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

Abstract

The rising demand for sustainable, nutritious, and functional food options has fueled growing interest in plant-based fermented foods. These products offer enhanced sensory, functional, and health-promoting properties, largely driven by microbial activity during fermentation. This review examines recent advances in microbial biotechnology—including the use of novel starter cultures, strain engineering, CRISPR-based genome editing, and precision fermentation that are reshaping the nutritional landscape of plant-based fermented foods. Key benefits such as improved protein digestibility, bioactive compound synthesis, antinutrient reduction, and micronutrient bioavailability are explored. Additionally, the review highlights the potential of microbial innovations to enhance sustainability, address global nutrition challenges, and improve consumer acceptance through better sensory quality. It also discusses challenges related to regulatory frameworks, scalability, and consumer perception. This review aims to provide a comprehensive understanding of how microbial processes can optimize the nutritional and functional value of plant-based fermented foods in alignment with future food system goals.

1. Introduction

Fermented foods have been an integral part of human diets for centuries, offering a unique combination of taste, texture, and health benefits [1]. In recent years, plant-based fermented foods have attained significant attention due to the growing consumer demand for sustainable, nutritious, and functional foods. Consumers are increasingly adopting plant-based diets due to concerns about animal welfare, environmental sustainability, and personal health [2]. Fermented plant-based foods cater to these preferences by offering alternatives to traditional dairy and meat products [1,3]. Plant-based diets are recognized for their lower environmental impact compared to animal-based diets. Plant proteins, such as those from legumes, cereals, and oilseeds, have a lower carbon footprint and require fewer resources for production [4]. Plant-based fermented foods are rich in bioactive compounds, such as peptides, polyphenols, phytochemicals, flavonoids and vitamins, which offer significant health benefits [5]. These compounds are generated during fermentation and have been linked to improved digestion, immune function, and chronic disease prevention [6].

The global plant-based functional food market has experienced significant growth in recent years, driven by consumer demand for healthier, sustainable, and ethical food options. The plant-based functional food market varies significantly across different regions.

The global plant-based food market is projected to grow at a compound annual growth rate (CAGR) of 12.3% from 2024 to 2031, reaching an estimated value of USD 113.1 billion by 2031. This growth is fueled by factors such as rising consumer intolerance to animal proteins, the expanding vegetarian population, the rising demand for plant-derived proteins, increasing venture capital investments in plant-based food startups, advancements in food technology, and increased awareness of animal welfare and environmental sustainability [7]. According to recent data, the global plant-based protein market is projected to reach over USD 27 billion by 2030, driven by increasing consumer demand for sustainable and healthy food options [8]. The global plant-based meat market was valued at USD 1.6 billion in 2019 and is projected to reach USD 3.5 billion by 2026, indicating significant growth opportunities in the plant-based functional food market [9]. In the United States, the plant-based product market reached USD 7.4 billion in 2021, up from USD 4.8 billion in 2018, with significant opportunities for growth driven by the rising demand for meat alternatives [9,10]. In Europe, the market for plant-based foods has also seen substantial growth. Sales data from Nielsen Market Track (2017–2020) reveal that the market has expanded significantly (European Plant-Based Foods Sales Data 2017–2020 [11]. In Asia also, the market is growing rapidly, with countries like Indonesia witnessing significant growth in the food sector. A study on plant-based jerky products in Indonesia found high consumer satisfaction levels (83.8–86.8%), indicating a promising market for plant-based functional foods in the region [9].

Traditional plant-based fermented foods such as tempeh, kimchi, sauerkraut, and miso have long been valued for their rich microbial diversity and enhanced nutrient profile. However, modern scientific advancements in microbial biotechnology are now unlocking new possibilities to further enhance their nutritional value and functionality. Modern perspectives on plant-based fermentation emphasize the scientific understanding of microbial interactions, advancements in fermentation technology, and consumer interest toward health-oriented and sustainable food products [12]. The adaptability of fermentation technology facilitates the production of diverse range of plant-based food alternatives, thereby contributing to dietary variety and inclusivity. Advances in product development driven by fermentation are enabling unique flavors, textures, and aromas to the plant-based food industry, enhancing the consumer preference and acceptance [13,14]. Recent studies have shown that fermentation can enhance the sensory properties and nutritional attributes of plant-based foods, providing flavors and textures that appeal to contemporary palates [14]. Notably, the sensory experiences provided by fermented products can differ significantly based on the microbial strains used and the fermentation conditions, thus driving innovations in the food industry [15,16]. The resurgence of interest in traditional fermentation practices, combined with modern food science, has catalyzed the development of novel plant-based fermented products that prioritize health benefits and cater to a growing market demand for sustainable and ethical food options [12,14]. Furthermore, the escalating interest in functional foods that provide health benefits beyond basic nutrition has enhanced the relevance of plant-based fermented foods. These foods are distinguished by their nutritional content and potential health-promoting properties, such as improved gut health, enhanced immunity, and reduced risk of chronic diseases [17,18].

Despite significant advancements made in understanding the nutritional benefits and sensory properties of fermented plant-based foods, there remains a notable research gap regarding specific microbial interactions and their impact on the final product quality. Much of the existing literature focuses on well-established products, with less emphasis on evaluating diverse microbial strains that could enhance the fermentation processes. Additionally, the regulatory landscape, consumer perception, scalability, and commercialization challenges surrounding fermented functional foods remain underexplored. Addressing these gaps could facilitate the development of tailored/specialized fermentation strategies that not only meet consumer demands but also enhance the functional properties of plant-based foods. In this context, the exploration of microbial innovations in fermentation presents significant opportunities for advancing plant-based food systems towards greater sustainability [12]. This review aims to explore the emerging role of microbial fermentation in enhancing the nutritional quality, functionality, and sustainability of plant-based fermented foods. It highlights recent innovations in microbial biotechnology such as precision fermentation, synthetic biology, and AI-based optimization that enable the development of nutritionally enriched, environmentally sustainable, and consumer-acceptable plant-based food alternatives. The review also identifies key challenges and future directions for advancing the field.

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

Microbial diversity plays a central role in plant-based fermentation by influencing the quality, safety, and health benefits of fermented foods. Traditional fermentative microbes have been the backbone of food fermentation processes for centuries, playing a pivotal role in enhancing the quality, safety, and nutritional value of plant-based foods. Traditional plant fermentation heavily relies on microbial populations that include lactic acid bacteria (LAB), yeasts, and fungi. These microbes are well-known for their ability to ferment a wide range of plant-based substrates, producing compounds that contribute to the sensory and nutritional properties of fermented foods [19]. LAB, such as a species from the Lactobacillus genus, is vital in the fermentation of various plant-based products, including vegetables and cereals. Their ability to convert sugars into lactic acid enhances the preservation and flavor of these foods while providing health benefits to consumers through probiotics [20,21]. LAB are the predominant bacteria, with species such as Lactobacillus, Leuconostoc, and Pediococcus being commonly identified [22,23,24]. In some cases, bacteria such as Enterobacter and Weissella have also been identified as key players in fermentation processes [25,26]. Microbial diversity associated with plant-based fermentation is illustrated in Figure 1, highlighting the range of microorganisms involved.

The ecological distributions of LAB can be influenced by various environmental factors such as the plant materials used and existing microbiota. For instance, it has been documented that LAB populations can significantly fluctuate depending on the composition of the phyllosphere—the portion of a plant that is exposed to the air [27].

Yeasts also play a crucial role in plant fermentation, often working alongside LAB to create complex flavor profiles and improve the nutritional content of fermented products [28,29]. In this context, Arlosan et al. explored an innovative strategy to enhance the nutritional quality of lentil-whey protein (LP-WP) complexes by combining pH-shifting with fermentation using water kefir microorganisms (yeasts, LAB, and acetic acid bacteria). The approach significantly improved protein solubility, digestibility, and overall structure. Key findings of the study included increased phenolic content, better flavor, and favorable changes in secondary protein structures (α-helix and random coil) [30].

Fungi, particularly filamentous strains like those from the Aspergillus and Rhizopus genera, are involved in the breakdown of complex carbohydrates during the fermentation of plant-based products, enriching the quality and nutritional value of the final product [31].

The interactions among these traditional fermentative microbes can lead to enhanced fermentation processes. LAB and yeast co-cultures have been shown to positively influence the sensory attributes and nutritional outcomes of fermented foods like yogurt and kimchi [32,33]. By understanding these interactions, it is possible to optimize fermentation processes and improve the overall quality of plant-based foods.

The emergence of engineered and novel probiotic strains, categorized as next-generation fermentative microbes (NGFM), further expands the potential benefits of fermentation. These microbes have been deliberately selected or engineered to optimize health benefits and functional properties in fermented foods. Recent advancements in biotechnology allow for the development of tailored probiotic strains that can withstand harsh fermentation conditions while delivering specific health benefits. Next-generation fermentative microbes, such as genetically modified LAB and Bacillus species, are being increasingly used in plant-based fermentation to enhance the quality, safety, and nutritional value of fermented products. These microbes are engineered to produce specific enzymes or bioactive compounds, such as carotenoids and bacteriocins, which can tailor the properties of fermented plant-based matrices for specific applications, such as yellow cheese or red meat analogs [34,35]. The meticulous design of microbial communities that include these engineered strains can lead to more predictable and enhanced fermentation outcomes, incorporating beneficial interactions that have previously been less understood.

One of the most significant aspects of plant-based fermentation is the production of microbial metabolites, which includes an array of bioactive compounds, vitamins, and postbiotics. Microbial metabolites, such as bacteriocins, exopolysaccharides, and bioactive peptides, play a significant role in enhancing the quality and safety of plant-based fermented products. These compounds are known for their ability to inhibit the growth of pathogenic microorganisms, extend the shelf life of fermented products, and contribute to the nutritional and functional properties of plant-based foods [4,36].

Bioactive compounds derived from fermentation have gained substantial attention due to their potential health benefits. For example, fermented vegetables can be rich in vitamins C and K due to microbial activity during fermentation [37,38]. Furthermore, postbiotics, which are metabolic byproducts released by live microbes, have been found to enhance gut health and systemic immunity, acting independently of the viability of probiotics [39].

Consideration of the transformational capabilities of these microbial metabolites can assist in optimizing fermentation processes to enhance the nutritional aspects of plant-based foods. In this context, studies utilizing advanced meta-omics techniques have provided insights into understanding the diversity of microbial metabolites produced during fermentation [40,41].

Microbial consortia, which are communities of different microbial species, exhibit synergistic interactions that can significantly improve fermentation processes and outcomes. These consortia are known for their ability to degrade complex plant-derived molecules, such as hexanal, into simpler compounds, improving the flavor and texture of fermented products. Additionally, microbial consortia are known for their ability to produce a wide range of bioactive compounds, such as polyphenols and peptides, which contribute to the nutritional and functional properties of fermented products [19,42]. Consortia including LAB, yeasts, and various fungi can optimize flavor profiles and enhance the bioavailability of nutrients by synergistically breaking down dietary fibers and other complex carbohydrates present in plants [43].

Table 1. Microbial consortia in plant-based fermented foods and key characteristics.

Food Type	Dominant Microbes	Key Characteristics	Reference
Chinese Fermented Vegetables	Lactobacillus sakei, Lactobacillus acetotolerans, Pediococcus pentosaceus	Flavor development through organic acids and volatile compounds; inhibition of spoilage microorganisms	[44]
Vegetable Ferments	Lactobacillus, Pediococcus, Leuconostoc	High LAB diversity, pathways for carbohydrate degradation	[23,24]
Legume Ferments	Bacillales, Enterobacterales	Enriched with protein and lipid degradation pathways	[23,45]
Red Beetroot Ferments	Lactobacillus plantarum, Weissella cibaria	Complex volatilome, lactic acid fermentation	[46]
French Fermented Vegetables	Lactiplantibacillus pentosus, Levilactobacillus brevis	Dominance of LAB, no pathogenic bacteria detected	[22]
Pea Protein Gels	Geotrichum candidum, Lactococcus lactis, Lactobacillus rhamnosus	Decreased pea note intensity in pea gels, bitterness increased after fermentation, enhanced cheesy perception	[47]
African Fermented Maize	Lactobacillus, Weisella, Curvibacter	Environmental selection shapes microbial composition	[45]
Novel Miso Varieties	Lactococcus lactis, Lactobacillus rhamnosus	Substrate-dependent microbial composition, carotenoid biosynthesis genes	[48]

provides key insights into the role of microbial consortia in plant-based fermented foods.

Studies have demonstrated that co-culturing LAB with yeasts can yield products with extended shelf life and improved sensory characteristics [49]. Co-fermentation strategies, where different microbial species are used together, are being increasingly used in plant-based fermentation to enhance the efficiency and diversity of fermentation processes. These strategies are known for their ability to produce a wide range of bioactive compounds, such as carotenoids and bacteriocins, which can tailor the properties of fermented plant-based matrices for specific applications [34,35]. Synthetic microbial communities (SynComs) are a novel approach to plant-based fermentation, where microbial communities are designed and constructed to perform specific functions. These communities are known for their ability to simplify complex microbial interactions, allowing for targeted design of microbial communities that can enhance the quality and safety of fermented products. SynComs are also known for their ability to reduce hazardous compounds and improve the flavor of traditional fermented foods [42].

Recent advances in multi-omics technologies, such as genomics, proteomics, and metabolomics, have revolutionized the field of plant-based fermentation. These technologies allow for the characterization of microbial communities involved in fermentation and their functional roles, enabling the optimization of fermentation processes. Multi-omics approaches have been used to identify microbial strains that can improve the properties of plant-based beverages, such as flavor, texture, and nutrient availability [40,50]. Fermentation technology has undergone significant advancements in recent years, with the integration of modern biotechnology, genetic engineering, and process optimization. Economically viable fermentation processes. For instance, the use of genetically modified microbes and novel bioreactor designs has improved the efficiency of fermentation processes, reduced energy consumption and enhancing scalability [51]. As research continues to evolve, integrating new biotechnological advancements with traditional fermentation methods will enhance our understanding of microbial roles and functions in plant-based fermentation, ensuring the continued development of nutritious and flavorful foods.

3. Nutritional Enhancement of Plant-Based Foods Through Fermentation

In recent years, the fermentation of plant-based foods has gained significant attention for its role in enhancing the nutritional profile of these products. The fermentation of plant-based foods presents a robust method for improving their nutritional value by enhancing bioavailability, enriching protein quality, biosynthesizing vitamins and minerals, and producing functional metabolites.

Table 2. Effects of fermentation on nutritional and sensory properties across different plant-based matrices.

Plant-Based Matrix	Nutritional Enhancement	Sensory Improvement	Reference
Legumes	Increased vitamins (folate, riboflavin), minerals (iron, zinc)	Reduced beany off-flavor, improved texture	[52,53]
Cereals	Enhanced bioactive compounds, antioxidants	Improved palatability, aroma	[54]
Chickpea-Based Beverages	Enhanced phosphorus (478 vs. 331 mg/kg), calcium (165 vs. 117 mg/kg), reduced raffinose	Increased viscosity, consumer acceptability	[55]
Rice-Based Foods	Increased antioxidants, reduced antinutrients	Enhanced flavor, reduced off-flavors	[56]
Meat Analogues	Tailored carotenoid production for color	Mimicked meat-like texture and flavor	[14,57]
Legume Matrices	Carotenoid production	Improved texture and flavor	[35]
Plant-based beverages (mixtures of Hibiscus sabdariffa (zobo) and Raphia hookeri wine)	Increased antioxidant activity	Improved color and taste	[58]
Vegetable Matrices	Increased bioavailability of nutrients	Pleasant sensory characteristics	[59]
Fermented brown rice	Increased soluble dietary fiber, total phenolic content, and antioxidant capacity	Improved texture	[60]
Vegetable Matrices (African black nightshade and African spiderplant)	Increased phenolic compounds and flavonoid contents	Improved sensory acceptability	[61]
Bian-Que Triple-Bean Soup	Increased total flavone contents and phenol contents	Improvedflavors	[62]
Pea and rice protein concentrate blend	Increase in protein’s Digestible Indispensable Amino Acid Score (DIAAS) to an “excellent source” for humans Reduced antinutrients like phytates and protease inhibitors	Reduction in off-note compounds substantially improving its organoleptic performance	[63]

summarizes the effects of fermentation on nutritional and sensory properties across different plant-based matrices. The applications of fermentation technologies in the food industry not only help meet the rising global demand for nutritious plant-based foods but also contribute to food security and health enhancement. Here we discuss various dimensions of nutritional enhancement through fermentation, including bioavailability and nutrient release, protein enrichment, vitamin and mineral biosynthesis, and the production of functional metabolites (Figure 2).

3.1. Bioavailability and Nutrient Release

The bioavailability of nutrients in plant-based foods is often hindered by the presence of anti-nutritional factors such as phytates, tannins, and oxalates, which can bind essential minerals and impede their absorption [64]. Fermentation has been employed to effectively break down these anti-nutritional factors (ANFs), thereby improving nutrient release and availability. During fermentation, microorganisms produce enzymes, such as phytases and tannases, that catalyze the degradation of phytates and tannins, respectively. This enzymatic activity releases the minerals that were previously bound to these compounds, increasing their solubility and making them more readily available for absorption in the small intestine. This process significantly improves the nutritional value of plant-based foods.

Research indicates that the fermentation process activates endogenous enzymes that degrade anti-nutritional compounds. For instance, phytase production during fermentation has been shown to decrease phytic acid levels significantly. Phytic acid, primarily found in legumes and cereals, can severely limit the bioavailability of phosphorus and essential minerals such as iron and zinc [65,66]. Soybean meal (SBM) is one of the key sources of plant-based protein widely utilized in the livestock and poultry industry. A study by Qi et al. investigated the impact of fermentation of SBM with a novel probiotic strain, Bacillus licheniformis B4. Fermentation with B4 for 24 h significantly reduced the phytic acid in SBM by 73.3%. It also enhanced the degree of protein hydrolysis (from 15.9% to 25.5%) and crude protein (from 44.8% to 54.3%). Additionally, fiber content was notably reduced, enhancing the nutritional quality of SBM. The findings support B4-fermented SBM as a viable alternative to conventional phytase supplementation [67]. Reduced levels of phytate have been correlated with enhanced mineral absorption, showcasing the efficacy of fermentation in releasing bound nutrients.

Moreover, fermentation also leads to the breakdown of tannins and oxalates, further enhancing nutrient bioavailability. Tannins, which are polyphenolic compounds, can negatively affect protein digestibility and hinder the absorption of iron. The fermentation process can alleviate these concerns by degrading tannins, leading to improved iron bioavailability [68,69]. Furthermore, the reduction in oxalates through fermentation can aid in calcium absorption, in foods such as spinach where oxalates present a challenge to calcium bioavailability [70,71]. In this context, a study on sesame seeds highlighted the fact that fermentation reduced oxalate levels by 69% over a 12-day period [72]. Similarly, a 20.8% reduction in total oxalate content was observed during the fermentation of green amaranth (Amaranthus viridis L.) seeds in calabash pots uniformly lined with banana leaves [73]. Naseem et al. evaluated the impact of fermentation on nutritional quality and reducing antinutritional factors in spinach harvested at three growth stages [70]. Fermentation using Lactiplantibacillus plantarum significantly increased protein (2.53% to 3.53%) and fiber content (19.33% to 22.03%). Furthermore, fermentation resulted in significant decline in the alkaloids (6.45 to 2.20 mg/100 g), oxalates (0.07 mg/100 g to 0.02 mg/100 g), phytates (1.97 to 0.43 mg/100 g) and glucosinolates (201 to 10.50 µmol/g. The antioxidant activity and total phenolic content remained unaffected [70]. The findings highlight fermentation as a promising bioprocess approach to enhance spinach’s nutrient bioavailability. Spinach powder derived from this process could serve as a cost-effective, plant-based protein supplement. In another study, Subedi et al. investigated the impact of fermentation on the functional attributes of kale (Brassica oleracea L.). The findings demonstrated that fermentation enhanced kale’s functional properties, with a mixed culture of Lactococcus lactis and Lactobacillus acidophilus. This treatment increased total polyphenols from 8.5 to 10.7 mg GAE/g and sulforaphane from 960.8 to 1777 μg/g. Antinutritional factors including oxalate and tannins were significantly reduced by 49% and 55–65%, respectively. Antioxidant capacity was notably improved, while anti-inflammatory effects remained similar to unfermented kale. This highlights fermentation as an effective strategy to boost kale’s nutritional value [74].

Additionally, fermentation increases the release of bound nutrients. Research indicates that various fermentation techniques can enhance the bioavailability of minerals in plant-based foods. The breakdown of cell wall components during fermentation makes amino acids, vitamins, and minerals more accessible. In this regard, fermentation with algae has been shown to enhance the biosynthesis of minerals like iron and zinc, improving the nutritional profile of algae-based products [69]. One study demonstrated that five LAB strains—Lactobacillus fermentum B4655 (Limosilactobacillus fermentum), L. plantarum B4495, L. casei B1922 (Lacticaseibacillus casei), L. bulgaricus CFR2028 (Lactobacillus delbrueckii), and L. acidophilus B4496 significantly improved mineral bioavailability in soymilk. After 24 h of fermentation at 37 °C, these strains notably reduced the phytic acid content while increasing magnesium and calcium levels compared to the control [75]. In another study, Bahaciu et al. explored the effects of germination and LAB fermentation on soybean seeds. Germination for four days at 25 °C elevated zinc, magnesium, iron, and calcium content by 28.04%, 15.77%, 22.31%, and 48.76%, respectively, over untreated seeds. Subsequent fermentation further enhanced these levels to 40.87%, 43.41%, 59.56%, and 53.4%, respectively [76]. Dhull et al. investigated the impact of solid-state fermentation (SSF) on three lentil cultivars (HM-1, LL-931, and Sapna) by employing A. awamori (MTCC 548). The Aspergillus-fermented lentil (AFL) exhibited significantly improved mineral content. Among the various minerals analyzed, copper exhibited the most pronounced enhancement in all AFL extracts, showing an increase ranging from 46.4% to 60.0% post-fermentation. Notably, the in vitro bioavailability of iron and zinc improved significantly (p ≤ 0.05) in fermented samples, reaching peak levels on the 6th day of fermentation. These findings emphasize the potential of bio transformed lentils as valuable components in the development of functional foods and innovative nutraceutical products with enhanced health benefits [77]. In a separate study, Cao et al. highlighted the enhancement of soybean meal through yeast fermentation, resulting in crude protein and acid-soluble protein levels of 542.5 g/kg and 117.2 g/kg, respectively, and increase in essential amino acid content by 17.9% [78]. The results support the role of fermentation in enhancing the nutritional quality and digestibility of legume proteins.

Incorporating cereals into milk-based products can result in enhanced nutrition and improved functional characteristics. In this regard, Samtiya et al.’s study evaluated the impact of selective fermentation on the nutritional and techno-functional properties of a millet-skim milk-based product using HHB-311 biofortified pearl millet and skim milk powder. Fermentation was carried out with Limosilactobacillus fermentum (LF) and Lacticaseibacillus rhamnosusGG (LGG) for 8, 16, and 24 h at 37 °C. Protein digestibility significantly improved in LF (16 h) and LGG (24 h) samples, reaching 90.75 ± 1.6% and 93.76 ± 3.4%, respectively, compared to 62.60 ± 2.6% in the control (p < 0.05). LF (16 h) fermentation also enhanced iron and zinc bioavailability by 39% and 14%, respectively. The findings indicate that LF with 16 h fermentation yields a product with optimal nutritional quality and improved micronutrient bioavailability [79].

Further research emphasizes how microbial fermentation can also enhance the availability of trace elements like selenium and zinc by decreasing the binding interactions with phytates, thus increasing their absorption from plant-based sources [80,81]. In this context, Rangaswamaiah evaluated SSF as a method to enhance zinc (Zn) and selenium (Se) uptake and reduce phytic acid in sorghum grain. Using Aspergillus oryzae, Bacillus subtilis, and their co-culture, SSF was applied to both coarsely ground and whole grain sorghum. The highest Zn absorption was recorded at 50 μg/g zinc acetate, while 3.2 μg/g selenium aspartate led to optimal Se uptake. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and UV/VIS spectroscopy analysis confirmed that all organisms could grow in Zn- or Se-enriched media. Notably, A. oryzae and the co-culture significantly reduced phytic acid levels in coarsely ground samples. This suggests that SSF can improve mineral bioavailability, making the fermented biomass a promising Zn- and Se-enriched functional food ingredient [82]. These studies highlight the potential of fermentation to address mineral deficiencies, particularly in populations that rely heavily on plant-based diets.

3.2. Protein Enrichment and Quality Improvement

Protein quality is critical in plant-based diets, and fermentation can significantly enhance both protein content and its digestibility. During the fermentation process, microbial proteolysis occurs, which breaks down complex protein structures into simpler peptides and amino acids [83]. This process not only increases the protein content but also improves its digestibility and absorption in the body [14]. Studies have demonstrated that microbial fermentation enhances the levels of essential amino acids in plant-based foods. In this context, Moore et al. investigated the free amino acid (FAA) composition of fresh, acidified, naturally fermented, and starter culture fermented cucumbers using liquid chromatography triple quadrupole mass spectrometry. Fermented cucumbers exhibited significantly higher total FAA content (1302 ± 102 mg/kg) compared to acidified ones (635 ± 35 mg/kg), regardless of brine salt concentration (2–6% NaCl) or the addition of starter cultures. In fresh cucumbers, glutamine (1491.4 ± 69.3 mg/kg), γ-aminobutyric acid (GABA) (269.6 ± 21.4 mg/kg), asparagine (113.0 ± 6.4 mg/kg), and citrulline (110.3 ± 8.5 mg/kg) were most abundant. The predominant free amino acids found in fermented cucumber were GABA (181.3 ± 21.5 mg/kg), isoleucine (165.2 ± 11.2 mg/kg), leucine (129.8 ± 10.9 mg/kg), and lysine (110.9 ± 5.0 mg/kg). The formation of GABA and ornithine during fermentation indicates glutamate decarboxylase and arginine deiminase activity, respectively. Notably, ornithine levels were substantially higher in naturally fermented cucumbers (63.3 ± 31.5 mg/kg) compared to those fermented with starter cultures (3.0 ± 0.7 mg/kg). These findings underscore the influence of fermentation method on FAA profiles, offering insights into optimizing cucumber fermentation for enhanced nutritional value and consumer health benefits [84]. Gientka et al. explored the effect of spontaneous fermentation on the amino acid profile of sliced carrot and celeriac, both with and without apple addition, to develop diversified plant-based fermented products. Fermentation effectively reduced pH, ensuring microbiological safety, while the inclusion of apple significantly enhanced the viability of lactic acid bacteria throughout the process. Notably, fermentation decreased the levels of acidic amino acids (aspartic and glutamic acid) but boosted several essential amino acids, improving the overall protein quality. Although leucine remained the limiting amino acid across all variants, its concentration increased during fermentation. The Essential Amino Acid Index (EAAI) was higher in apple-enriched samples, 1.13 for carrot with apple and 1.03 for celeriac with apple, thereby highlighting the nutritional benefits [85]. These findings underscore the potential of combining root vegetables with fruits to produce microbiologically safe, nutritionally enhanced, and sustainable fermented plant-based foods.

SSF has been reported to increase the protein content in plant-based foods. In this regard, Filipe et al. highlighted the fact that solid-state fermentation of a plant feedstuff mixture (25% each of rapeseed meal, soybean meal, rice bran, and sunflower meal) using Aspergillus ibericus and two strains of Aspergillus niger enhanced its nutritional profile. Protein content increased by 5% across all fungi, while cellulose and hemicellulose contents decreased by 9–11% and 21–34%, respectively. A. niger CECT 2088 showed the highest enzyme activity: cellulase (123.7 U/g), xylanase (431.8 U/g), and β-glucosidase (117.9 U/g). Principal component analysis revealed positive correlations between fermentation, enzyme production, protein enhancement, fiber reduction, and digestibility [86]. These findings underscore SSF as an effective strategy to improve the feed value of plant-based materials. In another study, Hsieh et al. demonstrated that SSF of fourth-day Chenopodium formosanum sprouts in a bioreactor resulted in enhanced antioxidant capacity, peptide yield, and enzyme activity compared to traditional plate fermentation. Fermentation in a bioreactor (35 °C, 0.4 vvm aeration at 5 rpm) resulted in higher free peptide content (99.56 ± 7.77 mg casein tryptone/g) and enzyme activity (amylase, glucosidase, and proteinase are 2.21 ± 0.01, 54.57 ± 10.88, and 40.81 ± 6.52 U/g, respectively) than traditional plate fermentation (PF). Over 20 new metabolites were identified in the bioreactor-based fermentation setup, including aromatics and fatty acids [87]. These findings suggest that bioreactor-based fermentation is a scalable and nutritionally superior method for enhancing the functional properties of C. formosanum sprouts.

In contrast, some studies have observed a decrease in protein digestibility following fungal SSF. For example, lupin flour fermented with Aspergillus sojae, Aspergillus ficuum, and their co-cultures exhibited reduced protein digestibility [88]. This decline was attributed to proteins becoming entrapped within the fiber matrix of lupin, limiting their accessibility to proteolytic enzymes. Additionally, the partial denaturation of proteins during the drying process was suggested to impair protein dispersibility and solubility, further contributing to reduced digestibility. The authors emphasized the need to consider physical changes occurring during processing that may influence digestion. Similar findings were reported by Ranjan et al. who observed that SSF using Rhizopus oryzae adversely affected the protein digestibility of dry defatted rice bran [89].

Co-culture SSF is another approach that typically enhances the protein digestibility of substrates, it is important to note that the improvement is often less significant compared to that achieved with single-strain SSF. In this context, Terefe et al. reported a significant enhancement in the protein digestibility of maize flour following 48 h of SSF. Among the fermentation setups, Lactobacillus plantarum showed the most substantial improvement, increasing protein digestibility by 40%, followed by Saccharomyces cerevisiae with a 36% increase. In contrast, the co-culture fermentation exhibited a comparatively lower enhancement of 34%, indicating that single-strain fermentation may be more efficient in boosting protein digestibility [90]. In another study involving the co-fermentation of grass pea seeds with Rhizopus microsporus var. chinensis and Aspergillus oryzae, protein digestibility improved only when the inoculum size of A. oryzae was kept lower than that of R. microsporus var. chinensis [91]. This suggests that microbial competition in co-culture systems can suppress the growth or activity of strains with higher proteolytic potential, thereby limiting the overall improvement in protein digestibility. These findings highlight the importance of carefully optimizing microbial ratios and fermentation conditions in co-culture SSF to achieve desirable nutritional outcomes.

With the increasing popularity of plant-based foods, there is growing interest in developing innovative strategies to enhance the bioaccessibility of plant-derived proteins. In this regard, in a standardized in vitro upper gastrointestinal tract (UGIT) digestion model, seven probiotic strains including Bifidobacterium animalis subsp. lactis B420 and Lactobacillus acidophilus NCFM were assessed for their ability to enhance the digestion of soy and pea protein ingredients. All strains significantly improved protein hydrolysis, with an observed increase in free α-amino nitrogen (FAN) ranging from 13% to 33%, depending on the strain and protein substrate. Additionally, several strains elevated the concentration of free amino acids, indicating enhanced protein bioaccessibility. The survival of probiotic strains during digestion was variable and strain-dependent, directly influencing their proteolytic activity. These results highlight the potential of probiotic-assisted strategies to improve the digestibility and amino acid release from plant proteins, a critical factor in optimizing the nutritional quality of plant-based diets [92]. In addition, the production of bioactive peptides during fermentation also offers health benefits, including antioxidant, antihypertensive, and immune-modulating effects, thereby contributing to the functional properties of fermented plant-based foods [12,93]. These advancements underscore the potential of fermentation to transform plant-based proteins into high-quality nutritional sources.

3.3. Enhanced Vitamin Synthesis

Fermentation is remarkably effective in biosynthesizing essential vitamins, particularly B vitamins, and increasing the bioavailability of minerals. Certain strains of bacteria and yeasts involved in fermentation have been shown to elevate the content of B-group vitamins, including B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin) which is often absent in plant foods [94,95]. In this regard, Van Bokhorst-van De Veen et al. explored the in-situ production of vitamin B12 using Propionibacterium freudenreichii and Priestia megaterium in a protein-enriched (53%) brewers’ spent grain (BSG). Initial lab-scale trials achieved up to 21 μg VitB12/100 g BSG after optimization. Scale-up fermentation (12 kg) with stabilized pH yielded 7.7 μg VitB12/100 g. These findings demonstrate the feasibility of low-cost BSG fortification through microbial fermentation. P. freudenreichii showed strong potential as a VitB12 producer in this context. The fortified BSG could serve as a sustainable, plant-based protein source enriched with VitB12 for food and feed applications [96].

Rana et al. in their study developed vitamin B2-enriched soymilk using co-fermentation by two riboflavin-producing Lactiplantibacillus plantarum strains (MTCC 25432, 25433) and Lactobacillus acidophilus NCIM 2902. Optimization via central composite design identified ideal conditions: 36 °C, pH 5.5, 11 h fermentation, with 2% inoculum of both L. plantarum strains and 0.43% of L. acidophilus. These parameters led to a threefold increase in riboflavin (481 µg/L) and probiotic viability of 9 log CFU/mL. Enhanced protease activity improved protein hydrolysis (6259 nm), water holding capacity, and sensory properties. The approach offers a novel, dairy-free strategy to address B2 deficiency, especially in vegan and lactose-intolerant populations [97]. In another study, Diez-Ozaeta et al. investigated the potential of Weissellacibaria BAL3C-5 C120T as a multifunctional starter culture for the development of biofortified plant-based beverages. Among the tested substrates, oat-based drinks showed the most promising results, where fermentation for 24 h led to a significant increase in riboflavin content up to 3.4 mg/L, addressing dietary vitamin B2 deficiencies through in situ biofortification. The strain also produced 3.2 g/L of dextran and 6.6 g/L of panose, enhancing both the nutritional and prebiotic value of the beverage. The fermented oat drink demonstrated a marked pH reduction from 7.0 to 3.8, along with 80% cell viability after one month of storage, indicating strong shelf stability. Rheologically, the product exhibited a thixotropic, gel-like structure, improving its texture and sensory appeal. Furthermore, the strain’s tolerance to gastrointestinal conditions and its autoaggregation ability reinforce its potential as a probiotic. Overall, W. cibaria BAL3C-5 C120T presents a promising strategy for riboflavin enrichment and the creation of functional, health-promoting plant-based beverages [98].

Vitamin C (Vc), the most abundant water-soluble vitamin in orange juice, offers potent antioxidant properties and significant nutritional benefits for human health [99]. Quan et al. evaluated six lactic acid bacteria strains for their impact on fermented orange juice’s physicochemical, antioxidant, and sensory properties. All strains showed good growth, but Lactiplantibacillus plantarum and Lacticaseibacillus paracasei notably enhanced bioactive compounds like vitamin C and shikimic acid. In the original orange juice, the vitamin C (Vc) content was measured at 59.27 mg/100 g. Following fermentation, Vc levels increased in samples fermented with Lactiplantibacillus plantarum (Lp), Limosilactobacillus fermentum (Lf), Lactobacillus acidophilus (La), and Bifidobacterium lactis (Bl) by 19.42%, 16.72%, 16.25%, and 6.80%, respectively, compared to the control. Conversely, Vc content decreased in the Limosilactobacillus reuteri (Lr) and Lacticaseibacillus casei (Lc) groups [100]. The observed increase may be attributed to microbial biosynthesis of Vitamin C during fermentation, while the decline could be due to degradation through chemical or enzymatic oxidation potentially mediated by ascorbate oxidase activity induced by certain microorganisms.

Plant-based milk is known for its rich nutritional profile, containing essential vitamins, minerals, and amino acids. Sooklim et al. investigated the enhancement of the biochemical and functional qualities of rice milk through fermentation with a novel yeast strain, Saccharomyces cerevisiae RSO4, recognized for its superior fermentative capacity. Using an integrated omics approach, the study identified genetic variants in key genes associated with aroma and flavor development (e.g., ARO10, ADH1-5, SFA1), and proteomic analysis revealed upregulation of enzymes involved in glycogen branching (Glc3), glycolysis (Eno1, Pgk1, Tdh1/2), stress response (Hsp26, Hsp70), amino acid metabolism, and cell wall maintenance. Biochemical and metabolomic profiling of fermented rice milk using Homali (Jasmine) and Riceberry varieties exhibited increased levels of bioactive compounds such as β-glucan, vitamins, di- and tripeptides, along with enhanced aroma and flavor [101]. These findings emphasize the critical role of yeast strain selection and rice variety in developing functional plant-based beverages.

Microbial fermentation may also yield certain valuable metabolites. For example, fermentation processes have been shown to boost the concentration of vitamin K, especially in fermented soy products, such as natto, which is rich in menaquinone (vitamin K2) produced by Bacillus subtilis during fermentation. In this regard, Słowik-Borowiec et al. evaluated the impact of fermentation duration on vitamin K2 MK-7 content in ten different plant-based materials (seeds and beans) employing Bacillus subtilis var. natto. Analysis was performed using HPLC UV/DAD. Among the samples, sunflower seeds, mung beans, and peas demonstrated the highest MK-7 levels, reaching 1080.18 ± 55.11 µg/100 g, 806.45 ± 60.95 µg/100 g, and 636.92 ± 59.86 µg/100 g, respectively. A fermentation period of 5–6 days was found to significantly enhance MK-7 yield. The findings indicate that nearly all fermented seeds and beans, with the exception of soybean, can serve as excellent sources of MK-7 and offer a promising alternative with reduced phytoestrogen content [102]. The fermentation process can also convert certain vitamin precursors into more bioactive forms [103,104]. Some vitamins exist in inactive precursor forms in plant-based foods. During fermentation, microorganisms can convert these precursors into their active forms, enhancing their bioavailability and biological activity. For instance, certain bacteria can convert beta-carotene, a precursor to vitamin A, into retinol, the active form of vitamin A. This conversion can significantly improve the vitamin A nutritional value of fermented plant-based foods.

3.4. Production of Functional Metabolites

The fermentation process not only enhances nutritional value but also results in the generation of various functional metabolites, including short-chain fatty acids (SCFAs), polyphenols, and bioactive peptides. These metabolites possess beneficial health properties and contribute to the overall functionality of fermented plant-based foods.

SCFAs, such as butyrate, propionate, and acetate, are produced during the fermentation of dietary fibers by gut microbiota. They play a crucial role in gut health by serving as energy sources for colonic cells, regulating fat storage, and exhibiting anti-inflammatory properties [69,105]. The production of SCFAs is particularly relevant in fermented foods, as these compounds can enhance gut barrier function and modulate immune responses [106]. In this context, Wang et al. assessed the bioaccessibility of phenolic compounds, antioxidant capacity, and SCFA production in four tomato varieties, Oxheart, Green Zebra, Kumato, and Roma during simulated in vitro gastrointestinal digestion and colonic fermentation. Roma demonstrated the highest total phenolic content (TPC) at 0.31 mg gallic acid equivalents (GAE)/g and DPPH radical scavenging activity of 0.12 mg Trolox equivalents (TE)/g after gastrointestinal digestion. Kumato exhibited the highest total flavonoid content (TFC) at 2.47 mg quercetin equivalent (QE)/g after 8 h of colonic fermentation. Oxheart and Roma showed comparable ferric reducing antioxidant power (FRAP) values of approximately 4.30 mg QE/g after 4 h of faecal fermentation. Catechin was the most bioaccessible phenolic compound but was entirely degraded after intestinal digestion, while other bound phenolics were released via microbial fermentation. Notably, Kumato and Green Zebra produced higher levels of both individual SCFAs (acetate, propionate, and butyrate) and total SCFAs, particularly after 16 h of colonic fermentation, suggesting a more favorable impact on gut health through enhanced microbial activity and fermentation efficiency [19]. In another study, Wongsurawat et al. analyzed 65 Thua Nao (a Thai traditional fermented soybean food) samples (30 wet, 35 dried) from six northern Thai provinces to evaluate bacterial diversity and SCFA associations. Differences among the fermented soybean types were analyzed using PERMANOVA (Permutational Multivariate Analysis of Variance) tests. Wet samples exhibited significantly higher bacterial diversity than dried ones. Firmicutes (92.7%) was the dominant phylum, with Bacillus (67%) as the most prevalent genus. Wet samples were enriched in Lactobacillus, Enterococcus, and Globicatella. SCFA analysis showed significantly higher levels of acetate (p = 2.8 × 10⁻⁸), propionate (p = 0.0044), butyrate (p = 0.0021), and isovalerate (p = 0.017) in wet samples. High butyrate and propionate levels correlated with Clostridiales, while high acetate was linked to Weissella. These findings support the potential for SCFA-enriched Thua Nao production using targeted microbial starter cultures [107].

Additionally, fermentation often leads to the enhancement of polyphenolic content in plant foods. These compounds are known for their antioxidant properties, which can help combat oxidative stress and reduce the risk of chronic diseases. Fermentation processes can either release bound polyphenols or enhance their bioavailability through microbial action, increasing their beneficial effects [108]. For example, the fermentation of fruits and vegetables has been shown to improve their antioxidant activity significantly, indicating a dual benefit of improved nutrient density alongside enhanced functional characteristics [38]. Tang et al. developed a fermented beverage (FB) from apple and cantaloupe using a two-stage fermentation process: 21% sugar-supplemented juice inoculated with 9% yeast (27 °C, 11 days), followed by 9% LAB inoculation (36 °C, 16 days). In vitro assays revealed enhanced antioxidant activity post-fermentation, with increased total phenolic content (TPC), total flavonoid content (TFC), DPPH and ABTS radical scavenging activity, and Fe³⁺ reducing power. In vivo studies on Caenorhabditis elegans showed that 6.25% FB significantly prolonged lifespan, boosted SOD and GSH-Px enzyme activity, and reduced MDA levels, without affecting growth, reproduction, or movement. Untargeted metabolomics identified 624 metabolites, with major changes in lipids, organic acids, and heterocyclic compounds. The findings support FB as a functional beverage with notable antioxidant and anti-stress properties [109]. In another study, Yaqoob et al. investigated the impact of multi-frequency ultrasound-assisted (20/28/40 kHz) fermentation using various LAB strains (both mono- and co-cultures) on mulberry juice. Ultrasound treatment notably altered the juice powder’s microstructure, creating rougher, more porous surfaces. The best-performing sample (S10) showed a significant increase in total phenolic (365.36 mg GAE/mL) and flavonoid content (139.20 mg RE/mL). Antioxidant activity improved markedly, with DPPH scavenging reaching 87.45% and FRAPS values rising to 3.27 mM TE/mL (p < 0.05). HPLC-UV analysis detected elevated levels of cyanidin-3-rutinoside (47.47 mg/L) and peonidin-3-O-glucoside (66.86 mg/L) in sample S2. E-nose and sensory evaluations revealed enhanced fruity and floral aromas, particularly in co-culture fermented samples S10, S7, and S14. Overall, the combined approach significantly improved antioxidant potential, flavor, and structural quality of mulberry juice [110].

The production of bioactive peptides during fermentation also deserves attention, as they can exert multiple health benefits, including antihypertensive and antimicrobial properties. Such peptides, created through the hydrolysis of proteins by microbial enzymes, can act as functional additives, enhancing the nutritional profile of the final product. Bioactive peptides, typically consisting of 2 to 20 amino acids, exhibit a range of biological activities, including antimicrobial, antioxidant, and antifungal properties [4]. Plant-based proteins are a valuable source of antibacterial peptides, antioxidative peptides, antifungal peptides as well as antiviral peptides, all of which demonstrate significant bioactive potential. Fermentation serves as an efficient method for producing these peptides, offering advantages such as reduced processing time and enhanced peptide yield. Moreover, it mitigates issues like allergenicity, bitterness, and toxicity often associated with bioactive peptides [111]. Tonini et al. investigated lentil protein isolate (LPI) as a fermentation substrate for selected LAB—Lacticaseibacillus rhamnosus LR32, Lactiplantibacillus plantarum 299v, and Lacticaseibacillus casei LC01—and demonstrated its effectiveness in supporting microbial growth, with final cell concentrations ranging from 7.93 to 8.52 log10 CFU/mL. After 24 h of fermentation at 37 °C, the pH dropped from 6.7 to between 4.71 and 5.08, indicating strong acidification. Fermentation significantly enhanced proteolysis, increasing soluble peptide content by up to 44.1% with L. casei LC01. Antioxidant activity, measured by DPPH radical scavenging, rose from 49.2% in the unfermented control to 69.3% with L. plantarum 299v. ACE (angiotensin I converting enzyme)-inhibitory activity also improved, reaching up to 81.4% inhibition, indicating potential antihypertensive benefits. LC-MS/MS peptide profiling revealed the formation of unique bioactive peptides with antioxidant, anti-inflammatory, and ACE-inhibitory properties. These findings support the use of LPI as a valuable plant-based substrate for developing functional fermented foods enriched with health-promoting bioactive compounds [112].

In another study, Hsieh et al. highlighted the production and functional validation of glycine-rich bioactive peptides (GRPs) derived from Chenopodium formosanum fermented with Rhizopus oligosporus. The GRP fraction, enriched through proteolytic activity during fermentation, demonstrated potent antioxidant, anti-aging, and cytoprotective effects. In UVA-irradiated Hs68 fibroblasts, GRP treatment (50–100 μg/mL) significantly reduced ROS by 33%, enhanced Nrf2 expression (3.86-fold), and downregulated pro-aging markers p53 (2.81-fold) and p21 (0.23-fold). In C. elegans, GRP extended lifespan by up to 13.4%, improved oxidative stress survival to ~80%, and upregulated detoxification genes gcs-1 (5.75-fold) and gst-7 (3.99-fold). Molecular docking further supported GRP’s interaction with the Keap1-BTB domain (−5.22 kcal/mol), facilitating Nrf2 activation [113]. These findings underscore the value of fermentation-based peptide generation for developing functional food ingredients targeting oxidative stress and aging.

4. Microbial Innovations for Next-Gen Plant-Based Fermented Foods

Emerging microbial biotechnological innovations will continue to transform the production of plant-based fermented foods by enabling the creation of next-generation products with enhanced nutritional value, improved functionality, and greater sustainability. As demand for sustainable dietary innovations continues to grow, advancements in biotechnological tools are being leveraged to improve the nutritional and functional properties of plant-based substrates, as illustrated in Figure 3. Central to this transformation is the development of CRISPR-Cas and synthetic biology approaches, which allow for the precise editing of microbial genomes to synthesize essential micronutrients, amino acids, and bioactive compounds. CRISPR-Cas-edited microbes capable of synthesizing vitamin B12, folate, and lysine—nutrients often deficient in plant-based diets—will help address nutritional inequities in plant-based food systems [114].

In addition, precision fermentation technologies enable the production of high-value metabolites in a controlled manner using specific microbial hosts tailored for particular plant-based food matrices. Furthermore, the real-time optimization of fermentation parameters, selection of ideal microbial strains, and prediction of product outcomes using machine learning (ML) and artificial intelligence (AI) enhance consistency and yield in food production, while enabling on-the-fly adjustments for large-scale applications [115]. To improve the sensory quality of plant-based fermented foods, exopolysaccharide-producing microbes are being explored. Exopolysaccharides, or biopolymers, enhance the viscosity, mouthfeel, and stability of plant-based fermented products, such as dairy alternatives including plant-based yogurt and cheese. They also demonstrate prebiotic potential, supporting gut health and adding functional value to the final product [116]. Altogether, these microbial innovations will continue to drive the convergence of biotechnology, sustainability, and food science in next-generation plant-based fermented foods that are nutritionally sound, environmentally sustainable, and tailored to evolving consumer preferences.

4.1. CRISPR and Synthetic Biology Approaches: Engineering Microbes for Targeted Nutrient Synthesis

4.1.1. CRISPR-Cas Approaches

The emergence and implementation of CRISPR-based genome-editing approaches have transformed microbial biotechnology, especially in improving the nutritional value of plant-based fermented foods. CRISPR-Cas systems, particularly CRISPR-Cas9, offer an accurate and efficient method for editing the genomes of microorganisms, enabling targeted enhancement of nutrient synthesis in microbiomes, as shown in Figure 4. These genetic modifications can help address common nutritional deficiencies identified in plant-based diets, which often lack certain vitamins, amino acids, and bioactive compounds typically found in animal-based products [117].

Precision Genome Editing with CRISPR-Cas9

CRISPR-Cas9 is a genome-editing tool initially discovered in bacteria as part of an adaptive immune defense mechanism. In recent years, it has been widely adopted in microbial biotechnology due to its precision, efficiency, and predictability in gene editing. This technology enables the targeted insertion or deletion of genes, including those involved in nutrient biosynthesis pathways, allowing for the development of microbial strains with enhanced functional and nutritional characteristics.

One of the key advantages of CRISPR is its ability to make specific genetic modifications without introducing foreign DNA, potentially avoiding some of the regulatory constraints associated with traditional genetically modified organisms (GMOs). However, it is important to note that the regulatory status of CRISPR-edited organisms varies globally. While some countries do not classify certain CRISPR-edited microbes as GMOs when no transgenic DNA is present, others still impose restrictions or apply similar regulatory frameworks. As such, the global adoption of CRISPR-based food innovations will depend on evolving national policies and public perception. Several studies have demonstrated the application of CRISPR in enhancing plant-based fermented foods. For instance, researchers have used CRISPR-Cas9 to edit Lactococcus lactis (a lactic acid bacterium used in dairy fermentation) to increase folate biosynthesis. Folate, or vitamin B9, is essential for DNA synthesis, cell division, and overall health. Enhancing folate production in L. lactis is beneficial, as population-wide diets may be deficient in this nutrient. Additionally, a gene involved in vitamin B12 biosynthesis was introduced into Escherichia coli using CRISPR, enabling E. coli to produce vitamin B12—an important nutrient often lacking in plant-based diets—which is critical for nerve function and red blood cell formation [118].

Lee et al. used CRISPR-Cas9 genome editing technology to improve both the quality and quantity of fermented food products using Saccharomyces cerevisiae [119]. This study involved the deletion of the glucose sensor genes RGT2 and SNF3 to shift the yeast’s energy metabolism from fermentation to respiration, thereby increasing carbon dioxide production. This metabolic shift resulted in an approximately 18% increase in dough volume, thereby enhancing the final product yield. Additionally, deletion of the URE2 gene, a nitrogen regulator, improved amino acid production during the fermentation of rice wine and, more importantly, enhanced the overall fermentation process. These data demonstrate that a simple, targeted genetic modification using CRISPR-Cas9 can significantly improve the yield and taste of fermented foods without introducing foreign DNA.

Xie et al. aimed to enhance the commercial viability of Lacticaseibacillus rhamnosus GG (LGG) by using the endogenous type II-A CRISPR-Cas9 system for genome editing [120]. This work included the construction of lactose-positive strains of LGG (MJM570), involving the deletion of a transcriptional terminator upstream of the lacT gene and the correction of a premature stop codon in the lacG gene. These genetic modifications restored lactase activity, enabling the strain to metabolize lactose and resulting in improved growth characteristics during milk or yogurt fermentation. The fermentation process yielded increased biomass, as measured by cell counts, and the milk was chemically coagulated and remained viable during storage at refrigeration temperatures. This study demonstrates how CRISPR-mediated genome editing can be strategically applied to enhance the functional characteristics and yield of probiotics for dairy applications.

Han et al. revealed that CRISPR-Cas9 technology could be used to edit a food-grade, high-yielding Acetobacter pasteurianus Ab3 strain to produce higher levels of pyrroloquinoline quinone (PQQ), an important antioxidant that supports mitochondrial function and maintains redox balance [121]. Through genomic editing, they upregulated gene expression in the PQQ biosynthetic pathway, thereby increasing the metabolic flux toward PQQ production. The rationally genome-edited strains did not contain any antibiotic resistance markers, thus preserving their food-grade status for application in the nutraceutical and food industries. Their findings highlight the potential of CRISPR-Cas9 as a precise and timely tool to optimize metabolic pathways and enhance the yields of important industrial microorganisms.

Haryani et al. demonstrated that the CRISPR/Cas9 system can be used to reprogram the metabolic pathways of LAB strains to increase the synthesis of antimicrobial compounds [122]. Metabolite-based genetic engineering, using a two-plasmid CRISPR/Cas9 system to knock out the lactate dehydrogenase (ldh) genes, shifted the carbon flux from lactic acid production to the synthesis of bacteriocin-like inhibitory substances (BLIS). The metabolic reprogramming of LAB strains resulted in significant antimicrobial activity against foodborne pathogens, with certain strains exhibiting up to a 78% improvement in activity compared to the wild-type. Notably, Enterococcus faecalis with the ldh deletion displayed pronounced bactericidal effects, surpassing the antimicrobial capabilities of the wild-type strain. This study highlights how metabolic engineering via CRISPR/Cas9 technology can be strategically applied to enhance the accumulation of desirable antimicrobial compounds, thereby improving food safety and quality in LABs.

These studies collectively highlight how CRISPR can serve as a precise and versatile tool for improving the nutritional, functional, and safety attributes of fermented foods. As emerging regulatory frameworks and public acceptance continue to evolve, CRISPR-based microbial strain development may offer promising, scalable, and potentially non-GMO-compliant solutions for the next generation of sustainable and health-enhancing food systems.

Engineering Microbes for Amino Acid and Fatty Acid Production

In addition to vitamins, CRISPR is being utilized to improve the biosynthesis of amino acids and fatty acids that are components of a balanced diet. For example, essential amino acids such as lysine, methionine, and tryptophan are important but can be limited in the diet, particularly in vegetarian or vegan diets that do not contain sufficient quantities of animal-based protein. CRISPR-Cas9 has been used to enhance the biosynthesis of these essential amino acids in microbial strains such as E. coli and Corynebacterium glutamicum. CRISPR-Cas9 has also been used to engineer the metabolism and function of S. cerevisiae (baker’s yeast), enabling it to express omega-3 fatty acids such as docosahexaenoic acid (DHA), which are essential for brain health and typically obtained from fish or algae. Researchers have now introduced genes from marine organisms into yeast strains and have successfully engineered microbial cell factories capable of producing omega-3 fatty acids, providing an example of CRISPR-Cas9 as a solution to omega-3 overexploitation from marine sources [123,124].

CRISPR-based metabolic engineering has made significant advancements in microbial biosynthesis of proteinogenic amino acids and omega-3 fatty acids, offering a sustainable alternative to nutrient inputs that have historically been animal-based. For example, Chen et al. engineered E. coli for improved substrate utilization by deleting the mlc gene and adding heterologous gene constructs, resulting in L-lysine production of 204.00 g/L, with a yield of 72.32% and a productivity of 5.67 g/(L·h) during fed-batch fermentation [125]. Similarly, Wang et al. employed CRISPR-based metabolic engineering in C. glutamicum by deleting regulatory genes (thrB, mcbR) and overexpressing feedback-inhibition-resistant homm, lysCm, and the brnFE cluster, leading to L-methionine production of 6.3 g/L after 64 h of fermentation [126]. Cleto et al. used CRISPR interference (CRISPRi) to target central metabolic genes (pgi, pck, pyk) in C. glutamicum using a catalytically inactive Cas9 (dCas9) system, achieving up to 98% repression of the target genes while maintaining or improving yields of L-lysine and L-glutamate [127]. In the context of fatty acid biosynthesis, Han et al. leveraged metabolic engineering of oxidative stress response genes (ALDH, GPO, TRXR) in Schizochytrium sp., improving DHA yield from 4.3 g/L in the wild-type strain to 13.3 g/L in the engineered strain, resulting in a 114.5% increase in DHA yield [128].

These examples demonstrate the efficiency and scalability of CRISPR-based metabolic engineering and the production of essential nutrients (i.e., L-lysine, L-methionine, and DHA) relevant to plant-based diets and nutrition that would not be available from marine or animal sources to combat global nutrition issues.

Xin et al. found that the RecE/T-assisted CRISPR/Cas9 system achieved gene deletion efficiencies of 50% to 100% in LAB strains such as Lactobacillus plantarum WCFS1 and Lactobacillus brevis ATCC 367 within less than seven days [129]. This system enabled gene knock-out, knock-in, and point mutation efficiencies in L. plantarum WCFS1 of 53.3%, 58.3%, and 62.5%, respectively. These results highlight the potential of CRISPR/Cas9 technology for enhancing genetic manipulation of LAB, thereby improving their metabolism and advancing their industrial applications in the production of probiotics, bioactive compounds, and fermented food products.

Addressing Nutritional Deficiencies in Plant-Based Diets

The potential uses of CRISPR to combat nutritional deficiencies within plant-based diets are enormous. One notable example involves vitamin B12, an essential micronutrient for human health, responsible for the normal functioning and development of brain cells, nerve cells, and red blood cells. Since vitamin B12 is naturally absent in plant-based foods, B12-rich products are often fortified using UV light or animal-derived nutrients. CRISPR can make an ecological impact by enabling the incorporation of microbes that synthesize vitamin B12 into the fermentation of plant-based foods. For B12-deficient vegan populations, CRISPR-modified fermentation microbes offer a solution to the B12 bioavailability issue, demonstrating how CRISPR can address one of the greatest nutritional challenges to food security [130].

Lactobacillus and Propionibacterium strains can be genetically modified to produce bioavailable vitamin B12 during fermentation, making fermented plant-based foods such as soy milk or vegetables excellent non-animal sources of this vital nutrient [131]. The advent of CRISPR-modified B12 production may significantly influence dietary behavior by supporting the development of affordable, plant-based alternatives that address key nutrient gaps traditionally filled by animal-based products.

In addition, CRISPR can be used to enhance the production of bioactive peptides in plant-based foods through fermentation, offering nutritional benefits beyond vitamin B12 [132]. Bioactive peptides are short protein fragments derived from food proteins and are known for their positive physiological effects. By biotransforming plant-based proteins during fermentation, these peptides can increase both the nutritional value and health benefits of the resulting food products [133]. For instance, Lactobacillus strains have been engineered to produce bioactive peptides with antioxidant and immunomodulatory properties, enhancing the functional attributes of fermented products [93].

While the nutritional quality of plant-based fermented foods with CRISPR optimizes health impacts, CRISPR-engineered fermentation microbes also support sustainable and efficient food production processes. This technology contributes to a wider degree of sustainability by decreasing reliance on animal-based products and potentially increasing consumer interest in plant-based products. Animal agriculture has significant environmental burdens associated with its operations, such as greenhouse gases, higher water use, and land clearing for cattle, fish, and hens. CRISPR provides a direct conversion for necessary vitamins and nutrients into live microorganisms that can be utilized to produce plant-based foods. Each of the optimization characteristics from CRISPR helps to reduce the environmental impacts of food production due to more sustainable manufacturing of nutrients, supporting greener food systems in response to consumer demand [12,134].

By using CRISPR to create engineered microbes for nutrition, it can reduce our reliance on animal farming at commercial scales while continuing to nutritionally satisfy consumers [135]. CRISPR can also play an important role in optimizing microbes for fer-mentation to produce nutrients for human consumption. For example, microbes have metabolic pathways in producing vitamins and essential fatty acids that can be enhanced through CRISPR technology to produce the nutrients more efficiently, decreasing time, energy, and materials used to optimize nutrient production during the fermentation process. Each CRISPR optimization stands to reduce the number of re-sources for sustainability, along with creating functional, plant-based foods, with efficiency and minimizing material impacts [129].

4.2. Precision Fermentation and AI-Driven Optimization

Recent advances in fermentation control systems have been facilitated by sensing technologies, metabolic models, and machine learning. These technologies are revolutionizing how fermentation processes are controlled and monitored, thereby improving efficiency, sustainability, and product yield without requiring changes to the bioreactor design [136]. Reinforcement learning (RL) has proven to be an effective and adaptive control paradigm for fermentation process optimization. Unlike traditional control paradigms, RL does not rely on a pre-established mathematical model; instead, the agent learns through interaction with the environment. The goal in RL is to maximize the long-term cumulative reward (e.g., product yield and stability) in a given environment through trial-and-error exploration of different combinations of actions (or policies). While RL is fundamentally a model-free method of learning, most practical fermentation applications utilize RL agents that have been trained on model-based simulations, or digital twins of the bioprocess, which provide an efficient and safe training environment without interfering with the actual production system [137].

RL has been validated in batch, fed-batch, and microbial co-culture systems by dynamically adjusting critical control parameters such as temperature, pH, agitation speed, or nutrient feeding rate over time to optimize growth conditions and maximize product synthesis. In fed-batch fermentation, RL agents have learned optimal feeding strategies that balance substrate availability and metabolic stress to enhance overall productivity. RL also integrates effectively with certain Model Predictive Control (MPC) applications. MPC offers short-term guarantees that are beneficial in more complex scenarios, such as controlling substrate gradients and managing metabolic pathway transitions in co-cultures.

While the RL-MPC approach holds great promise, it faces several challenges. One major issue is dimensionality; as the number of available control variables increases, the state and action spaces grow exponentially, making the RL agent’s exploration process more complex [138]. This complexity can lead to longer training times, increased computational costs, and a reduced likelihood of policy convergence (i.e., suboptimal learning). Additionally, biochemical systems are particularly sensitive to variability and noise, as they are ultimately governed by biological processes. Therefore, developing generalized policies that account for this variability while enabling efficient learning from environmental noise is essential. Potential solutions include the use of function approximation techniques (including but not limited to deep learning), dimensionality reduction methods for both model-based simulations and digital twins, and transfer learning from simulated environments to real-world systems [139].

The efficiency and accuracy of fermentation processes can be significantly enhanced by combining artificial intelligence (AI)-based optimization with traditional statistical approaches such as Response Surface Methodology (RSM) [140]. In bacterial exopolysaccharide (EPS) production, AI-based optimization methods such as artificial neural networks (ANN) and genetic algorithms (GA) have outperformed RSM alone and even RSM in combination with AI. While RSM is valuable for understanding factor interactions and identifying near-optimal conditions through polynomial regression models, AI techniques are better suited for capturing non-linear and complex interactions. In a comparative study conducted by Rabiya et al., an ANN-GA-based optimization improved EPS production by 25–30% compared to RSM, increasing predicted yields from 6.2 g/L to 8.1 g/L [141]. The AI-based models also exhibited higher R² values (>0.98) and lower root mean square errors (RMSE), indicating superior accuracy and robustness. These models not only streamline medium optimization and save time but also reduce costs by minimizing the need for exhaustive experimental trials, making them especially useful and cost-effective for scaling up industrial fermentation processes.

4.3. Microbial Exopolysaccharides and Textural Modifications

The sensorial attributes, specifically the texture and mouthfeel of plant-based fermented food products, are tremendously important to consumer acceptance and overall product quality. One of the most innovative microbial approaches for enhancing these sensory and functional properties involves the production of exopolysaccharides (EPSs) by (LAB) and other beneficial microbes. These polysaccharides, which are high-molecular-weight molecules, are produced extracellularly during fermentation. Their significance lies in their ability to increase viscosity, enhance water-binding capacity, and contribute to the overall stability of the product [36]. Microbial EPSs significantly contribute to changes in the rheological properties of plant-based matrices, mimicking the creaminess and smooth texture typically associated with dairy-based products.

For instance, Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus, employed in yogurt fermentation, produce ropy and capsular EPSs that improve product viscosity and gel strength [142]. However, with the growing preference for vegetarian diets, plant-based beverages like yogurt are increasingly being developed, where the main challenges remain in achieving desirable taste and optimal texture. When microorganisms are added to a non-dairy substrate such as soy milk, oat milk, and almond milk, they produce the same desirable properties after fermentation [143]. Fermentation of soy milk with Weissella confusa wild-type or sac mutant strains significantly improved water holding capacity and viscosity which highlights their potential to boost EPS production in fermented plant-based milk alternatives, helping to mimic the texture of traditional dairy products [144]. Similarly, LAB are used in bakeries for sourdough production owing to their EPS production, which improves dough characteristics by increasing thickness [145]. EPSs also act as stabilizers by preventing phase separation in plant-based fermented beverages and sauces through their ability to stabilize emulsions. In such beverages, EPSs contribute emulsifying capacity and help retain a homogeneous distribution of nutrients and flavor throughout the product’s shelf life. This not only enhances the overall sensory experience for consumers but also reduces the reliance on synthetic stabilizers [146].

Moreover, EPSs have demonstrated potential synergistic interactions with plant proteins and dietary fibers. These interactions can support the formation of gels and structures sufficient to mimic the viscosity and mouth-coating characteristics of dairy products and meat analogues. EPSs also help retain water, contributing to the creation of soft, moist textures in products made through baking or cultured methods [147].

Microbial EPSs function not only as textural enhancers in functional foods but have also shown prebiotic capabilities, immunomodulatory effects, and cholesterol-lowering properties, enabling them to serve as dual-purpose bioactive compounds [148]. This positions EPS-producing microbes as promising ingredients in the development of next-generation plant-based functional foods, offering both health benefits and improved consumer acceptance.

Advances in genetic engineering and fermentation control have further enabled the customization of microbial strains for high EPS yield and structural diversity. Additionally, omics tools and ML models are being used to screen and optimize EPS biosynthetic pathways, allowing food developers, bakers, and producers to modulate both texture and nutritional functionality in a single step [149]. In short, microbial EPSs represent a sustainable and innovative approach to improving the texture, viscosity, stability, and functional value of plant-based fermented foods. They make important technological, sensory, and nutritional contributions to plant-based product formulation and serve as key players in bioactive innovation for future food systems [150].

5. Health Benefits and Functional Properties

5.1. Fermented Foods and Gut Microbiota

Fermented foods are increasingly recognized as important modulators of gut microbiota and overall gastrointestinal health. Foods rich in live microorganisms, particularly (LAB) contain high concentrations of these beneficial microbes at the time of fermentation. When such foods are consumed regularly as part of the diet, they can positively influence gut health. Continuous intake of LAB-rich foods (e.g., yogurt, kefir, kimchi, sauerkraut) has been shown to enhance not only microbial diversity but also the metabolic activity of the gut microbiota [151]. Improvements in these key indicators reflect favorable changes in the gut microbiome, as illustrated in Figure 5. The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines probiotics as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” [152]. While many traditional fermented foods contain live microorganisms, they often do not fulfill the full measure of defined strains, quantify doses, or prove a health benefit to be considered a probiotic. Synbiotics are also defined as “a mixture of live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host” [153]. Therefore, fermented foods with undefined microbial populations should not be interchangeably regarded as probiotic or synbiotic unless those claims are supported by rigorously collected evidence that follows the ISAPP criteria. Some recent research has leveraged consumption of these fermented foods (e.g., yogurt, kefir, kimchi, sauerkraut) and their effects on gut microbial communities and host metabolism. Wastyk et al. found that a diet high in fermented foods, increased diversity of gut microbiota and decreased biomarkers of inflammation such as IL-6 and IL-10 [154]. Fermented foods likely influence microbial ecosystems not directly as probiotics, but indirectly by changing the microbial environment, increasing SCFA production, and competitive exclusion of pathogenic bacteria.

5.1.1. Mechanisms of Action: Host-Microbiota Interactions

Recent studies in microbiome research have revealed several important pathways through which probiotics and synbiotics interact with host systems. These pathways include the modulation of immune function, maintenance of epithelial integrity, and microbial metabolite signaling. The health benefits of fermented foods on gut health rely heavily on specific microbial metabolites and host immune pathways that are activated. One such pathway involves the production of SCFAs—butyrate, acetate, and propionate generated from the anaerobic bacterial fermentation of dietary fiber [155]. SCFAs not only serve as an energy source for colonocytes but also possess immune-modulating functions. For example, butyric acid is a histone deacetylase (HDAC) inhibitor that alters gene expression to upregulate anti-inflammatory cytokines and enhance the differentiation of regulatory T cells (Tregs), which promote immune homeostasis [156,157]. SCFAs also activate G-protein-coupled receptors (GPR41, GPR43, and GPR109A) on immune and epithelial cells, thereby inhibiting the NF-κB signaling pathway and reducing the production of TNF-α, IL-6, and other pro-inflammatory cytokines [158].

In addition, surface molecules and metabolites of probiotic strains (including Lactobacillus and Bifidobacterium) interact with pattern recognition receptors (such as TLR2 and TLR4) on intestinal epithelial and antigen-presenting cells. These interactions activate innate immune pathways, leading to the production of anti-inflammatory cytokines—particularly IL-10—and suppression of the pro-inflammatory cascade [28,159]. Probiotic strains also contribute to maintaining epithelial barrier integrity by upregulating genes encoding tight junction proteins (e.g., occludin and claudins) and enhancing mucin secretion, which collectively protect against pathogen invasion and systemic endotoxemia. Collectively, these pathways highlight the role of fermented foods in immune modulation, pathogen resistance, and anti-inflammatory responses [160].

5.1.2. Prebiotics: Fuel for Beneficial Bacteria

Prebiotics are defined as non-digestible dietary components, primarily fibers and oligosaccharides, that selectively stimulate the growth and activity of beneficial microorganisms along the gastrointestinal (GI) tract, such as Lactobacillus spp. [161]. The key characteristic of prebiotic compounds is that they are non-digestible carbohydrates that escape digestion in the upper GI tract and reach the colon intact. Once in the colon, prebiotics serve as fermentable substrates for the resident microbiota. Common prebiotics include inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS), which are naturally present in foods such as garlic, onions, bananas, globe artichokes, and whole grains [162].

One of the principal benefits of prebiotic fermentation in the gut is the production of SCFAs—including acetate, propionate, and butyrate by gut bacteria. These SCFAs are metabolically significant, serving as energy sources for colonic epithelial cells (colonocytes), supporting intestinal barrier integrity, and modulating local immune responses [163]. The fermentation of prebiotic substrates also contributes to the acidification of the colonic environment, which inhibits the growth of pathogenic bacteria while enhancing beneficial microbial populations. This helps maintain the resilience and functional stability of the gut microbiota, supporting overall intestinal homeostasis.

Prebiotics are believed to enhance microbial diversity and metabolic activity, thereby promoting gut homeostasis and potentially alleviating the symptoms or reducing the risk of gastrointestinal disorders such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) [158]. Consequently, prebiotics have been associated with improvements in barrier function, reduction in inflammation, and mitigation of other disease states. These benefits underscore their utility in dietary management and the prevention of various GI-related conditions [164].

5.1.3. Synergistic Effects of Fermented Foods and Prebiotics

Synbiotics are a combination of fermented foods and prebiotics that foster gut health by delivering beneficial microorganisms along with substrates that support their growth. Fermented foods such as yogurt, kefir, kimchi, and sauerkraut contain significant amounts of probiotics, which can enhance gut microbiota diversity, digestion, gut barrier integrity, and immune function [165]. Prebiotics, on the other hand, are non-digestible fibrous substances found in foods like bananas, garlic, onions, and whole grains. They selectively stimulate the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium, helping to maintain a balanced gut microbiome [166].

Prebiotics promote gut health, which in turn influences digestion, inflammation, and nutrient absorption. By providing a substrate for beneficial microbes to thrive, prebiotics support the colonization and activity of probiotics when consumed together with fermented foods. This synergy improves gut barrier function and enhances immune responses [167]. The prebiotics present in fermented foods are metabolized by gut microbiota into SCFAs, which regulate inflammation, strengthen the gut lining, and provide energy to colonocytes [168].

Simon et al. found that synbiotics—combinations of fermented foods and prebiotics improve microbiome diversity, enhance bowel regularity, and reduce symptoms associated with (IBS) and bloating [169]. Ford et al. reported that synbiotics help modulate the population of beneficial gut bacteria and may offer protection against inflammatory diseases by supporting gut and immune health [170]. Furthermore, synbiotics can improve nutrient bioavailability and promote the production of microbial metabolites that aid in the absorption of fat-soluble vitamins and minerals, which is especially beneficial for individuals with specific dietary needs, such as those following a vegan diet [171].

Moreover, synbiotics are known to support gut motility and may alleviate symptoms associated with constipation and (IBD) [172]. Overall, synbiotics represent a promising dual approach to enhancing gut health, immune function, and nutrient absorption, with growing potential for both therapeutic and preventive healthcare applications.

5.2. Metabolic and Anti-Inflammatory Benefits: Role in Obesity, Diabetes, and Cardiovascular Health

Fermented foods are effective in improving metabolic health and reducing inflammation, both of which are key factors in the treatment and management of diseases such as obesity, diabetes, and cardiovascular disease. In fermented foods, probiotic microbes (e.g., Lactobacillus and Bifidobacterium species) modulate the gut microbiota, contributing to metabolic functions including insulin sensitivity, glucose homeostasis, and lipid metabolism [173]. These probiotic microbes also influence the biosynthesis of (SCFAs), which have been shown to improve metabolic health through anti-inflammatory effects [159]. During the fermentation process, SCFAs such as butyrate are produced, playing important roles in regulating adipocyte differentiation and reducing inflammatory markers associated with obesity [158]. Probiotics and certain bioactive peptides released during fermentation may also modulate cholesterol levels and improve cardiovascular health by regulating lipid metabolism, lowering blood pressure, and enhancing endothelial function [174]. Overall, studies have shown a correlation between the consumption of fermented dairy products such as kefir and yogurt and a reduced risk of hypertension and atherosclerosis, suggesting a potential impact on cardiovascular disease morbidity [175].

5.3. Cognitive and Neurological Impact: Neuroprotective Metabolites from Fermented Foods

In recent years, the neuroprotective effects of fermented foods have received increased attention in the literature. This interest stems from the metabolites generated during the fermentation of food, which may have implications for brain health. The gut–brain axis—through which the gut microbiota communicates with the central nervous system—has established links to cognitive function and emotional health [176]. Fermented foods may act as key agents in this relationship due to the probiotic strains present in fermentation cultures, which remain bioactive upon consumption. These probiotics can produce metabolites such as (GABA), serotonin, and dopamine, all of which play essential roles in regulating stress, cognition, and mood [177,178].

Fermented foods like kimchi and sauerkraut contain bioactive compounds such as small peptides and SCFAs, which have been correlated with neuroprotective effects, reduced anxiety, and improved memory function [179]. Although the specific mechanisms by which these metabolites exert their effects remain unclear, it is hypothesized that they may modulate neuroinflammation and oxidative stress—two factors implicated in neurodegenerative diseases such as Alzheimer’s and Parkinson’s [180]. Not surprisingly, evidence suggests that dietary supplementation with probiotics can alter gut microbiota composition, thereby influencing cognitive function and mental health [181].

5.4. Allergen Reduction and Digestibility Improvements: Mitigation of Food Intolerance Risks

Fermentation is also important for reducing allergens and improving the digestibility of certain food products, making them safer for individuals with food intolerances. For instance, people with lactose intolerance can often tolerate fermented dairy products like yogurt and kefir better than other dairy products, as the fermentation process breaks down lactose into glucose and galactose [182]. Fermentation and its associated enzymes can also lower the allergenic potential of some proteins (e.g., soy and wheat). By breaking down protein structures and reducing immunoreactivity, fermentation can be beneficial for managing food intolerances and allergies [183]. Fermented foods are also used to help address gluten sensitivities. LAB in wheat-based products can degrade gluten, significantly decreasing its presence in the final product and reducing related digestive discomfort [184]. Finally, fermented plant-based foods are often easier to digest than their unfermented counterparts. This improved digestibility results from the fermentation process, which enhances the bioavailability of nutrients such as amino acids, minerals, and vitamins, thereby offering better nutrition for individuals with malabsorption or digestive issues [185].

6. Sustainability and Future Trends in Plant-Based Fermentation

6.1. Fermentation for Food Waste Valorization

Fermentation has demonstrated great potential for food waste valorization by offering the possibility to transform agricultural by-products into valuable, functional food products with improved nutritional properties—efficiently and sustainably. Food waste is a major environmental concern, with millions of tons of fruit peels, seeds, and pulp discarded every year. This not only generates greenhouse gases but also depletes the planet’s natural resources [186]. Fermentation can redirect food waste into useful fermentable ingredients for human consumption and animal feed, serving as a functional ingredient beneficial to both human health and the environment. By repurposing food waste through fermentation, several goals can be achieved: food waste reduction, a lower carbon footprint, and the incorporation of bioactive compounds that enhance the nutritional value of plant-based food products [187].

One of the most frequently fermented agricultural by-products is fruit and vegetable peels. Although these peels are nutrient-dense, they are often discarded due to their unique texture or perceived lack of value. Commonly considered the ultimate by-products of food processing, they are in fact rich in fiber, vitamins, and antioxidant nutrients. Microbial fermentation of these materials can convert complex structural organic components into bioactive ingredients such as organic acids, peptides, and vitamins. Table 3 highlights the diversity of fermentation techniques applied to food waste valorization.

LAB plays a pivotal role in enhancing bioavailability during fermentation. LAB can break down complex carbohydrates and proteins in agricultural by-products into simpler, more digestible forms. This biodigestion process not only improves the nutritional value of the final product but also increases the bioavailability of nutrients and vitamins, making food healthier and more suitable for human consumption. LAB fermentation also produces organic acids like lactic acid, which act as natural preservatives and extend the shelf life of fermented products. Additionally, fermentation enhances the digestibility of by-products, making nutrients more easily absorbed [188].

Fermentation can also yield bioactive peptides with various health benefits. These peptides may possess antioxidant, anti-inflammatory, or antimicrobial properties that further improve the health value of fermented plant-based foods [189]. For example, fermentation of soy—an agricultural byproduct has produced bioactive peptides with hypotensive and anti-cholesterol effects, underscoring their importance in functional foods [38].

The growing interest in upcycling agricultural waste into nutrient-dense fermented products not only benefits the food industry but also reduces environmental impact. This approach supports the development of sustainable food production by integrating waste into the creation of functional foods, thereby contributing to a circular economy. As consumer preferences shift toward plant-based diets and sustainable lifestyles, this model becomes increasingly relevant [190]. Moreover, food waste valorization through fermentation can enhance food security by providing affordable, locally sourced, functional food options. Converting surplus and low-cost agricultural by-products into high-value foods reduces reliance on traditional agricultural resources and improves resilience to environmental and market fluctuations. With a growing global population and increasing food insecurity, sustaining access to nutritionally dense foods is essential [38]. Fermentation-based valorization has the potential to positively transform the food system by reducing waste, boosting nutritional density, and supporting sustainability. If agricultural by-products can generate bioactive compounds that promote gut health, immunity, and disease prevention, they can significantly contribute to human health. Continued research and innovation in fermentation technologies offer great promise for addressing modern challenges in food systems.

Table 3. Fermentation approaches for food waste valorization.

Fermentation Approach	Microorganism/s Involved	Substrate	Key Products	Yield/Key Characteristics	Reference
SSF	Starmerella bombicola	oil cake and molasses	Sophorolipids	0.2 g SL g−1	[191]
Submerged Fermentation (SmF)	Aspergillus niger	Pineapple waste	Single-cell proteins (SCPs)	Protein content-9.79 ± 0.11 g/L after 10 days	[192]
Mixed Solid-State Fermentation (M-SDF)	Trichoderma reesei and A. niger	Orange peel by-products	Soluble dietary fiber	The water holding capacity and oil holding capacity of M-SDF were 5.68 ± 0.36 g/g and 5.04 ± 0.04 g/g, respectively, approximately six times and two times greater than those of Untreated soluble dietary fiber.	[193]
SSF	Trichoderma harzianum	Grass clippings and pruning waste	Indole-3-acetic acid (IAA) and Conidial spore	101.46 µg g−1 dry matter IAA and 3.03 × 109 spore g−1 dry matter	[194]
Lactic Acid Fermentation	L. plantarum	cocoa bean shell	Lactic acid	19.00 g/100 g of lactic acid after 24 h of fermentation	[195]
SSF	Pseudomonas aeruginosa PTCC 1074s	Soyabean meal	Rhamnolipid	14.63 g/kg substrate	[196]
SSF	Clostridium tyrobutyricum	Wheat bran, rice polishings and molasses	Butyric acid	5.63 mg/100 g from rice polishing	[197]
Yeast fermentation	Saccharomyces cerevisiae	Pineapple crumbs by-product	Fermented pineapple juice	Alcohol content: 5–6 %v, Soluble solids concentration: 13–14 °Bx.	[198]
SSF	A. fumigatus TXD105	Sugarcane bagasse	Paclitaxel	145.61 mg/kg	[199]
Fungal Fermentation (SSF)	A. terreus	mixed food waste	Glucose, free amino nitrogen, inorganic phosphate	Glucose-0.57 g/g, free amino nitrogen-185 mg/L, inorganic phosphate-195 mg/L	[200]
SSF	Bacillus subtilis D19	Wheat bran	Amylase	1239 U/g	[201]
Fungal Fermentation (SSF)	Neurospora intermedia	Okara	Fermented food	Increased protein content from 25% to 28% and lipid content from 12% to 14%.	[202]

Table 3. Fermentation approaches for food waste valorization.

Fermentation Approach	Microorganism/s Involved	Substrate	Key Products	Yield/Key Characteristics	Reference
SSF	Starmerella bombicola	oil cake and molasses	Sophorolipids	0.2 g SL g−1	[191]
Submerged Fermentation (SmF)	Aspergillus niger	Pineapple waste	Single-cell proteins (SCPs)	Protein content-9.79 ± 0.11 g/L after 10 days	[192]
Mixed Solid-State Fermentation (M-SDF)	Trichoderma reesei and A. niger	Orange peel by-products	Soluble dietary fiber	The water holding capacity and oil holding capacity of M-SDF were 5.68 ± 0.36 g/g and 5.04 ± 0.04 g/g, respectively, approximately six times and two times greater than those of Untreated soluble dietary fiber.	[193]
SSF	Trichoderma harzianum	Grass clippings and pruning waste	Indole-3-acetic acid (IAA) and Conidial spore	101.46 µg g−1 dry matter IAA and 3.03 × 109 spore g−1 dry matter	[194]
Lactic Acid Fermentation	L. plantarum	cocoa bean shell	Lactic acid	19.00 g/100 g of lactic acid after 24 h of fermentation	[195]
SSF	Pseudomonas aeruginosa PTCC 1074s	Soyabean meal	Rhamnolipid	14.63 g/kg substrate	[196]
SSF	Clostridium tyrobutyricum	Wheat bran, rice polishings and molasses	Butyric acid	5.63 mg/100 g from rice polishing	[197]
Yeast fermentation	Saccharomyces cerevisiae	Pineapple crumbs by-product	Fermented pineapple juice	Alcohol content: 5–6 %v, Soluble solids concentration: 13–14 °Bx.	[198]
SSF	A. fumigatus TXD105	Sugarcane bagasse	Paclitaxel	145.61 mg/kg	[199]
Fungal Fermentation (SSF)	A. terreus	mixed food waste	Glucose, free amino nitrogen, inorganic phosphate	Glucose-0.57 g/g, free amino nitrogen-185 mg/L, inorganic phosphate-195 mg/L	[200]
SSF	Bacillus subtilis D19	Wheat bran	Amylase	1239 U/g	[201]
Fungal Fermentation (SSF)	Neurospora intermedia	Okara	Fermented food	Increased protein content from 25% to 28% and lipid content from 12% to 14%.	[202]

6.2. Eco-Friendly Fermentation Technologies: Bioreactor Innovations and Low-Energy Processes

Sustainable fermentation technologies are poised to play a key role in advancing sustainability and the production of environmentally friendly, plant-based food systems. Fermentation is widely recognized as a traditional food preservation method that has been practiced for centuries. It not only extends shelf life but also enhances food flavor and nutritional value. However, industrial-scale fermentation processes often consume significant amounts of energy due to requirements such as temperature control, aeration, mixing, and sterilization.

Given the urgent need to reduce emissions and minimize environmental impact, there is growing interest in developing low-impact fermentation alternatives that maintain productivity while consuming fewer resources. Innovations in bioreactor technology, including membrane bioreactors, immobilized cell systems, and continuous stirred-tank reactors (CSTRs), have notably improved the environmental performance of fermentation systems. These advanced designs create more controlled environments for microbial growth and metabolite production, optimizing mass transfer, enhancing substrate utilization, and enabling microbial biomass recycling. This leads to reduced microbial inactivation and lower biowaste generation [203]. CSTRs offer specific advantages, as they operate in a steady state that consistently produces metabolites, reducing batch decoupling time and improving productivity and energy-to-yield ratios. When integrated with solar energy for heating, aeration, and mixing, CSTRs can also decrease fuel requirements and recover heat and power [38].

Low-energy fermentation strategies such as cold fermentation—where psychrotolerant microorganisms remain efficient at lower temperatures and anaerobic or microaerophilic conditions that eliminate the need for mechanical aeration, can significantly reduce energy input and emissions. For instance, naturally occurring LAB and yeasts can perform fermentations at lower temperatures without compromising metabolite output, eliminating the need for energy-intensive thermal control systems [204]. Moreover, smart fermentation systems are increasingly incorporating AI and IoT sensors to optimize energy use. These systems can process large datasets to predict inefficiencies, minimize energy consumption, and enable automated energy-saving functions (e.g., disabling unused heating elements) [205].

Innovative fermentation practices align with green biotechnology principles and contribute to the decarbonization and de-intensification of resource-heavy food production. By adopting eco-friendly bioreactors, low-energy fermentation methods, and AI-enhanced smart systems, the plant-based fermentation industry can greatly reduce its environmental footprint. These advancements support the development of a circular, sustainable bioeconomy that meets consumer expectations for ecologically responsible, plant-based food solutions.

6.3. Personalized Fermented Foods: AI-Driven Formulation Based on Microbiome Profiling

The emergence of nano-scale AI and microbiome sciences signifies the rise in personalized nutrition and fermented foods, particularly in the realm of plant-based fermented products. Personalized fermented foods refer to food developments created using an individual’s microbiome data to address underlying physiological and health concerns. Data-driven AI and ML methods enable scientists to pinpoint specific health-related interactions between the gut microbiota and host health, fostering innovations through tailored formulations that improve microbial balance and optimize nutrient intake [206]. AI facilitates the evaluation of sequencing data from gut microbiome experiments and helps predict optimal probiotic strains, substrates, and bioactives derived from fermentation conditions that maximize health outcomes in personalized food environments. These platforms utilize data from macro- and micro-omics technologies such as metagenomics, metabolomics, and transcriptomics to enable precision fermentation that supports an individual’s unique microbiome signature [207].

The use of personalized foods based on microbiome signatures allows customization according to probiotic strain, fermentation conditions, and functional ingredients. For example, individuals with low Bifidobacterium counts may benefit from fermented foods containing prebiotics like inulin and targeted probiotic strains to restore microbial diversity [208]. AI can also be applied in fermentation to optimize parameters such as pH, temperature, and substrate, enhancing the production of bioactive compounds like (SCFAs) that are essential for gut health and anti-inflammatory effects [12]. Personalized fermented foods targeted at metabolic disorders have demonstrated microbiome-based dietary interventions that reduce postprandial glycemic responses, lower body weight, and improve associated cardiovascular outcomes [209].

These personalized applications, grounded in functional innovations and plant-based systems, can enhance the bioavailability of essential nutrients (e.g., iron, zinc, vitamin B12) while degrading anti-nutritional factors [80]. The personalized food approach lies at the intersection of functional efficacy and microbiome diversity, maximizing the benefits of fermented foods and addressing inter-individual variability. In conclusion, advances in nano-scale AI and microbiome sciences are converging to drive personalized fermented foods, leveraging data for health promotion while integrating sustainable plant-based innovations. This represents a promising paradigm shift in functional nutrition.

6.4. Space and Extreme Environment Fermentation: Potential Applications in Space Travel and Food Security

Fermentation in extreme environments, such as outer space, presents a potential paradigm shift in how we use fermentation technologies to address food insecurity on Earth and support space travel. Astronauts on prolonged missions face challenges in producing fresh food due to limited availability and the constraints imposed by zero gravity. Consequently, fermentation technologies offer a critical nutritional component providing vitamins, proteins, and bioactive compounds to help sustain astronauts on long-duration missions [210]. Additionally, microbial fermentation systems such as those that recycle waste products in closed-loop life support systems and produce functional foods in space—can supplement supply chains and enhance the logistics of planetary missions and operationally closed-loop systems in space [3].

Research provides evidence that designed fermentation approaches (e.g., engineered lactic acid bacteria) can be developed to meet the nutritional and metabolic requirements of space travelers [36]. Regarding food security on Earth, microbial fermentation technologies adapted to extreme environments can enable food production with minimal to no reliance on traditional farming resources (e.g., in arid or drought-prone regions). Populations in such areas often face limited food availability and difficulty accessing traditionally produced food products. Successful experiments demonstrating the conversion of non-food agricultural substrates (e.g., by-products) into nutrient-dense, functional foods efficiently have the potential to address pressing food insecurity challenges [211]. As with the use of engineered microorganisms to produce food ingredients such as proteins and fats in the harshest environments, these innovations can help meet global food demand sustainably and reduce the environmental footprint associated with conventional food production [210].

7. Challenges and Limitations

7.1. Regulatory Challenges

The rise of novel plant-based fermented foods has introduced a complex regulatory landscape, driven by consumer demand for sustainable, healthy, and innovative products. These foods, often produced through precision fermentation or traditional methods, pose unique challenges for regulatory bodies worldwide. The regulatory challenges governing novel plant-based fermented foods are multifaceted, encompassing safety assessments, labelling requirements, functional claims, and consumer trust. While significant progress has been made in developing frameworks for these products, gaps remain, particularly in harmonization and innovation support.

Regulatory frameworks for novel plant-based fermented foods vary significantly across regions, reflecting differences in legal structures, consumer preferences, and historical approaches to food safety. In the European Union (EU), the Novel Foods Regulation (EU) 2015/2283 provides a centralized framework for the authorization of novel foods, including plant-based fermented products. This regulation emphasizes safety assessments, labeling requirements, and the need for scientific evidence to support health claims [212,213,214].

In contrast, the United States relies on a decentralized system, where the Generally Recognized as Safe (GRAS) status is often used to evaluate new food ingredients. This approach allows industry proponents to self-affirm the safety of their products, with voluntary oversight by the FDA [215]. Canada, on the other hand, has a novel food regulation that requires pre-market approval for new foods and ingredients [215]. Despite efforts to harmonize regulations, significant disparities exist across jurisdictions. For instance, the EU’s stringent requirements for allergenicity assessments and nutritional claims often conflict with the more flexible approaches in the U.S. and Canada [215,216]. Additionally, the lack of a universal definition for functional foods and nutraceuticals further complicates regulatory efforts, as seen in the differing classifications across the EU, U.S., Japan, and India [217,218].

The regulatory challenges in engineering microbes and their metabolites for plant-based fermented foods are multifaceted, involving safety, classification, and harmonization issues. These challenges stem from the need to ensure consumer safety while fostering innovation in microbial engineering for food production. The complexity of these challenges is compounded by the diverse applications and potential risks associated with engineered microbes. Engineered microorganisms used in food production must undergo rigorous safety assessments to ensure they do not pose health risks. This is particularly important as some microbial strains, previously considered safe, have been linked to opportunistic infections [219]. The classification of food and feed cultures is ambiguous, as they do not fit neatly into existing categories of ingredients or additives. This lack of clear regulatory status can hinder international trade and product development [219].

Current regulatory frameworks often treat microbial products as non-living substances, which is not suitable for live microorganisms. This misalignment can impede the development and implementation of microbial technologies in agriculture and food production [220]. Harmonizing regulations across sectors could stimulate technical development and facilitate the use of plant-beneficial microorganisms, benefiting both agriculture and the environment [220]. Advances in microbial metabolic engineering have enabled the production of bioactive plant compounds, but transferring these laboratory-scale breakthroughs to industrial applications remains challenging due to regulatory and technical barriers [34]. The European Union’s E-classification system for food additives, while robust, presents bottlenecks in the metabolic pathways of engineered microbes, necessitating further research and development to overcome these challenges [221].

Precision fermentation has revolutionized the production of plant-based fermented foods, enabling the creation of novel ingredients with tailored nutritional profiles. However, the regulatory frameworks for these technologies are still evolving. In the EU, precision fermentation products are subject to the Novel Foods Regulation, requiring comprehensive safety assessments [214,222].

Traditional fermentation methods, while less technologically advanced, present their own challenges. The use of diverse microbial cultures and variable raw materials can lead to inconsistencies in product safety and quality. Regulatory bodies must balance the need for innovation with the protection of traditional practices, particularly in regions with rich fermentation cultures [223,224].

Novel plant-based fermented foods present unique safety challenges due to their production processes and ingredients. Chemical hazards may arise from natural toxins, environmental contaminants, or by-products of fermentation. For example, precision fermentation, while offering controlled environments, can introduce unintended chemical compounds if the production process is not meticulously monitored [222,225]. Microbiological hazards are another critical concern, particularly in traditional fermentation processes. While precision fermentation reduces the risk of contamination, traditional methods may carry over hazards from raw materials or uncontrolled environments [222,225]. Regulatory bodies must ensure that hazard analysis and critical control point (HACCP) plans are adapted to address these risks.

Assessing the allergenic potential of novel plant-based fermented foods is another significant challenge. The Codex Alimentarius Commission’s weight-of-evidence approach, adapted for genetically modified foods, is increasingly applied to novel foods. However, the reliance on literature reviews and the lack of standardized testing methods complicates allergenicity assessments [216]. For example, only a few regulatory submissions proactively include additional tests, highlighting the need for more robust scientific frameworks [216]. Toxicological assessments further add to the complexity. Novel foods derived from unconventional sources, such as mycelium or algae, require comprehensive evaluations of their bioactive compounds and potential interactions with human health [225,226].

Labeling is a critical aspect of regulatory compliance for novel plant-based fermented foods. The EU’s Novel Foods Regulation mandates clear labeling to ensure consumer transparency, particularly for products that may be mistaken for traditional foods. For instance, mycelium-based foods must be labeled to avoid confusion with animal-derived products [227]. In the U.S., the FDA focuses on ensuring that labels are truthful and non-misleading, with specific guidelines for health claims and allergen declarations. However, the lack of a unified approach to labeling across regions creates challenges for manufacturers seeking to market their products globally [215]. Functional and health claims for novel plant-based fermented foods are subject to rigorous scrutiny. In the EU, health claims must be supported by scientific evidence and approved by the European Food Safety Authority (EFSA) [213,214]. Similarly, Japan’s Foods with Function Claims (FFC) system requires manufacturers to demonstrate the efficacy of their products [217]. The global regulatory landscape for functional foods is further complicated by the lack of harmonization in claim substantiation. While the Codex Alimentarius provides general guidelines, regional differences persist, creating barriers for manufacturers seeking to enter multiple markets [217,228].

Consumer trust is a foundation of the successful market integration of novel plant-based fermented foods. Transparent communication about production processes, ingredients, and health benefits is essential to build confidence. However, the complexity of regulatory frameworks and the lack of standardized labeling often leave consumers confused or skeptical [223,229]. Collaboration between regulators, manufacturers, and consumers is critical to addressing these challenges. Regulatory bodies must work closely with industry stakeholders to develop clear guidelines and ensure compliance. Additionally, public education campaigns can help consumers understand the benefits and risks of novel foods, fostering a more informed market environment [224,230].

7.2. Scalability and Commercialization Challenges

The rise of plant-based fermented foods has been driven by increasing consumer demand for sustainable, health-conscious, and environmentally friendly products. However, the scalability and commercialization of these products face significant challenges, including supply chain issues, technological hurdles, and regulatory challenges.

One of the primary challenges in scaling plant-based fermented foods is the availability and cost of raw materials. Plant-based proteins, such as legumes, cereals, and oilseeds, are the foundation of these products. However, the availability of these raw materials can be inconsistent due to factors like seasonal variations, geopolitical issues, and competing demands from other industries [231]. Additionally, the cost of high-quality plant proteins can be prohibitively expensive, especially for small-scale producers, making it difficult to achieve economies of scale [232]. The quality of raw materials is another critical issue. Plant-based ingredients often contain anti-nutritional factors, such as phytates and lectins, which can affect the nutritional value and digestibility of the final product [233]. Ensuring consistent quality and safety of these ingredients requires robust sourcing and quality control measures, which can be resource-intensive and challenging to implement, particularly for smaller manufacturers. Fermented plant-based products are highly perishable and require careful storage and distribution to maintain their quality and safety. The lack of adequate cold chain infrastructure in some regions can lead to spoilage and contamination, further complicating the supply chain [234]. Additionally, the need for specialized packaging to maintain the integrity of live cultures in fermented products adds to the logistical challenges [235].

Fermentation is a critical step in the production of plant-based fermented foods. However, optimizing the fermentation process to achieve consistent flavor, texture, and nutritional profiles remains a significant challenge. The metabolism of lactic acid bacteria and other microorganisms used in fermentation can vary depending on factors such as temperature, pH, and substrate composition, leading to inconsistencies in the final product [204]. Moreover, the production of bioactive compounds during fermentation, such as bioactive peptides, requires precise control over fermentation conditions to maximize their health benefits [189]. Enzymes play a crucial role in improving the digestibility and functionality of plant-based proteins. However, the production of enzymes with high activity and specificity is a significant technological challenge. Native enzymes often lack the required efficiency and stability for large-scale industrial applications, necessitating the use of engineered enzymes [14]. The development of novel enzymes through precision fermentation and synthetic biology has shown promise, but scaling up their production while maintaining cost-effectiveness remains a bottleneck [236]. The global market for plant-based fermented foods is fragmented, with varying regulatory standards across regions. Differences in food safety regulations, labelling requirements, and ingredient approvals can create barriers to entry for manufacturers seeking to expand into international markets. Furthermore, trade agreements and tariffs on plant-based ingredients can impact the cost-effectiveness of production and distribution in different regions [231,232].

Despite the challenges, there are significant opportunities for innovation and growth in the plant-based fermented foods industry. Advances in precision fermentation, synthetic biology, and enzyme engineering are enabling the production of high-quality, sustainable ingredients with improved functionality and nutritional profiles [236]. Additionally, the development of novel processing technologies, such as high-pressure processing and 3D printing, offers new avenues for creating plant-based products with enhanced texture and flavor [14,126].

7.3. Consumer Perception and Market Acceptance

Plant-based fermented foods have gained significant attention in recent years due to their potential to address health, environmental, and ethical concerns. These products offer a sustainable alternative to traditional animal-based foods, leveraging fermentation to enhance nutritional value and sensory properties. However, their market acceptance is influenced by consumer perception, which is shaped by factors such as taste, texture, health benefits, and environmental impact. Consumer perception of plant-based fermented foods is a complex interplay of sensory, nutritional, and psychological factors. Studies have shown that while these products are perceived as healthier and more sustainable, they often face challenges related to taste, texture, and familiarity [81,237]. Sensory properties, such as flavor, texture, and aroma, play a critical role in consumer acceptance. Plant-based fermented foods often struggle to replicate the sensory characteristics of their animal-based counterparts. For instance, plant-based dairy alternatives are perceived as having weaker aromas and flavors compared to traditional dairy products [238,239]. Similarly, plant-based meat analogues often lack the juiciness and texture of traditional meat [238,240].

Consumers are increasingly drawn to plant-based fermented foods due to their lower environmental impact. These products require fewer resources, produce less greenhouse gas emissions, and generate less waste compared to animal-based foods [241,242]. Additionally, the ethical appeal of plant-based products resonates with consumers who prioritize animal welfare and sustainability [241,243]. While plant-based fermented foods have gained traction, their market acceptance is not universal. Skepticism arises from several factors, including unfamiliarity with fermentation processes, concerns about taste, and misconceptions about nutritional content.

The sensory profile of plant-based fermented foods often differs significantly from traditional products, which can be a barrier for consumers who prefer familiar flavors and textures [239,240]. Consumers who are hesitant to try new or unfamiliar foods are less likely to adopt plant-based fermented products [237,244]. Some consumers perceive plant-based products as less nutritious than their animal-based counterparts, despite evidence to the contrary [244].

Consumer acceptance of plant-based fermented foods varies across regions and cultures. For example, Asian consumers may be more familiar with fermented foods due to their cultural significance, while Western consumers may be more skeptical due to limited exposure [242,245].

To overcome skepticism and enhance market acceptance, education and communication strategies are essential. These strategies should focus on highlighting the benefits of plant-based fermented foods while addressing consumer concerns. Educating consumers about the nutritional and health benefits of plant-based fermented foods can increase their appeal. For example, emphasizing the presence of probiotics and bioactive compounds can attract health-conscious consumers [81,246]. Highlighting the environmental benefits of plant-based fermented foods can resonate with eco-conscious consumers. This includes information about reduced greenhouse gas emissions and resource efficiency [241,242]. Demonstrating the versatility of plant-based fermented foods through recipes and cooking tips can encourage consumers to incorporate these products into their diets [243]. Clear and transparent labeling is critical for building consumer trust. Labels should emphasize the product’s nutritional content, environmental benefits, and production processes. For example, terms like “high in protein” or “sustainably sourced” can enhance perceived value [247,248]. To address sensory concerns, manufacturers can focus on improving the taste and texture of plant-based fermented foods. This may involve the use of advanced fermentation techniques or the incorporation of natural flavor enhancers [81,238]. Education and awareness campaigns are vital for promoting the adoption of plant-based fermented foods. These campaigns should target both consumers and stakeholders in the food industry.

Continued investment in research and development is essential for improving the sensory and nutritional quality of plant-based fermented foods [238]. Governments and regulatory bodies can support the growth of the plant-based fermented food industry through subsidies, tax incentives, and labeling standards [244,248].

Plant-based fermented foods offer a promising solution to the environmental, health, and ethical challenges associated with traditional animal-based products. While consumer perception and market acceptance are influenced by sensory, nutritional, and psychological factors, education and communication strategies can play a pivotal role in addressing skepticism and promoting adoption. By highlighting the benefits of these products and addressing consumer concerns, the plant-based fermented food industry can achieve greater market penetration and contribute to a more sustainable food system.

8. Conclusions

In summary, microbial fermentation presents a powerful and sustainable approach to enhancing the nutritional quality, functionality, and sensory attributes of plant-based foods. Innovations in microbial biotechnology—including CRISPR-based genome editing, precision fermentation, and the use of synthetic microbial consortia—have significantly expanded the potential of plant-based fermented foods to address global nutrition challenges. These advancements not only improve protein digestibility and micronutrient bioavailability but also contribute to the reduction in antinutritional factors, leading to more health-promoting food products.

Looking ahead, emerging tools such as metagenomics, metabolomics, and other multi-omics platforms will be instrumental in deepening our understanding of host-microbiota interactions and optimizing fermentation outcomes for targeted health benefits. Importantly, the application of microbial fermentation aligns closely with the United Nations Sustainable Development Goals (SDGs), particularly SDG 2 (Zero Hunger), through enhanced nutrient density and food security; SDG 3 (Good Health and Well-being), by supporting preventive nutrition and gut health; SDG 12 (Responsible Consumption and Production), by promoting resource-efficient, plant-based food systems. Continued research and interdisciplinary collaboration are essential to scale these innovations and ensure equitable access to nutritionally enriched, sustainable plant-based fermented foods.