (page 1, lines 17-43), “Background: Metabolic syndrome, a clinical condition defined by central obesity, impaired glucose regulation, elevated blood pressure, hypertriglyceridemia, and low high-density lipoprotein cholesterol across the lifespan, is now a major public health issue typically managed with lifestyle, behavioral, and dietary recommendations. However, “one-size-fits-all” recommendations often yield modest, heterogeneous responses and poor long-term adherence, creating a clinical need for more targeted and implementable preventive and therapeutic strategies. Objective: To synthesize evidence on how the gut microbiome can inform precision nutrition and exercise approaches for metabolic syndrome prevention and management, and to evaluate readiness for clinical translation. Key findings: The gut microbiome may influence cardiometabolic risk through microbe-derived metabolites and pathways involving short-chain fatty acids, bile acid signaling, gut barrier integrity, and low-grade systemic inflammation. Diet quality (e.g., Mediterranean-style patterns, higher fermentable fiber, or lower ultra-processed food intake) consistently relates to more favorable microbial functions, and intervention studies show that high-fiber/prebiotic strategies can improve glycemic control alongside microbiome shifts. Physical exercise can also modulate microbial diversity and metabolic outputs, although effects are typically subtle and may depend on baseline adiposity and sustained adherence. Emerging “microbiome-informed” personalization, especially algorithms predicting postprandial glycemic responses, has improved short-term glycemic outcomes compared with standard advice in controlled trials. Targeted microbiome-directed approaches (e.g., Akkermansia muciniphila–based supplementation and fecal microbiota transplantation) provide proof-of-concept signals, but durability and scalability remain key limitations. Conclusions: Microbiome-informed personalization is a promising next step beyond generic guidelines, with potential to improve adherence and durable metabolic outcomes. Clinical implementation will require standardized measurement, rigorous external validation on clinically meaningful endpoints, interpretable decision support, and equity-focused evaluation across diverse populations.”

 

Comment 3

Language and Readability: Several sentences are long and complex, reducing clarity. For example: “Novel evidence suggests that the gut microbiome could play key role in several pathways related to diet-host interactions…” Suggested rewrite: “Emerging evidence indicates that the gut microbiome plays a central role in diet–host interactions, influencing energy harvest, glucose and lipid metabolism, bile acid signaling, and inflammatory pathways.” Frequent passive voice and redundant phrases should be minimized.

 

Response 3: We are most grateful for the reviewers’ highly valued comments regarding language use. The authors have revised the entire manuscript to improve clarity and readability using track-changes.

 

Comment 4

Introduction: While informative, the introduction could better highlight the clinical gap: why microbiome-informed personalization is needed beyond standard guidelines. Add a sentence on clinical relevance (e.g., improved adherence and metabolic outcomes).

 

Response 4: Using the reviewer’s comment, the introduction was modified as now stated (page 2, lines 215-227) “In routine care, this combination of variable response and poor adherence translates into repeated cycles of weight regain and persistent cardiometabolic risk. Highlighting a practical clinical gap: clinicians need implementable strategies to match dietary and lifestyle prescriptions to the patients most likely to benefit and adhere [14]. Recent studies have shown interindividual variability in postprandial glycemic and lipemic responses to standardized meals, even among individuals with similar clinical characteristics, highlighting substantial biological heterogeneity and suggesting that generalized dietary prescriptions may be suboptimal for many patients with or at risk of MetS [15-17]. Therefore, personalization is clinically relevant not only as a mechanistic refinement, but also to improve the “fit” of recommendations to patient biology and preferences, potentially strengthening adherence and yielding more durable improvements in glycemic control, lipemia, and other MetS components [18].”

Comment 5

Figures and Tables: The review lacks figures and tables, which could help readability and interest from readers. Consider adding at least a schematic figure illustrating the diet–microbiome–host axis and key mechanistic pathways and a summary table of intervention studies (Mediterranean diet, prebiotics, probiotics, exercise).

 

Response 5: Two new figures and one table have been added to the manuscript asking the reviewer’s comment.

 

Comment 6

Discussion and Conclusion: Strong synthesis, but could better emphasize practical implications: How can clinicians use microbiome data today? What are the next steps for implementation?

 

Response 6: Using the reviewer’s comment, a new section was made and now state (pages 15-16, lines 1139-1190), “6.5. How clinicians can use microbiome data today and next steps for implementation

At present, clinically actionable use of microbiome science remains uneven across indications. The strongest evidence base and clearest care pathways are concentrated in selected gastrointestinal settings [19], particularly with recurrent Clostridioides difficile infection, where fecal microbiota–based therapies and microbiota restoration strategies have demonstrated clinical benefit and are increasingly reflected in clinical guidance and pivotal trials [203-205]. In contrast, for MetS, most outputs from 16S rRNA gene sequencing or metagenomics remain insufficiently validated for routine decision-making. As emphasized by recent consensus efforts urging caution when translating microbiome test reports into clinical recommendations without rigorous validation and clear clinical action thresholds [206]. Consequently, when microbiome testing is obtained in MetS-like populations, results should generally be interpreted as hypothesis-generating and contextualized alongside diet quality, medication exposures (including antibiotics and acid-suppressing drugs), adiposity distribution, hepatic steatosis markers, and glycemic patterns, rather than used as stand-alone determinants of dietary prescriptions [206].

A feasible implementation pathway in cardiometabolic care requires moving beyond descriptive “dysbiosis” labels toward reproducible, function-centered outputs that can be audited clinically. First, microbiome measurement must become more reproducible through harmonized pre-analytics, sequencing, and bioinformatic workflows, and through transparent reporting standards; adoption of structured reporting frameworks such as STORMS is a necessary foundation to improve comparability and interpretability across human studies [190]. Second, methodological choices across the analytic chain can materially change results; comparative evaluations show that different differential-abundance methods and pipelines can yield meaningfully different “discoveries” on identical datasets, directly affecting biomarker credibility and downstream clinical claims [187]. Third, translation will depend on demonstrating incremental value over standard risk stratification using clinically meaningful endpoints (e.g., glycemic trajectories, blood pressure, lipids, hepatic fat, and weight maintenance), with external validation before adoption—an approach aligned with expert recommendations for clinical microbiome testing and interpretation [206]. Fourth, implementation should prioritize clinician-facing decision support that produces interpretable. Moreover, guideline-compatible recommendations rather than long lists of taxa, reflecting the broader consensus that clinical usefulness depends on actionable outputs with explicit uncertainty and validated thresholds [206].

Finally, feasibility, privacy, and equity must be treated as core design requirements. Public microbiome datasets are geographically skewed toward high-income settings, which constrains generalizability and risks widening disparities if biomarkers and models are deployed without validation in diverse ancestries, diets, and environments [202]. At the same time, microbiome-based precision approaches increasingly intersect with sensitive omics and digital phenotypes, raising privacy and governance challenges that require robust safeguards, particularly when data are handled through commercial or cross-institutional pipelines [207]. Together, these considerations reinforce that near-term progress in MetS will be driven less by additional associative findings and more by standardized measurement, rigorous validation, equity-conscious cohort building, and privacy-preserving translational infrastructure [187,190,202,206,207].”

 

Comment 7

Minor suggestions are:

Ensure consistency in reference formatting (DOI spacing, journal abbreviations).

 

Response 7: Using the reviewer’s comment, the references were modified.

 

Comment 8

Check for minor grammatical issues (e.g., “Nowadays is among the major public health issues” → “It is now a major public health issue”).

 

Response 8: Using the reviewer’s comment the sentence was modified.

 

Comment 9

Keywords are appropriate; consider adding “precision nutrition” explicitly.

 

Response 9: Using the reviewer’s comment, the keyword was added.

 

Comment 10

I would like to recommend “Minor revisions”. The manuscript is promising and highly relevant but requires improvements in language clarity, abstract conciseness, and inclusion of visual elements to enhance readability and impact.

 

Response 10: Thank you for your input on our manuscript. We have incorporated the modifications suggested by the reviewer.

 

Comment 11

Language and Readability: Several sentences are long and complex, reducing clarity. For example: “Novel evidence suggests that the gut microbiome could play key role in several pathways related to diet-host interactions…” Suggested rewrite: “Emerging evidence indicates that the gut microbiome plays a central role in diet–host interactions, influencing energy harvest, glucose and lipid metabolism, bile acid signaling, and inflammatory pathways.” Frequent passive voice and redundant phrases should be minimized.

 

Response 11: We are most grateful for the reviewers’ highly valued comments regarding language use. The authors have revised the entire manuscript to improve clarity and readability using track-changes.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

nutrients-4090220-peer-review-v1

 

The present paper is interesting basic for the development of full manuscript. However, at current form is just a basic material that will need an extensive upgrade. Authors have summarized several relevant topics to the metabolic syndromes, however, in most of the cases the topics are simply presented without really going deeper and with sufficient details and examples from the cited literature.

Abstract is informative and present principle points later discussed in the current review; however, some specific details and hot topics results can be specified.

Introduction section is a bit extended and in fact tourn around same topics repeated and presented in repetitive way. Maybe authors can consider reorganizing the section and compact, taking out not needed replications.

Section 2.2.1. regarding SCFA is described in popular way, providing importance of the SCFA, but not really giving details and pointing on the mechanisms behind the importance of SCFA. Authors supposed to extend this is other sections, but extend them not as popular text, but as focus scientific manuscript. Details on evidence, details of mechanisms involve behind these factors will need to be produced and discussed.

Same recommendations needs to be taken to the following section - 2.2.2. In fact, discussing importance of bile acids and FXT/TGR5 represent only in 14 lines is a bit telegraphic. Their role was extensively studied and merit a bit more attention.

Section 2.2.4. make sense to be moved earlier and even combined with 2.2.1.

Authors have touching different topics, but in fact do not profound them. In most of the presented cases information provided is in general way, in style of popular magazine. Please, for all topics under section 2. details, mechanisms, specific examples needs to be provided.

Maybe help from more experienced colleagues will be a good option in improving the text of the manuscript. Moreover, authors will need to generate some figures, some tables where principle mechanisms and reported facts can be visually presented and thus will make the manuscript more attractive and easier to follow.

In my opinion sections 2 and 3 can be changed to their position. In fact, section 3 in kind of manifest where authors presents their concept and state the terminology and way of application, way of interfering to the health status by the nutritional frames. Maybe, make sense that this section to be moved one place earlier in the manuscript.

Section 4 is again missing details. It is generally informative, but missing deepness and do not really provide examples and details regarding explored topics. In some cases, authors simply cite several references, but then nothing represent, nothing extracted from these literature sources. Please, enrich your text with examples, with data from the presented references and discuss these results critically, providing your opinion in accordance with or against previously published data.

Section 5 in fact shows some improvements in the preparation of the manuscript. Maybe different sections were prepared by different authors of the manuscript. However, in section 5 authors started to present more details and be more linked and objective to the explored topics. However, in some cases can be observed repetitions form the previous sections, an point that merit attention form the authors, and these repetitions needs to be removed and text adjusted.

 

Author Response

January 12^th, 2026

Ms. Letty Lei
Assistant Editor

Nutrients

 

Thank you for providing us with the opportunity to submit a revised version of our manuscript entitled “Personalized Nutrition Through the Gut Microbiome in Metabolic Syndrome and Related Comorbidities”. The authors thank the reviewers for their thoughtful comments and suggestions on our manuscript. We have considered all of the comments and incorporated them into the revised manuscript. Changes to the original document are highlighted as track changes, and an itemized point-by-point response to the reviewers’ comments is presented below.

 

COMMENTS FROM REVIEWER #2

 

Comment 1

The present paper is interesting basic for the development of full manuscript. However, at current form is just a basic material that will need an extensive upgrade. Authors have summarized several relevant topics to the metabolic syndromes, however, in most of the cases the topics are simply presented without really going deeper and with sufficient details and examples from the cited literature.

 

Response 1: We are thankful to the reviewer for his/her comment about our manuscript.

 

Comment 2

Abstract is informative and present principle points later discussed in the current review; however, some specific details and hot topics results can be specified.

 

Response 2: The abstract was modified using your comment and now state (page 1, lines 17-43), “Background: Metabolic syndrome, a clinical condition defined by central obesity, impaired glucose regulation, elevated blood pressure, hypertriglyceridemia, and low high-density lipoprotein cholesterol across the lifespan, is now a major public health issue typically managed with lifestyle, behavioral, and dietary recommendations. However, “one-size-fits-all” recommendations often yield modest, heterogeneous responses and poor long-term adherence, creating a clinical need for more targeted and implementable preventive and therapeutic strategies. Objective: To synthesize evidence on how the gut microbiome can inform precision nutrition and exercise approaches for metabolic syndrome prevention and management, and to evaluate readiness for clinical translation. Key findings: The gut microbiome may influence cardiometabolic risk through microbe-derived metabolites and pathways involving short-chain fatty acids, bile acid signaling, gut barrier integrity, and low-grade systemic inflammation. Diet quality (e.g., Mediterranean-style patterns, higher fermentable fiber, or lower ultra-processed food intake) consistently relates to more favorable microbial functions, and intervention studies show that high-fiber/prebiotic strategies can improve glycemic control alongside microbiome shifts. Physical exercise can also modulate microbial diversity and metabolic outputs, although effects are typically subtle and may depend on baseline adiposity and sustained adherence. Emerging “microbiome-informed” personalization, especially algorithms predicting postprandial glycemic responses, has improved short-term glycemic outcomes compared with standard advice in controlled trials. Targeted microbiome-directed approaches (e.g., Akkermansia muciniphila–based supplementation and fecal microbiota transplantation) provide proof-of-concept signals, but durability and scalability remain key limitations. Conclusions: Microbiome-informed personalization is a promising next step beyond generic guidelines, with potential to improve adherence and durable metabolic outcomes. Clinical implementation will require standardized measurement, rigorous external validation on clinically meaningful endpoints, interpretable decision support, and equity-focused evaluation across diverse populations.”

 

Comment 3

Introduction section is a bit extended and in fact tourn around same topics repeated and presented in repetitive way. Maybe authors can consider reorganizing the section and compact, taking out not needed replications.

 

Response 3: We understand the reviewer’s comment; however, we also incorporated additional information based on another reviewer’s suggestion, and several sentences were revised accordingly.

 

Comment 4

Section 2.2.1. regarding SCFA is described in popular way, providing importance of the SCFA, but not really giving details and pointing on the mechanisms behind the importance of SCFA. Authors supposed to extend this is other sections, but extend them not as popular text, but as focus scientific manuscript. Details on evidence, details of mechanisms involve behind these factors will need to be produced and discussed.

 

Response 4: Using the reviewer’s comment the section was modified and now stated (pages 5-6, lines 399-502), “ 3.2.1. Short-chain fatty acids and other metabolites

SCFAs, primarily acetate, propionate, and butyrate, are the main end-products of bacterial fermentation of dietary fibers and resistant starches. They act as key mediators of diet–microbiome–host interactions [62,63]. Their biological relevance in MetS extends beyond being “beneficial metabolites,” because SCFAs operate at the interface of (i) epithelial energy metabolism and barrier function, (ii) endocrine signaling, and (iii) immunometabolic regulation [62,63]. Butyrate is the preferred oxidative fuel for colonocytes and supports epithelial respiration, which helps maintain a low-oxygen luminal environment that favors obligate anaerobes and limits expansion of facultative taxa [64]. Thus, SCFAs can contribute to ecosystem stability while simultaneously supporting host mucosal homeostasis [65]. At the barrier level, SCFAs have been shown to enhance epithelial integrity through increased expression and/or assembly of tight junction com-ponents (e.g., occludin/claudins/ZO proteins) [66]. In addition, the activation of mucus-associated pathways and the enhancement of antimicrobial defenses and epithelial repair responses act together to reduce intestinal permeability and limit the translocation of pro-inflammatory microbial products [67]. In parallel, SCFAs exert immunomodulatory effects via both receptor-dependent and epigenetic routes, including inhibition of histone deacetylases and signaling through SCFA-sensing receptors expressed on epithelial and immune cells [68], thereby shaping cytokine profiles and supporting regulatory immune phenotypes relevant to the low-grade inflammation characteristic of MetS [69].

Endocrine and metabolic effects are mediated in part by activation of G protein–coupled receptors—notably FFAR2/GPR43 and FFAR3/GPR41—which are expressed on enteroendocrine L cells and other cell types [70-73]. SCFA signaling in L cells promotes secretion of incretins and satiety hormones, particularly GLP-1 and PYY, linking microbial fermentation to improved postprandial glycemic control, appetite regulation, and gastric emptying dynamics [70-73]. Beyond gut hormone release, SCFAs can influence systemic metabolism through effects on hepatic lipid handling (including lipogenesis and substrate partitioning), adipose tissue biology, and vascular tone, providing plausible pathways for observed associations with triglycerides, insulin sensitivity, and blood pressure [74]. Mechanistically, these effects are best interpreted as networked outputs of SCFA signaling across tissues (gut–liver–adipose–vasculature), rather than as a single linear pathway [70-74].

In MetS and related phenotypes, multiple cohorts report depletion of SCFA-producing taxa and altered fecal and/or circulating SCFA patterns, although the direction and magnitude of associations are not uniform [75,76]. Importantly, fecal SCFA concentrations reflect the net balance of production, microbial cross-feeding, host absorption, and colonic transit. Therefore, do not always track “SCFA benefit” monotonically across populations; habitual diet composition, sampling matrix (fecal vs plasma), and analytical methods further contribute to this heterogeneity [75,76]. Despite these measurement caveats, the convergent interpretation across human and mechanistic literature supports a model in which fiber-poor diets and reduced community capacity for fer-mentation-related functions are linked to impaired incretin signaling, weakened barrier integrity, and a more pro-inflammatory metabolic milieu, features that align with core pathophysiology of MetS [77].

Trimethylamine N-oxide (TMAO), produced from dietary choline, was related to atherosclerosis, CVD events and mortality [78-80]. Moreover, bacteria-driven alterations in branched-chain amino acid metabolism have been linked to insulin resistance, im-paired glucose tolerance and type 2 diabetes (T2D) risk [81-83]. This association was possibly through effects on mTOR signalling and ectopic lipid accumulation [81-83]. Aromatic amino acid–derived indoles and phenolic compounds can influence intestinal barrier integrity, aryl hydrocarbon receptor signalling, incretin secretion, and hepatic inflammation, thereby connecting dietary patterns, microbial metabolism, and NAFLD/MASLD progression [84]. Taken together, these findings support a model in which the gut microbiome functions as a metabolic endocrine organ, producing a complex mixture of small molecules that collectively modulate host metabolic pathways central to MetS.”

 

Comment 5

Same recommendations needs to be taken to the following section - 2.2.2. In fact, discussing importance of bile acids and FXT/TGR5 represent only in 14 lines is a bit telegraphic. Their role was extensively studied and merit a bit more attention.

 

Response 5: Using the reviewer’s comment the section was modified and now stated (pages 6-7, lines 503-591), “3.2.2. Bile acids and FXR/TGR5 signalling

BAs are not only detergents that facilitate lipid absorption but also endocrine-like signaling molecules that regulate glucose, lipid, and energy homeostasis through nuclear and membrane receptors, particularly the farnesoid X receptor (FXR) and the G protein–coupled receptor TGR5 [85]. BA signaling is inherently microbiome-sensitive because intestinal microbes shape both the composition and signaling potency of the BA pool [86]. Primary BAs synthesized from cholesterol in the liver are conjugated (glycine/taurine) and secreted into the intestine [87], where bacterial bile salt hydrolases (BSH) deconjugate them and enable downstream transformations (e.g., 7α-dehydroxylation, oxidation/epimerization) that generate a diverse set of secondary BAs with distinct receptor affinities [87]. Consequently, changes in microbiome structure and functional capacity translate into shifts in BA diversity, hydrophobicity, and the relative abundance of BA species that act as agonists/antagonists or partial agonists of FXR- and TGR5-driven pathways [88].

Mechanistically, BA–FXR signaling contributes to metabolic regulation through coordinated control of BA synthesis and transport (e.g., feedback inhibition of hepatic BA synthesis), as well as broader effects on hepatic glucose and lipid metabolism [89]. FXR activation influences pathways relevant to MetS, including regulation of gluconeogenesis, lipogenesis, and very-low-density lipoprotein secretion, and it also intersects with enterohepatic signaling through endocrine mediators such as fibroblast growth factor signaling from the gut to the liver (often discussed as a key FXR-linked gut–liver axis mechanism) [90,91]. In parallel, TGR5 activation in metabolically relevant tissues has been linked to energy expenditure and glucose control, in part via effects on thermogenic programs and incretin physiology, providing a plausible route by which BA composition can influence postprandial metabolism and insulin sensitivity [92]. Importantly, BA signaling also integrates with gut barrier and inflammatory biology, because BA species differ in their antimicrobial activity and their capacity to shape microbial niches, while BA receptor signaling can modulate inflammatory tone, features that are highly relevant to chronic low-grade inflammation in MetS [93].

In obesity and MetS, accumulating human and experimental evidence supports a model of dysregulated BA–microbiome crosstalk, characterized by altered BA composition, impaired receptor-mediated signaling, and associations between specific BA signatures, microbial features, and metabolic outcomes such as insulin resistance, dyslipidemia, and hepatic steatosis within the NAFLD/MASLD spectrum [94]. Several studies report that altered BA pools track with hepatic fat content and other cardiometabolic traits, consistent with the concept that BA profiles can serve as both functional readouts of microbiome activity and candidate mediators linking diet to metabolic phenotypes [95]. However, inter-individual variation in diet, medication exposure, and host factors (e.g., liver function, intestinal transit, and enterohepatic circulation dynamics) can influence BA measurements and partially explain heterogeneity across cohorts.

Intervention evidence further supports the therapeutic relevance of this axis. Dietary patterns that restructure the microbiome can shift BA pools, and pharmacologic strategies such as BA sequestrants and receptor-targeting agents (FXR/TGR5 agonists) provide proof-of-concept that modifying BA signaling can influence cardiometabolic risk factors [96,97]. Nevertheless, despite strong biological plausibility, direct causal pathways in humans remain incompletely resolved, and translation to clinical personalization will require studies that link intervention-induced BA changes to downstream receptor signaling, metabolomic outputs, and durable clinical endpoints (e.g., insulin sensitivity, hepatic fat, triglycerides) in well-characterized populations [96,97].”

 

Comment 6

Section 2.2.4. make sense to be moved earlier and even combined with 2.2.1.

Authors have touching different topics, but in fact do not profound them. In most of the presented cases information provided is in general way, in style of popular magazine. Please, for all topics under section 2. details, mechanisms, specific examples needs to be provided.

 

Response 6: Following the reviewer’s comment, this section was moved to the SCFAs section, and additional mechanistic details were added.

Comment 7

Maybe help from more experienced colleagues will be a good option in improving the text of the manuscript. Moreover, authors will need to generate some figures, some tables where principle mechanisms and reported facts can be visually presented and thus will make the manuscript more attractive and easier to follow.

 

Response 7: Two new figures and one table have been added to the manuscript asking the reviewer’s comment.

 

Comment 8

In my opinion sections 2 and 3 can be changed to their position. In fact, section 3 in kind of manifest where authors presents their concept and state the terminology and way of application, way of interfering to the health status by the nutritional frames. Maybe, make sense that this section to be moved one place earlier in the manuscript.

 

Response 8: Using the reviewer’s comment, the sections were modified.

 

Comment 9

Section 4 is again missing details. It is generally informative, but missing deepness and do not really provide examples and details regarding explored topics. In some cases, authors simply cite several references, but then nothing represent, nothing extracted from these literature sources. Please, enrich your text with examples, with data from the presented references and discuss these results critically, providing your opinion in accordance with or against previously published data.

 

Response 9: Using the reviewer’s comment the section was modified and now stated (pages 9-11, lines 732-915), “4. Physical Exercise, Gut Microbiome, and Metabolic Syndrome

4.1. Exercise as a core component of lifestyle management in metabolic syndrome

MetS management usually is based on Lifestyle changes. Structured physical activity or physical exercise repeatedly showing clinically meaningful benefits across the main MetS domains [116-118]. Contemporary syntheses and clinical reviews consistently highlight improvements in insulin sensitivity and glycemic control, blood pressure, atherogenic dyslipidemia, and central and visceral adiposity [116-118]. Importantly, these improvements are observed across multiple exercise modalities (aerobic, resistance, and combined training), although the magnitude of benefit typically depends on baseline cardiometabolic risk, adherence, training volume, and whether concomitant dietary energy restriction is present [119]. Importantly, implementation in practice and even in many guideline-adjacent documents still tends to treat them as parallel “pillars” rather than as a single adaptive intervention [116-118]. From a mechanistic perspective, this separation is artificial: exercise modifies substrate flux, inflammation, gut motility, bile acid dynamics, and intestinal barrier physiology [116-118]. Each of which can plausibly influence microbial ecology and microbial metabolite production, creating a biologically coherent route linking physical activity to gut microbiome-mediated metabolic effects [120].

4.2. Effects of exercise on the gut microbiome

4.2.1. Microbiome composition and diversity

Physical exercise is frequently associated with higher microbial diversity and detectable changes in community microbial structure. Randomized clinical trials (RCTs) and controlled interventions provide particularly valuable evidence [121]. In adults with overweight/obesity, a 6-month RCT reported a small but significant increase in Shannon diversity in the vigorous-intensity arm and measurable beta-diversity shifts across exercise groups versus control [122]. Notably, the “signal” in such trials is often stronger for community-level structure (beta-diversity) than for single taxa, suggesting that physical exercise may act as a broad ecological perturbation rather than a selective “one-bacterium” intervention [121,122]. Controlled training studies also indicate that exercise can alter the microbiome in ways that depend on baseline adiposity. In one study, compositional and functional changes differed by obesity status and were largely reversible after stopping exercise [123]. This reversibility is an important translational constraint: it implies that microbiome changes may require sustained training to persist, and that studies with short-term interventions or poor adherence are likely to underes-timate true effects. At the taxonomic level, many studies and reviews describe enrichment of taxa often linked to SCFA production, including butyrate-associated genera (e.g., Faecalibacterium and Roseburia in some cohorts). However, results are heterogeneous and not uniformly replicated, likely reflecting differences in participant characteristics, exercise prescription (aerobic vs resistance vs type), study duration, diet control, and sequencing/analytic pipelines [124-127]. For example, some interventions report increases in taxa typically considered “beneficial” in metabolic health (often within butyrate-producing guilds), whereas other studies show minimal genus-level changes despite clear physiological improvements, implying that the functional output of the microbiome may shift even when taxonomy appears stable [124-127]. A critical interpretation is that physical exercise effects on taxonomy may be contingent on the dietary substrate envi-ronment, as without adequate fermentable fiber intake, expansion of saccharolytic/butyrate-producing communities may be constrained, which could partially explain inconsistent taxonomic findings across cohorts with different habitual diets [122-125].

 

4.2.2. Microbial metabolites and host physiology

Mechanistically, exercise–microbiome links are increasingly interpreted through the lens of microbial metabolites [128]. SCFAs are a leading candidate pathway because they connect microbial fermentation to gut barrier integrity, inflammatory tone, and metabolic regulation [128]. In controlled human training, exercise increased fecal SCFAs in lean participants and exercise-related changes in microbial functional potential aligned with shifts in SCFA-producing capacity [123]. This is consistent with a model in which physical exercise increases intestinal transit dynamics and substrate availability to distal colonic fermenters, while also lowering systemic inflammation, conditions that may favor SCFA-producing consortia and/or their metabolic activity [123]. Broader reviews converge on the idea that exercise can support SCFA-related functionality and improve gut barrier and systemic metabolic signalling [125,129,130]. Although the magnitude and durability of these effects likely depend on baseline metabolic health and the sustainability of the activity pattern [125,129,130].

However, an important nuance is that higher fecal SCFAs do not necessarily imply higher host absorption or beneficial signaling, because fecal concentrations reflect the balance between production, host uptake, and transit time [131,132]. Therefore, future studies should triangulate fecal SCFAs with circulating SCFAs, targeted metabolomics, and host signaling readouts (e.g., GLP-1/PYY, inflammatory markers) to strengthen mechanistic inference [133,134]. Beyond SCFAs, exercise may influence microbial pathways linked to branched-chain amino acid metabolism, lactate cross-feeding, and aromatic amino acid derivatives, which are increasingly implicated in insulin sensitivity and inflammatory tone [135]. However, evidence remains less consistent than for SCFA-related functions and requires more standardized functional profiling [136].

Exercise may also influence BA profiles indirectly through changes in the gut microbiome and host metabolism [137,138]. This could be done by FXR/TGR5-mediated signalling pathways implicated in lipid and glucose homeostasis. The biological plausibility of microbiome-driven BA modulation as a metabolic lever is well supported by authoritative reviews of BA–microbiome–receptor biology [137,138]. From a physiological standpoint, exercise can alter BA circulation through effects on hepatic metabolism, in-testinal motility, and enterohepatic cycling. These host-driven changes can then feed back to the microbiome because BA composition and concentration shape microbial selection pressures and antimicrobial constraints [139]. Nevertheless, BA outcomes are particularly sensitive to sampling context (fasting vs postprandial), diet composition, and analytical platform [140]. Thus, discrepancies across studies may reflect methodological rather than biological differences, emphasizing the need for harmonized BA profiling in exercise–microbiome research [120,128].

Collectively, these observations support a synergy model. Diet provides the sub-strate environment for microbial metabolism, while exercise can reshape intestinal physiology and microbial ecology, together amplifying metabolic benefits [125,141,142]. This synergy framework predicts that the largest microbiome-mediated benefits occur when physical exercise is paired with dietary patterns that provide fermentable substrates (e.g., Mediterranean-style, fiber-rich diets), whereas exercise in a low-fiber dietary context may yield smaller or more variable microbiome shifts [143].

4.3. Exercise–microbiome interventions in metabolic syndrome and obesity

Intervention evidence in obesity/MetS-adjacent populations increasingly supports the idea that exercise, alone or combined with diet, can remodel gut ecology [144]. However, also makes clear that effects are often subtle, context-dependent, and require careful interpretation [144]. RCTs in adults with overweight/obesity demonstrate that structured exercise can shift beta-diversity and inferred functional potential, even when genus-level changes are limited [122,144,145]. This pattern suggests that exercise may primarily affect microbial “activity states” (functional capacity/expression) rather than producing large, consistent taxonomic turnover—an interpretation aligned with the observation that physiological improvements can occur in parallel with modest compo-sitional changes [122,144,145]. Complementary controlled trials show that exercise-induced microbial changes can differ by obesity status and may revert when training stops. Moreover, highlighting the importance of adherence and long-term maintenance for durable microbiome modulation [123,145]. From a clinical perspective, this indicates that microbiome modulation should not be framed as an automatic consequence of prescribing exercise; it depends on sustained behavior change and may require comple-mentary dietary design to support ecological stability [123,145].

Beyond exercise-only designs, combined lifestyle interventions provide a pragmatic template closer to real clinical care. In PREDIMED-Plus, a 1-year lifestyle intervention incorporating an energy-restricted Mediterranean diet and physical activity was associ-ated with gut microbiota changes linked to SCFA-producing bacteria [141]. This is particularly relevant because it reflects a real-world intervention package where diet provides fermentable substrate and exercise may reinforce barrier and metabolic improvements, which are conditions expected to favor SCFA-related ecology [141]. A more recent RCT in the same framework has extended these observations to the gut metabo-lome and microbiota in relation to cardiometabolic risk factors [146]. The addition of metabolomic readouts is important because it enables testing whether microbiome changes translate into functional chemical outputs that plausibly mediate cardiometabolic improvements, rather than relying on taxonomy alone [146]. In metabolically compromised patients (NAFLD with prediabetes), a four-arm randomized controlled trial showed that the combined aerobic exercise + diet intervention was associated with diversified and stabilized keystone taxa and that baseline microbial network properties could help predict individual liver-fat response [142]. An important proof-of-concept for microbi-ome-informed stratification [142]. Critically, such results suggest that microbial network features (i.e., community connectivity/keystones) may provide more clinically useful “response biomarkers” than single taxa, because they capture ecological stability and resilience—properties likely relevant to long-term metabolic maintenance [142]. At the same time, network metrics can be sensitive to sequencing depth, compositionality, and analytic choices. Therefore, replication across cohorts and standardized network pipelines are essential before these approaches can be translated into clinical tools [142].

Taken together, these trials suggest three clinically relevant messages: (i) exercise can influence the gut microbiome in humans, (ii) the most translational signals may lie in functional/metabolite readouts and network properties rather than single taxa, and (iii) heterogeneity of response is not noise to be averaged away but a feature that precision lifestyle strategies should aim to explain and harness [123,141,142,146].”

 

Comment 10

Section 5 in fact shows some improvements in the preparation of the manuscript. Maybe different sections were prepared by different authors of the manuscript. However, in section 5 authors started to present more details and be more linked and objective to the explored topics. However, in some cases can be observed repetitions form the previous sections, an point that merit attention form the authors, and these repetitions needs to be removed and text adjusted.

 

Response 10: In response to the reviewer’s comment, the section was revised to avoid duplicating information.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Authors have improve the manuscript and provided requested information and updates. In my opinion paper can be suggested to the editor.