Nutritional Enhancement of Plant-Based Fermented Foods: Microbial Innovations for a Sustainable Future

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript “Nutritional Enhancement of Plant-Based Fermented Foods: Microbial Innovations for a Sustainable Future” presents extensive information about very well-known benefits of plant-based fermentation and less in new approaches. Authors should revise the content of the review and avoid repetitive sections and information. For instance, the information of section 3.1 (Bioavailability and nutrient release) is repetitive with mineral bioavailability of section 3.3. Section 3.3 (Enhanced vitamin synthesis and mineral bioavailability) is repetitive with section 4.3 (Biofortification strategies). The same case for section 3.2 (Protein enrichment and quality improvement) and 3.3 (Enhanced vitamin synthesis and mineral bioavailability) where solid fermentation and vitamin production is discussed as well as in section 4.3 (Biofortification strategies).

Metabolites from fermentation and their properties also are repetitive across the full manuscript.

Section 3 presents well known and reported nutritional enhancements about fermentation. Thus, the section should be reduced to basic context for the readers. Also, avoid presenting the same information in other sections.

The information on section 4.4 is well known for traditional fermentation of foods such yogurt and kefir. Thus, authors should include novelty findings if they want to include the section.

Section 5 should be removed because no new or deep information is presented about the health benefits and functional properties of fermented foods, prebiotics, symbiotics. Moreover, the benefits and metabolites of long traditional foods (yogurt, kefir, kimchi, sauerkraut) have been exhaustive report and no new information is presented here. In addition, in selected sentences authors suggest all fermented foods are probiotics and it is not correct. The criteria to denominate probiotic/symbiotic food and probiotic/symbiotic fermented food should be included to avoid confusion. Consider revising the ISAPP criteria.

Section 7. Regulatory challenges should be addressed the engineering microbes and their metabolites

Section 7.3 contradicts the previous framework of sustainability and demand/acceptability of plant-based fermented food.

Authors should revise and re-structure the manuscript focusing and deep in the innovations of plant-based fermentation to gain the attention of readers.

Other considerations are as follows:

L15. The review did not present a new approach of probiotics, thus, should be deleted.

The objective of the Abstract and Introduction sections must be similar. Revised and correct. The appropriate objective is presented in the Introduction.

L138. Increase the size of font because it is unclear.

L142. The current term of microbial flora is microbiota.

L353. Is the amount 1.302 or 1302? Please, revise and correct.

L356. Revise 1.491.4

L356-358. Clear if the high content of GABA was into fermented or fresh cucumbers. Please, revise and correct.

L379. Delete (SSF).

L482 and 484. Update the genus of Lactobacillus fermentum and Lactobacillus reuteri according to the new nomenclature.

L507-508. Update the genus of Lactobacillus rhamnosus according to the new nomenclature.

L963. Delete one LAB.

L1234-1237. This information was repetitive.

L1316. Delete one ML.

L1413-1416. Delete the sentence, the topic is not for this review.

L1537-1549. Repetitive from other sections.

Revise the citations format from journal guidelines.

Author Response

Comment 1: Authors should revise the content of the review and avoid repetitive sections and information. For instance, the information of section 3.1 (Bioavailability and nutrient release) is repetitive with mineral bioavailability of section 3.3. Section 3.3 (Enhanced vitamin synthesis and mineral bioavailability) is repetitive with section 4.3 (Biofortification strategies). The same case for section 3.2 (Protein enrichment and quality improvement) and 3.3 (Enhanced vitamin synthesis and mineral bioavailability) where solid fermentation and vitamin production is discussed as well as in section 4.3 (Biofortification strategies). Metabolites from fermentation and their properties also are repetitive across the full manuscript.

Response 1: Thank you for your valuable feedback and for pointing this out. In response to your suggestion, we have eliminated the repetition in all such cases. Further we have merged section 4.3 (Bio-fortification strategies) in section 3 to avoid any repetition with sub section3.2 and sub section 3.3.

Comment 2: Section 3 presents well known and reported nutritional enhancements about fermentation. Thus, the section should be reduced to basic context for the readers. Also, avoid presenting the same information in other sections.

Response 2: Thank you for your valuable feedback and for pointing this out. Our intention is to provide in depth information on the core topic, so we have provided detailed information on various aspects of Nutritional Enhancement of Plant-Based Foods Through Fermentation. Furthermore, we have carefully revised the manuscript to avoid repetition of the same information explained various aspects. In response to your suggestion, we have elaborated all such cases in first instance.

Comment 3: The information on section 4.4 is well known for traditional fermentation of foods such yogurt and kefir. Thus, authors should include novelty findings if they want to include the section.

Response 3: Thank you for your valuable suggestion. We have incorporated a paragraph to include the novelty findings. Changes have been highlighted in red.

Comments 4: Section 5 should be removed because no new or deep information is presented about the health benefits and functional properties of fermented foods, prebiotics, symbiotics. Moreover, the benefits and metabolites of long traditional foods (yogurt, kefir, kimchi, sauerkraut) have been exhaustive report and no new information is presented here. In addition, in selected sentences authors suggest all fermented foods are probiotics and it is not correct. The criteria to denominate probiotic/symbiotic food and probiotic/symbiotic fermented food should be included to avoid confusion. Consider revising the ISAPP criteria.

Response 4: Thank you for your valuable suggestion. We have incorporated novel insights and revised content accordingly. The additions have been highlighted in red.

We further thank the reviewer for the insightful observation regarding the terminology and classification of probiotic and fermented foods. We acknowledge that not all fermented foods qualify as probiotics, and that a clear distinction is essential to avoid misinterpretation.

In response to your comment, we have carefully revised the relevant sections to ensure that the definitions align with the International Scientific Association for Probiotics and Prebiotics (ISAPP) guidelines. Specifically, we now clarify that:

Fermented foods may contain live microorganisms but do not inherently meet the criteria to be labeled as probiotics, unless the strains are well-characterized, safe, and shown to confer a health benefit in a defined dose.

We also distinguish probiotic foods, which contain added, scientifically validated probiotic strains, from symbiotic foods, which combine probiotics with prebiotics in a synergistic form.

These clarifications have been incorporated in Section 5.1 of the revised manuscript. We have also cited the ISAPP consensus paper (Hill et al., 2014; Swanson et al., 2020) to support these distinctions and ensure scientific accuracy.

We appreciate your guidance in improving the clarity and rigor of our manuscript.

Comment 5: Section 7. Regulatory challenges should be addressed the engineering microbes and their metabolites

Response 5: We sincerely appreciate the reviewer’s insightful suggestion. In response to this comment, we have incorporated a paragraph on the regulatory challenges in engineering microbes and their metabolites for plant-based fermented foods. The added content has been highlighted in red.

Comment 6: Section 7.3 contradicts the previous framework of sustainability and demand/acceptability of plant-based fermented food.

Response 6: We sincerely appreciate your thoughtful feedback and the opportunity to clarify our position. While we understand your concern, we respectfully want to clarify that the content presented in Section 7.3 does not contradict the previously discussed framework of sustainability and consumer demand for plant-based fermented foods. Rather, it is intended to complement and expand upon this framework by providing a more nuanced and realistic perspective on the topic.

In particular:

1. The section reinforces the sustainability benefits of plant-based fermented foods, highlighting their:

• Lower greenhouse gas emissions
• Reduced use of natural resources
• Ethical appeal, particularly for consumers concerned with animal welfare

These advantages are in direct alignment with the earlier sustainability principles outlined in the manuscript.

1. Furthermore, we emphasize the growing interest from health-conscious and environmentally aware consumers, which reflects and supports the notion of increasing market demand for sustainable plant-based alternatives.
2. Importantly, the discussion of barriers to wider adoption—such as taste, texture, cultural familiarity, and consumer skepticismwas not intended to contradict the idea of demand. Rather, it serves to acknowledge the real-world factors that influence consumer acceptance, and the areas where further innovation and education are needed to improve uptake.

We hope this clarification addresses your concern, and we are open to further refining the section if additional changes are recommended.

Comment 7: L15. The review did not present a new approach of probiotics, thus, should be deleted.

Response 7: We appreciate your valuable input and have deleted the mentioned word.

Comment 8: The objective of the Abstract and Introduction sections must be similar. Revised and correct. The appropriate objective is presented in the Introduction.

Response 8: We thank the reviewer for pointing out the need for alignment between the abstract and the introduction. In response, we have revised both sections to ensure that the objective of the review is clearly and consistently stated. Specifically, In the Introduction, we have now explicitly included a clear objective statement at the end of the section (highlighted red) to outline the focus and scope of the review.

The Abstract has been revised accordingly to reflect this objective, with emphasis on microbial innovations, nutritional enhancement, and sustainability in plant-based fermented foods.

We believe these changes improve the clarity and coherence of the manuscript and appreciate your valuable suggestion.

Comment 9: L142. The current term of microbial flora is microbiota.

Response 9: We have revised the term as per the reviewer suggestion.

Comment 10: L353. Is the amount 1.302 or 1302? Please, revise and correct.

Response 10: Thanks for point out the error. We have corrected it to 1302

Comment 11: L356-358. Clear if the high content of GABA was into fermented or fresh cucumbers. Please, revise and correct.

Response 11: Thanks for point out the error. We have revised and corrected the information.

Comment 12: L379. Delete (SSF).

Response 12: Deleted.

Comment 13: L482 and 484. Update the genus of Lactobacillus fermentum and Lactobacillus reuteri according to the new nomenclature.

Response 13: Updated.

Comment 14: L507-508. Update the genus of Lactobacillus rhamnosus according to the new nomenclature.

Response 14: Updated

Comment 15: L963. Delete one LAB.

Response 15: Deleted

Comment 16: L1234-1237. This information was repetitive.

Response 16: We have eliminated the repetition.

Comment 17: L1316. Delete one ML.

Response 17: Deleted

Comment 18: L1413-1416. Delete the sentence, the topic is not for this review.

Response 18: Deleted

Comment 19: L1537-1549. Repetitive from other sections.

Response 19: We have carefully revised the manuscript to avoid repetition.

Comments 20: Revise the citations format from journal guidelines.

Response 20: Thank you for your observation. We have carefully reviewed and revised the citation format to ensure they strictly adhere to the journal’s author guidelines regarding formatting, citation style, and consistency. We appreciate your attention to detail in helping improve the manuscript's overall quality.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The article summarized recent and relevant literature, offering a perspective on both beneficial and detrimental effects of different fermentation products. However, there could be deeper discussion on  the current literature.

1. Please improve the resolution of Fig 1.
2. What about the ligislation for different countries?
3. Conclusion is too long, please reduce some lines.
4. CRISPR is a new technology which may not be deemed as GMO, but is not accepted of all countries.
5. Some mechanistic explanations, particularly regarding specific microbial pathways or host immune responses, could benefit from more depth or clarification.
6. While the microbiota and host health connections are mentioned, future perspectives or emerging tools (like metagenomics or metabolomics) might be mentioned as well at where the field is heading.
7.  Some important references were missing and should be discussed:  a. Hsieh, CC, Yu, SH, Cheng, KW, Liou, YW, Hsu, CC, Hsieh, CW, Kou, CH, Cheng, KC. 2023. Production and analysis of metabolites from solid-state fermentation of Chenopodium formosanum (Djulis) sprouts in a bioreactor. Food Research International. 168:112707. b. Hsieh, CC, Lin, HW, Huang, HC, Khumsupan, D, Shen, SC, Lin, SP, Hsieh, CW, Tsai, TY, Jantama, SS, Kuo, HC, Cheng, KC. 2025. Peptide from tempeh-like fermented Chenopodium formosanum counters senescence while enhancing antioxidant ability in non-replicative aging. LWT. 222:117641.

Author Response

Comment 1: Please improve the resolution of Fig 1.

Response 1: Thank you for your valuable feedback. We have improved the resolution of Fig 1.

Comment 2: What about the ligislation for different countries?

Response 2: Thank you for your valuable feedback. We have covered regulatory frameworks for novel plant-based fermented foods across different regions such as European Union, United States, Canada etc.

Comment 3: Conclusion is too long, please reduce some lines.

Response 3: Thank you for your valuable feedback.In response, we have carefully revised and condensed the conclusion, retaining only the most essential points to ensure clarity and focus while avoiding repetition. The revised version presents a succinct summary of key findings, future perspectives, and their alignment with sustainability goals.

Comment 4: CRISPR is a new technology which may not be deemed as GMO, but is not accepted of all countries.

Response 4: Thank you for your important observation regarding the regulatory status of CRISPR technology. In response to your comment, we have revised the relevant section of the manuscript to explicitly state that CRISPR-edited microorganisms may not be classified as GMOs in some regions, but are still subject to strict regulations or limited acceptance in others.

This clarification helps contextualize the potential applications of CRISPR in microbial fermentation, while acknowledging the current global regulatory landscape and the need for responsible use and transparent communication with consumers and stakeholders.

Comment 5: Some mechanistic explanations, particularly regarding specific microbial pathways or host immune responses, could benefit from more depth or clarification.

Response 5: Thank you for your valuable comment highlighting the need for more detailed mechanistic explanations, particularly concerning microbial pathways and host immune responses. In response, we have expanded Section 5 to provide a deeper and more structured mechanistic explanations regarding specific microbial pathways/host immune responses. The changes have been highlighted in red color.

Comment 6: While the microbiota and host health connections are mentioned, future perspectives or emerging tools (like metagenomics or metabolomics) might be mentioned as well at where the field is heading.

Response 6: Thank you for your insightful suggestion regarding the inclusion of future perspectives and emerging technologies such as metagenomics and metabolomics. In response, we have expanded the conclusion to highlight how multi-omics toolsincluding metagenomics, metabolomics, and transcriptomicsare expected to play a pivotal role in advancing our understanding of host–microbiota interactions and optimizing fermentation processes.

These tools will enable more precise characterization of microbial communities, functional gene expression, and metabolite profiling, thereby facilitating:

• The identification of novel microbial strains and metabolic pathways relevant to health and nutrition.
• A deeper understanding of how fermented foods modulate the gut microbiome and host physiology at a systems level.
• The development of personalized fermented food products tailored to individual microbiome compositions and health needs.

Comment 7: Some important references were missing and should be discussed:  a. Hsieh, CC, Yu, SH, Cheng, KW, Liou, YW, Hsu, CC, Hsieh, CW, Kou, CH, Cheng, KC. 2023. Production and analysis of metabolites from solid-state fermentation of Chenopodium formosanum (Djulis) sprouts in a bioreactor. Food Research International. 168:112707. b. Hsieh, CC, Lin, HW, Huang, HC, Khumsupan, D, Shen, SC, Lin, SP, Hsieh, CW, Tsai, TY, Jantama, SS, Kuo, HC, Cheng, KC. 2025. Peptide from tempeh-like fermented Chenopodium formosanum counters senescence while enhancing antioxidant ability in non-replicative aging. LWT. 222:117641.

Response 7: We have now incorporated these references into the revised manuscript and discussed their relevance in the appropriate sections. Their inclusion has helped us strengthen the context and support our findings more robustly within the existing body of research. We greatly appreciate your recommendation, which significantly improved the comprehensiveness of our review.

Reviewer 3 Report

Comments and Suggestions for Authors

Dear Authors

This manuscript reviews and analyzes recent advances in the use of microbial innovations to improve the nutritional profile of plant-based fermented foods, highlighting the role of technologies such as precision fermentation, strain engineering, the use of probiotics, and biofortification strategies, all within the context of sustainable food production. However, I can send some additional comments to polish the final details of the manuscript.

Keywords

I recommend that the keywords be different from those that appear in the title.

2. Microbial Diversity and Functional Role in Plant-Based Fermentation

Page 3. Line 124-125. According to the MDPI guide, abbreviations should be defined the first time they are used. This abbreviation has been defined previously (LAB). Please identify this error throughout the document.

Figure 1. I recommend making the font size larger and checking the image sharpness.

3.2. Protein Enrichment and Quality Improvement

Page 10. Line 379. Same problem with this abbreviation (SSF). Review the entire manuscript.

4.3 Biofortification Strategies

Page 23. Line 947. Typically, a good table has at least 10 rows of information. I recommend adding another 5 references.

5.1 Fermented Foods and Gut Microbiota

Figure 4. I recommend removing the black background from the image.

I recommend updating the following references: Wood, 1985; Sybesma et al., 2003; Tavares et al., 2011. It is important to mention that the references are not more than 10 years old.

References

Review the references carefully; they do not follow the journal's author guidelines.

General comments

It is recommended to break up long paragraphs (e.g. lines 243–311) to improve readability.

Add conceptual diagrams or graphic summaries to the emerging technologies or CRISPR/SynCom sections to facilitate understanding.

Focus on sustainability: As part of the journal's approach, it is recommended to highlight more explicitly in the conclusion how the work contributes to the SDGs (Sustainable Development Goals), such as SDG 2 (Zero Hunger), SDG 12 (Responsible Consumption and Production), and SDG 3 (Good Health and Well-being).

Author Response

Comment 1: Keywords I recommend that the keywords be different from those that appear in the title.

Response 1: We appreciate the reviewer’s suggestion regarding the selection of keywords. In response, we have revised the keyword list to avoid repeating terms already present in the title. The updated keywords now focus on related concepts and indexing terms that enhance the discoverability of the manuscript while maintaining relevance to the content.

Comment 2: Microbial Diversity and Functional Role in Plant-Based Fermentation

Page 3. Line 124-125. According to the MDPI guide, abbreviations should be defined the first time they are used. This abbreviation has been defined previously (LAB). Please identify this error throughout the document.

Response 2: Thank you for pointing this out. In response, we have carefully reviewed the entire document and removed repeated definitions of the abbreviation. LAB is now only defined at its first occurrence, and used consistently thereafter without redefinition.

Comment 3: Figure 1. I recommend making the font size larger and checking the image sharpness.

Response 3: Thank you for your valuable feedback on Figure 1. We have revised the figure to enhance its readability by increasing the font size of all text elements and improving image resolution and sharpness. The updated figure has been replaced in the revised manuscript to ensure better clarity and visual quality

Comment 4: 3.2. Protein Enrichment and Quality Improvement

Page 10. Line 379. Same problem with this abbreviation (SSF). Review the entire manuscript.

Response 4: Thank you for highlighting the issue with the repeated definition of the abbreviation SSF (solid-state fermentation). In response, we have thoroughly reviewed the entire manuscript and ensured that SSF is defined only at its first occurrence and used consistently without repetition throughout the text.

Comment 5: 4.3 Biofortification Strategies

Page 23. Line 947. Typically, a good table has at least 10 rows of information. I recommend adding another 5 references.

Response 5: Thank you for the constructive suggestion. We have added 7 more references to the table (Now Table 2).

Comment 6: 5.1 Fermented Foods and Gut Microbiota

Figure 4. I recommend removing the black background from the image.

I recommend updating the following references: Wood, 1985; Sybesma et al., 2003; Tavares et al., 2011. It is important to mention that the references are not more than 10 years old.

Response 6: We acknowledge your concern regarding the black background from the Fig. 4. In response, we have removed the black background from the image. We have removed these references and updated the manuscript with more recent and relevant literature.

Comment 7: References: Review the references carefully; they do not follow the journal's author guidelines.

Response 7: Thank you for your observation. We have carefully reviewed and revised all references to ensure they strictly adhere to the journal’s author guidelines regarding formatting, citation style, and consistency. We appreciate your attention to detail in helping improve the manuscript's overall quality.

Comment 8: It is recommended to break up long paragraphs (e.g. lines 243–311) to improve readability.

Response 8: Thank you for your helpful suggestion. In response to this comment, we haverestructured and divided the lengthy paragraph spanning lines 243–311 into shorter, more focused paragraphs, each addressing a specific idea or subtopic.

Comment 9: Add conceptual diagrams or graphic summaries to the emerging technologies or CRISPR/SynCom sections to facilitate understanding.

Response 9: Thank you for your helpful suggestion to include conceptual diagrams to enhance the clarity of the sections on emerging technologies. In response, we have added new Fig. 3 (Conceptual summary of key microbial innovations driving nutritional and functional enhancement in next-generation plant-based fermented foods. These include CRISPR-based genome editing, precision fermentation, SynComs, AI-driven optimization, biofortification via engineered microbes, and functional starter cultures.

This figure has been added with an intention to support reader comprehension of complex concepts and summarize key innovations in a more accessible format. We appreciate your suggestion, which has strengthened the pedagogical value and visual engagement of the manuscript.

Comment 10: Focus on sustainability: As part of the journal's approach, it is recommended to highlight more explicitly in the conclusion how the work contributes to the SDGs (Sustainable Development Goals), such as SDG 2 (Zero Hunger), SDG 12 (Responsible Consumption and Production), and SDG 3 (Good Health and Well-being).

Response 10: Thank you for your thoughtful suggestion to highlight the manuscript's alignment with the United Nations Sustainable Development Goals (SDGs). In response, we have revised the Conclusion section to more explicitly articulate how the findings and discussions presented in the review contribute to key SDGs:

• SDG 2 (Zero Hunger): by exploring microbial innovations that enhance the nutritional quality and bioavailability of plant-based foods, thereby supporting global food and nutrition security.
• SDG 3 (Good Health and Well-being): through the promotion of fermented foods enriched with bioactive compounds, probiotics, and functional metabolites that contribute to improved gut health and chronic disease prevention.
• SDG 12 (Responsible Consumption and Production): by advancing sustainable food production systems that reduce resource use, waste, and reliance on animal-based products.

These points have been clearly integrated into the revised conclusion to better reflect the sustainability-driven impact of plant-based fermented foods. We appreciate your guidance in aligning the manuscript more closely with the journal’s objectives.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors attended most suggestions and completed the changes. Please consider the following suggestion:

L1077. The current term of gut flora is microbiota.

Author Response

Comment 1: L1077. The current term of gut flora is microbiota.

REPLY: Thank you for your observation. We have revised the manuscript accordingly and replaced the term "gut flora" with "gut microbiota" to reflect current and accurate scientific terminology.