FermFooDb: A database of bioactive peptides derived from fermented foods

Classification of bioactive peptides: A systematic benchmark of models and encodings

Bioactive peptides are short amino acid chains possessing biological activity and exerting physiological effects relevant to human health. Despite their therapeutic value, their identification remains a major problem, as it mainly relies on time-consuming in vitro tests. While bioinformatic tools for the identification of bioactive peptides are available, they are focused on specific functional classes and have not been systematically tested on realistic settings. To tackle this problem, bioactive peptide sequences and functions were here gathered from a variety of databases to generate a unified collection of bioactive peptides from microbial fermentation. This collection was organized into nine functional classes including some previously studied and some unexplored such as immunomodulatory, opioid and cardiovascular peptides. Upon assessing their sequence properties, four alternative encoding methods were tested in combination with a multitude of machine learning algorithms, from basic classifiers like logistic regression to advanced algorithms like BERT. Tests on a total of 171 models showed that, while some functions are intrinsically easier to detect, no single combination of classifiers and encoders worked universally well for all classes. For this reason, we unified all the best individual models for each class and generated CICERON (Classification of bIoaCtive pEptides fRom micrObial fermeNtation), a classification tool for the functional classification of peptides. State-of-the-art classifiers were found to underperform on our realistic benchmark dataset compared to the models included in CICERON. Altogether, our work provides a tool for real-world peptide classification and can serve as a benchmark for future model development.

ToxinPred 3.0: An improved method for predicting the toxicity of peptides

Toxicity emerges as a prominent challenge in the design of therapeutic peptides, causing the failure of numerous peptides during clinical trials. In 2013, our group developed ToxinPred, a computational method that has been extensively adopted by the scientific community for predicting peptide toxicity. In this paper, we propose a refined variant of ToxinPred that showcases improved reliability and accuracy in predicting peptide toxicity. Initially, we utilized a similarity/alignment-based approach employing BLAST to predict toxic peptides, which yielded satisfactory accuracy; however, the method suffered from inadequate coverage. Subsequently, we employed a motif-based approach using MERCI software to uncover specific patterns or motifs that are exclusively observed in toxic peptides. The search for these motifs in peptides allowed us to predict toxic peptides with a high level of specificity with poor sensitivity. To overcome the coverage limitations, we developed alignment-free methods using machine/deep learning techniques to balance sensitivity and specificity of prediction. Deep learning model (ANN - LSTM with fixed sequence length) developed using one-hot encoding achieved a maximum AUROC of 0.93 with MCC of 0.71 on an independent dataset. Machine learning model (extra tree) developed using compositional features of peptides achieved a maximum AUROC of 0.95 with MCC of 0.78. We also developed large language models and achieved maximum AUC of 0.93 using ESM2-t33. Finally, we developed hybrid or ensemble methods combining two or more methods to enhance performance. Our specific hybrid method, which combines a motif-based approach with a machine learning-based model, achieved a maximum AUROC of 0.98 with MCC 0.81 on an independent dataset. In this study, all models were trained and tested on 80 % of data using five-fold cross-validation and evaluated on the remaining 20 % of data called independent dataset. The evaluation of all methods on an independent dataset revealed that the method proposed in this study exhibited better performance than existing methods. To cater to the needs of the scientific community, we have developed a standalone software, pip package and web-based server ToxinPred3 (https://github.com/raghavagps/toxinpred3 and https://webs.iiitd.edu.in/raghava/toxinpred3/).

Bioinformatics tools for the study of bioactive peptides from vegetal sources: evolution and future perspectives

Bioactive peptides from vegetal sources have been shown to have functional properties as anti-inflammatory, antioxidant, antihypertensive or antidiabetic capacity. For this reason, they have been proposed as an interesting and promising alternative to improve human health. In recent years, the numerous advances in the bioinformatics field for in silico prediction have speeded up the discovery of bioactive peptides, also reducing the associated costs when using an integrated approach between the classical and bioinformatics discovery. This review aims to provide an overview of the evolution, limitations and latest advances in the field of bioinformatics and computational tools, and specifically make a critical and comprehensive insight into computational techniques used to study the mechanism of interaction that allows the explanation of plant bioactive peptide functionality. In particular, molecular docking is considered key to explain the different functionalities that have been previously identified. The assumptions to simplify such a high complex environment implies a degree of uncertainty that can only be guaranteed and validated by in vitro or in vivo studies, however, the combination of databases, software and bioinformatics applications with the classical approach has become a promising procedure for the study of bioactive peptides.

Fermented foods and gastrointestinal health: underlying mechanisms

Although fermentation probably originally developed as a means of preserving food substrates, many fermented foods (FFs), and components therein, are thought to have a beneficial effect on various aspects of human health, and gastrointestinal health in particular. It is important that any such perceived benefits are underpinned by rigorous scientific research to understand the associated mechanisms of action. Here, we review in vitro, ex vivo and in vivo studies that have provided insights into the ways in which the specific food components, including FF microorganisms and a variety of bioactives, can contribute to health-promoting activities. More specifically, we draw on representative examples of FFs to discuss the mechanisms through which functional components are produced or enriched during fermentation (such as bioactive peptides and exopolysaccharides), potentially toxic or harmful compounds (such as phytic acid, mycotoxins and lactose) are removed from the food substrate, and how the introduction of fermentation-associated live or dead microorganisms, or components thereof, to the gut can convey health benefits. These studies, combined with a deeper understanding of the microbial composition of a wider variety of modern and traditional FFs, can facilitate the future optimization of FFs, and associated microorganisms, to retain and maximize beneficial effects in the gut.

Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health

Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though the microbiota-gut-brain axis. Fermented foods offer themselves as a combined whole food microbiota modulating intervention. Indeed, they contain potentially beneficial microbes, microbial metabolites and other bioactives, which are being harnessed to target the microbiota-gut-brain axis for positive benefits. This review highlights the diverse nature of fermented foods in terms of the raw materials used and type of fermentation employed, and summarises their potential to shape composition of the gut microbiota, the gut to brain communication pathways including the immune system and, ultimately, modulate the microbiota-gut-brain axis. Throughout, we identify knowledge gaps and challenges faced in designing human studies for investigating the mental health-promoting potential of individual fermented foods or components thereof. Importantly, we also suggest solutions that can advance understanding of the therapeutic merit of fermented foods to modulate the microbiota-gut-brain axis.

Bioinformatics and bioactive peptides from foods: Do they work together?

We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.

Potential of milk-derived bioactive peptides as antidiabetic, antihypertensive, and xanthine oxidase inhibitors: a comprehensive bibliometric analysis and updated review

Bioactive peptides consist of small protein fragments, which are inactive in their original conformation, and they become active when released from these through enzymatic hydrolysis or fermentation processes. The bioactivity of such peptides has been extensively reported in the literature as contributors to organic homeostasis processes, as well as in immunomodulation, organism defense against oxidative processes, among others. In this study, reports of the activity of BPs isolated from milk with the potential glycemic control, antihypertensive activity, and inhibitors of uric acid formation were compiled. A systematic literature review and bibliometric analysis were conducted, using the PICO strategy for the research. The temporal analysis of publications revealed a growing interest in the investigation of bioactive peptides with potential antidiabetic, antihypertensive, and xanthine oxidase inhibitory activities, using dairy sources as products for their extraction. The literature analysis also revealed an increase in research involving non-bovine dairy products for bioactive peptide extraction. The collaboration network among authors exhibited weaknesses in scientific cooperation. Regarding the analysis of keywords, the usage of terms such as "bioactive peptides", "antioxidant", "antihypertensive", and "diabetes" was evident, constituting the main research clusters. Peptides with low molecular weight, typically < 10 kDa, of hydrophobic nature with aliphatic and aromatic chains, have significant implications in molecular interactions for the required activities. Although there is a growing interest in the industry regarding the utilization of bioactive peptides as potential drugs, there is a need to address gaps related to elucidating their interactions with cellular targets and their use in human therapy.

Umami-BERT: An interpretable BERT-based model for umami peptides prediction

Umami peptides have received extensive attention due to their ability to enhance flavors and provide nutritional benefits. The increasing demand for novel umami peptides and the vast number of peptides present in food call for more efficient methods to screen umami peptides, and further exploration is necessary. Therefore, the purpose of this study is to develop deep learning (DL) model to realize rapid screening of umami peptides. The Umami-BERT model was devised utilizing a novel two-stage training strategy with Bidirectional Encoder Representations from Transformers (BERT) and the inception network. In the pre-training stage, attention mechanisms were implemented on a large amount of bioactive peptides sequences to acquire high-dimensional generalized features. In the re-training stage, umami peptide prediction was carried out on UMP789 dataset, which is developed through the latest research. The model achieved the performance with an accuracy (ACC) of 93.23% and MCC of 0.78 on the balanced dataset, as well as an ACC of 95.00% and MCC of 0.85 on the unbalanced dataset. The results demonstrated that Umami-BERT could predict umami peptides directly from their amino acid sequences and exceeded the performance of other models. Furthermore, Umami-BERT enabled the analysis of attention pattern learned by Umami-BERT model. The amino acids Alanine (A), Cysteine (C), Aspartate (D), and Glutamicacid (E) were found to be the most significant contributors to umami peptides. Additionally, the patterns of summarized umami peptides involving A, C, D, and E were analyzed based on the learned attention weights. Consequently, Umami-BERT exhibited great potential in the large-scale screening of candidate peptides and offers novel insight for the further exploration of umami peptides.

Estimation of bioactive peptide content of milk from different species using an in silico method

This study assessed the bioactive peptides content of milk from different species, including humans, camel, bovine, buffalo, donkey, sheep, goat, and horse. The highest and lowest concentrations of total digestion-resistant peptides were estimated in sheep and human milk. Donkey milk casein contains a higher angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase III (DPP-III) inhibitory, DPP-IV inhibitory, and antioxidant peptides. On the other hand, camel whey protein contains the highest ACE-inhibitory peptides. To discover BPs with immunomodulatory and cholesterol-lowering functions, goat milk casein and sheep milk whey protein can be considered, respectively.

The inhibitory effects of plant additives on biogenic amine formation in fermented foods - a review

Fermented food has unique properties and high nutritional value, and thus, should constitute a basic element of a balanced and health-promoting diet. However, it can accumulate considerable amount of biogenic amines (BAs), which ingested in excess can lead to adverse health effects. The application of plant-derived additives represents a promising strategy to ensure safety or enhance the functional and organoleptic properties of fermented food. This review summarizes currently available data on the application of plant-origin additives with the aim to reduce BA content in fermented products. The importance of ensuring fermented food safety has been highlighted considering the growing evidence of beneficial effects resulting from the consumption of this type of food, as well as the increasing number of individuals sensitive to BAs. The examined plant-origin additives reduced the BA concentration to varying degrees, and their efficacy depended on the type of additive, matrix, autochthonous, and inoculated microorganisms, as well as the manufacturing conditions. The main mechanisms of action include antimicrobial effects and the inhibition of microbial decarboxylases. Further research on the optimization of bioactive substances extraction, standardization of their chemical composition, and development of detailed procedures for its use in fermented products manufacturing are needed.

Comparison of Neuroprotection and Regulating Properties on Gut Microbiota between Selenopeptide Val-Pro-Arg-Lys-Leu-SeMet and Its Native Peptide Val-Pro-Arg-Lys-Leu-Met In Vitro and In Vivo

Selenopeptides are promising candidates for intervening in neuroinflammation; however, the key role of selenium (Se) in selenopeptides remains poorly understood. To address this gap, we compared the neuroprotective effects of selenopeptide Val-Pro-Arg-Lys-Leu-SeMet (namely, Se-P1) and its native peptide Val-Pro-Arg-Lys-Leu-Met (namely, P1). Our results demonstrate that Se-P1 treatment exhibits superior antioxidant and antineuroinflammatory effects in PC12 cells and lipopolysaccharide (LPS)-injured mice compared to P1. Moreover, the administration of Se-P1 and P1 resulted in a shift in the gut microbiota composition. Notably, during LPS-induced injury, Se-P1 treatment demonstrated greater stability in maintaining gut microbiota composition compared to P1 treatment. Specifically, Se-P1 may have a positive impact on gut microbiota dysbiosis by modulating inflammatory-related bacteria such as enhancing Lactobacillus abundance while reducing that of Lachnospiraceae_NK4A136_group. Furthermore, the alteration of metabolites induced by Se-P1 treatment exhibited a significant correlation with gut microbiota, subsequently modulating the inflammatory-related metabolic pathways including histidine metabolism, lysine degradation, and purine metabolism. These findings suggest that organic Se contributes to the bioactivities of Se-P1 in mitigating neuroinflammation in LPS-injured mice compared to P1. These findings hold significant value for the development of potential preventive or therapeutic strategies against neurodegenerative diseases and introduce novel concepts in selenopeptide nutrition and supplementation recommendations.

Oenococcus oeni allows the increase of antihypertensive and antioxidant activities in apple cider

This study aimed to investigate the impact of the malolactic fermentation (MLF) carried out by Oenococcus oeni on antihypertensive and antioxidant activities in cider. The MLF was induced using three strains of O. oeni. The modification in phenolic compounds (PCs) and nitrogen organic compounds, antioxidant, and antihypertensive activities were determined after MLF. Among the 17 PCs analyzed caffeic acid was the most abundant compound and phloretin, (-)-epicatechin, and myricetin were detected only in malolactic ciders, however, (-)-epigallocatechin was not detected after MLF. The evaluation of nitrogen organic compounds revealed a drop in total protein concentration (from 17.58 to 14.00 mg N/L) concomitantly with a significant release of peptide nitrogen (from 0.31 to a maximum value of 0.80 mg N/L) after MLF. In addition, an extracellular proteolytic activity was evidenced in all MLF supernatants. The FRAP activity increased reaching a maximum of 120.9 μmol FeSO₄/mL and the ABTS radical-scavenging activity increased until 6.8 mmol ascorbic acid/L. Moreover, the angiotensin I-converting enzyme inhibitory activity reached a maximum value of 39.8%. The MLF conducted by O. oeni in ciders enables the increase of interesting biological activities and this finding could constitute a valuable tool to add value to final product.

Milk-Derived Antimicrobial Peptides: Overview, Applications, and Future Perspectives

The growing consumer awareness towards healthy and safe food has reformed food processing strategies. Nowadays, food processors are aiming at natural, effective, safe, and low-cost substitutes for enhancing the shelf life of food products. Milk, besides being a rich source of nutrition for infants and adults, serves as a readily available source of precious functional peptides. Due to the existence of high genetic variability in milk proteins, there is a great possibility to get bioactive peptides with varied properties. Among other bioactive agents, milk-originated antimicrobial peptides (AMPs) are gaining interest as attractive and safe additive conferring extended shelf life to minimally processed foods. These peptides display broad-spectrum antagonistic activity against bacteria, fungi, viruses, and protozoans. Microbial proteolytic activity, extracellular peptidases, food-grade enzymes, and recombinant DNA technology application are among few strategies to tailor specific peptides from milk and enhance their production. These bioprotective agents have a promising future in addressing the global concern of food safety along with the possibility to be incorporated into the food matrix without compromising overall consumer acceptance. Additionally, in conformity to the current consumer demands, these AMPs also possess functional properties needed for value addition. This review attempts to present the basic properties, synthesis approaches, action mechanism, current status, and prospects of antimicrobial peptide application in food, dairy, and pharma industry along with their role in ensuring the safety and health of consumers.

FDF-DB: A Database of Traditional Fermented Dairy Foods and Their Associated Microbiota

BACKGROUND

Fermented foods are attracting increasing interest due to their nutritional and health benefits, including a positive impact on gut microbiota exerted by their associated microbes. However, information relative to traditional fermented dairy products, along with their autochthonous microbiota, is still fragmented and poorly standardized. Therefore, our aim was to collect and aggregate data useful for obtaining a comprehensive overview translated in a classical database interface that can be easily handled by users.

METHODS

a preliminary inventory was built up by systematically collecting data from publicly available resources for the creation of a list of traditional dairy foods produced worldwide, including additional metadata useful for stratifying, and collapsing subgroups.

RESULTS

we developed the Fermented Dairy Food Database (FDF-DB), a feasible resource comprising 1852 traditional dairy foods (cheeses, fermented milks, and yogurt) for which microbial content and other associated metadata such as geographical indication label, country/region of origin, technological aspects were gathered.

CONCLUSIONS

FDF-DB is a useful and user-friendly resource where taxonomic information and processing production details converge. This resource will be of great aid for researchers, food industries, stakeholders and any user interested in the identification of technological and microbiological features characterizing traditional fermented dairy products.

Probiotic fermentation of polyphenols: potential sources of novel functional foods

Fermented functional food products are among the major segments of food processing industry. Fermentation imparts several characteristic effects on foods including the enhancement of organoleptic characteristics, increased shelf-life, and production of novel health beneficial compounds. However, in addition to macronutrients present in the food, secondary metabolites such as polyphenols are also emerging as suitable fermentable substrates. Despite the traditional antimicrobial view of polyphenols, accumulating research shows that polyphenols exert differential effects on bacterial communities by suppressing the growth of pathogenic microbes while concomitantly promoting the proliferation and survival of probiotic bacteria. Conversely, probiotic bacteria not only survive among polyphenols but also induce their fermentation which often leads to improved bioavailability of polyphenols, production of novel metabolic intermediates, increased polyphenolic content, and thus enhanced functional capacity of the fermented food. In addition, selective fermentation of combinations of polyphenol-rich foods or fortification with polyphenols can result in novel functional foods. The present narrative review specifically explores the potential of polyphenols as fermentable substrates in functional foods. We discuss the emerging bidirectional relationship between polyphenols and probiotic bacteria with an aim at promoting the development of novel functional foods based on the amalgamation of probiotic bacteria and polyphenols.

Graphical abstract

Formation and inhibition mechanism of novel angiotensin I converting enzyme inhibitory peptides from Chouguiyu

Angiotensin I converting enzyme (ACE) inhibitory peptides from fermented foods exhibit great potential to alleviate hypertension. In this study, the peptide extract from Chouguiyu exhibited a good inhibition effect on ACE, and the inhibition rate was significantly enhanced after fermentation for 8 days. The ACE inhibitory peptides were further identified, followed by their inhibition and formation mechanisms using microbiome technology and molecular docking. A total of 356 ACE inhibitory peptides were predicted using in silico, and most ACE inhibitory peptides increased after fermentation. These peptides could be hydrolyzed from 94 kinds of precursor proteins, mainly including muscle-type creatine kinase, nebulin, and troponin I. P1 (VEIINARA), P2 (FAVMVKG), P4 (EITWSDDKK), P7 (DFDDIQK), P8 (IGDDPKF), P9 (INDDPKIL), and P10 (GVDNPGHPFI) were selected as the core ACE inhibitory peptides according to their abundance and docking energy. The salt bridge and conventional hydrogen bond connecting unsaturated oxygen atoms in the peptides contributed most to the ACE inhibition. The cleavage proteases from the microbial genera in Chouguiyu for preparing these 7 core ACE inhibitory peptides were further analyzed by hydrolysis prediction and Pearson's correlation. The correlation network showed that P7, P8, and P9 were mainly produced by the proteases from LAB including Lactococcus, Enterococcus, Vagococcus, Peptostreptococcus, and Streptococcus, while P1, P2, P4, and P10 were mainly Produced by Aeromonas, Bacillus, Escherichia, and Psychrobacter. This study is helpful in isolating the proteases and microbial strains to directionally produce the responding ACE inhibitory peptides.

Cardioprotective Peptides from Milk Processing and Dairy Products: From Bioactivity to Final Products including Commercialization and Legislation

Recent research has revealed the potential of peptides derived from dairy products preventing cardiovascular disorders, one of the main causes of death worldwide. This review provides an overview of the main cardioprotective effects (assayed in vitro, in vivo, and ex vivo) of bioactive peptides derived from different dairy processing methods (fermentation and enzymatic hydrolysis) and dairy products (yogurt, cheese, and kefir), as well as the beneficial or detrimental effects of the process of gastrointestinal digestion following oral consumption on the biological activities of dairy-derived peptides. The main literature available on the structure–function relationship of dairy bioactive peptides, such as molecular docking and quantitative structure–activity relationships, and their allergenicity and toxicity will also be covered together with the main legislative frameworks governing the commercialization of these compounds. The current products and companies currently commercializing their products as a source of bioactive peptides will also be summarized, emphasizing the main challenges and opportunities for the industrial exploitation of dairy bioactive peptides in the market of functional food and nutraceuticals.

Conventional and in silico approaches to select promising food-derived bioactive peptides: A review

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Seaweed and edible insects are considered new sources of bioactive peptides.

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Conventional approaches are necessary to validate the bioactivity of peptides.

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Bioinformatics tools accelerate the obtaining of bioactive peptides.

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The integrated approach is a promising strategy to obtain bioactive peptides.

The interest for food-derived bioactive peptides, either from common or unconventional sources, has increased due to their potential therapeutic effect against a wide range of diseases. The study of such bioactive peptides using conventional methods is a long journey, expensive and time-consuming. Hence, bioinformatic approaches, which can not only help to predict the formation of bioactive peptides from any known protein source, but also to analyze the protein structure/function relationship, have gained a new meaning in this scientific field. Therefore, this review aims to provides an overview of conventional characterization methods and the most recent advances in the field of in silico approaches for predicting and screening promising food-derived bioactive peptides.

Antihypertensive effect of soybean bioactive peptides: A review

Hypertension is a global disease that is extremely harmful to humans. Timely lowering of blood pressure is necessary in order to avoid the occurrence of corresponding complications. This review shows that soy peptides are beneficial in resisting hypertension. One of the advantages is the abundance of raw materials for producing soybean peptides. Secondly, there are no reports of adverse reactions due to soy peptides. Moreover, they exert protective effect against hypertension-induced complications such as long-term memory impairment and kidney damage. However, there are still some obstacles associated with the development of soybean peptides. Therefore, this review is focused on statistical analysis of peptide sequences, amino acid residues, and possible targets of anti-hypertensive soybean peptides. Eventually, it proposes that application of genetic engineering technology to specifically modify the N- and C-terminal of the soybean peptides, and possible targets in identifying the likely drug targets involved in the antihypertensive effects of these peptides.

Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods

Ethnic fermented foods are known for their unique aroma, flavour, taste, texture and other sensory properties preferred by every ethnic community in this world culturally as parts of their eatables. Some beneficial microorganisms associated with fermented foods have several functional properties and health-promoting benefits. Bacteriocins are the secondary metabolites produced by the microorganisms mostly lactic acid bacteria present in the fermented foods which can act as lantibiotics against the pathogen bacteria. Several studies have been conducted regarding the isolation and characterization of potent strains as well as their association with different types of bacteriocins. Collective information regarding the gene organizations responsible for the potent effect of bacteriocins as lantibiotics, mode of action on pathogen bacterial cells is not yet available. This review focuses on the gene organizations, pathways include for bacteriocin and their mode of action for various classes of bacteriocins produced by lactic acid bacteria in some ethnic fermented foods.

Metaproteomics insights into fermented fish and vegetable products and associated microbes

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Increasing global population means higher demand for healthy food.

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Fish and vegetables are healthy foods, but overproduction leads to spoilage.

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Fermentation of fish/vegetables elongate their shelf lives, improved flavour and functions.

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Microbes associated with Fish/vegetable fermentation produce health conferring peptides.

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There is little review on peptides elicited during fish/vegetable fermentations.

The interest in proteomic studies of fermented food is increasing; the role of proteins derived from fermentation extends beyond preservation, they also improve the organoleptic, anti-pathogenic, anti-cancer, anti-obesogenic properties, and other health conferring properties of fermented food. Traditional fermentation processes are still in use in certain cultures, but recently, the controlled process is gaining wider acceptance due to consistency and predictability. Scientists use modern biotechnological approaches to evaluate reactions and component yields from fermentation processes. Pieces of literature on fermented fish and vegetable end-products are scanty (compared to milk and meat), even though fish and vegetables are considered health conferring diets with high nutritional contents. Evaluations of peptides from fermented fish and vegetables show they have anti-obesity, anti-oxidative, anti-inflammatory, anti-pathogenic, anti-anti-nutrient, improves digestibility, taste, nutrient content, texture, aroma properties, etc. Despite challenges impeding the wider applications of the metaproteomic analysis of fermented fish and vegetables, their potential benefits cannot be underestimated.