Enhancing the Nutritional Value of Foods Through Probiotics and Dietary Fiber from Fruit and Berry Pomace

Abstract

The growing demand for health-promoting food products has led to increased efforts to develop formulations enriched with probiotics and dietary fiber (DF). While traditional fermented foods remain widely recognized sources of probiotics, there is a pressing need to innovate novel, nutritious, and high-quality alternatives that also incorporate additional functional ingredients. In the context of sustainable consumption and health-conscious dietary trends, fruit and berry pomace has emerged as a promising source of DF with prebiotic potential, supporting the growth and activity of beneficial gut microorganisms. A growing body of research emphasizes the potential of pomace valorization, showcasing its relevance in the development of value-added food products. This review explores the key features and selection principles for probiotic strains, particularly those from the former group of Lactobacillus species, alongside opportunities for combining probiotics with fruit and berry pomace in functional food matrices. Special attention is given to the physiological and technological attributes of DF derived from pomace, which are critical for their successful application in food systems and their potential synergistic effects with probiotics. Although numerous probiotic-enriched products are currently available, DF remains an underutilized component in many of these formulations. Research has predominantly focused on dairy-based applications; however, the increasing demand for plant-based diets calls for a shift towards non-dairy alternatives. Looking forward, future innovations should prioritize the integration of probiotics and pomace-derived DF as symbiotic systems into plant-based food products, with an emphasis on their dual roles as nutritional enhancers and potential prebiotics.

1. Introduction

Consumer-buying behavior shows increasing interest in healthy and high-quality food products [1]. Correspondingly, the global market for probiotic food supplements is rapidly expanding, with an estimated value of USD 18.4 billion by 2031 [2]. This indicates the need for the use of probiotic bacteria in food products. Traditional fermented products are often considered a source of probiotics, but not all microorganisms present in these products are classified as probiotics [3]. In the 20th century, it was noticed that microorganisms present in food products can influence the intestinal microbiota of consumers, aid in the elimination of harmful microorganisms, and promote the growth of beneficial bacteria. The term ‘probiotics’ was first introduced in 1960. In 2001, the FAO and WHO provided the first official definition of probiotics. This definition was later refined by the International Scientific Association for Probiotics and Prebiotics (ISAPP) in 2013 as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” [4,5]. Probiotics were first isolated from fermented dairy products, breast milk, the oral cavity, and feces, and are generally recognized as safe (GRAS) [3,6]. Species belonging to the Lactobacillus and Bifidobacterium genera are commonly classified as probiotics [7]. However, the term “probiotics” refers specifically to well-defined strains of microorganisms that have been scientifically demonstrated to confer health benefits to the host. For example, a non-pathogenic strain of Escherichia coli (E. coli Nissle 1917) was isolated during the First World War, and used to treat salmonellosis and shigellosis [7]. Probiotics also include certain strains belonging to the Enterococcus, Saccharomyces, Pediococcus, Bacillus, Streptococcus, and Leuconostoc genera [6]. Due to a major taxonomic revision in 2020, the former group of Lactobacillus spp. was split into 25 new genera. As a result, many species previously classified as Lactobacillus now belong to different genera (e.g., Lacticaseibacillus casei was formerly Lactobacillus casei, Lactiplantibacillus plantarum was formerly Lactobacillus plantarum, Lacticaseibacillus rhamnosus was formerly Lactobacillus rhamnosus, and Limosilactobacillus fermentum was formerly Lactobacillus fermentum). For clarity and consistency, this review uses the abbreviated form (e.g., L. plantarum) throughout the text. Despite proven health benefits, successful application of probiotics in food depends on the selection of robust and viable strains [8,9].

Dietary fiber (DF) plays a crucial role in human health due to its various physiological effects and potential to reduce the risk of chronic diseases. The physiological effect of DF is related to reduced risk of certain diseases, like hypertension, obesity, and gastrointestinal disorders; moreover, certain DF is attributed to prebiotics [10]. It is recommended that adults consume approximately 25–35 g of DF per day [10,11,12]. Fruits and berries are an important source of DF and prebiotics. The pomace is usually left with skins, stems, and seed parts [13,14]. These by-products are rich in various bioactive compounds such as phenolic compounds and pigments as well as polysaccharides and oligosaccharides, which can be classified as DF [15,16]. Recently, the European Commission has been working to reduce waste and develop sustainable production, and published a Circular Economy Action Plan in 2015 [17]. The 2020 Farm to Fork strategy was launched with the aim of transforming the food system to make it sustainable. Among the objectives of this strategy are promoting more sustainable food consumption and healthy diets, as well as reducing food loss and waste [18]. These are particularly incorporated into baked goods, yogurt, and pasta as alternative ingredients, enhancing product properties while promoting both health and sustainability [19].

Recently, food products supplemented with probiotics and DF derived from berries and fruits have attracted increasing scientific interest [20,21,22]. Traditional fermented products (various vegetables) and dairy products are still the most popular foods supplemented with probiotics. As more consumers exclude milk from their daily diets, interest in plant-based probiotic products continues to grow [23]. Probiotic-enriched foods are generally preferred over supplements, as they align better with daily dietary habits. To enhance the nutritional value of food, products can be supplemented with both pomace and probiotics. While the scientific literature widely acknowledges agro-food by-products as valuable sources of DF and bioactive compounds—including carotenoids, organic acids, polyols, polyphenols, enzymes, peptides, and saccharides with prebiotic potential—their use in functional food formulations and related modification techniques has been extensively studied [24,25,26,27,28,29,30,31,32,33,34]. Nevertheless, the application of fruit and berry pomace specifically as a DF source combined with probiotic cultures in functional foods has been comparatively underexplored. This review focuses on the potential of probiotic strains, particularly those from the former group of Lactobacillus spp., combined with fruit and berry pomace, for the development of nutritionally enhanced food products.

2. Methodology

The relevant information regarding the Lactobacillus spp., including its probiotic benefits and selection criteria, as well as the physiological and technological properties of dietary fiber from fruit/berry processing by-products, were collected from published articles. Research publications on probiotic bacteria and dietary fiber from fruit/berry processing by-products were located through scientific resources, such as PubMed, Web of Science, Science Direct, Google Scholar, and SciFinder. The selection and evaluation of scientific articles for relevancy were based on titles, abstracts, and keywords. The keywords used were Lactobacillus spp. probiotic, lactic acid bacteria, L. plantarum, L. paracasei, L. acidophilus, L. casei, L. rhamnosus, Lactobacillus bulgaricus as a probiotic, berry and fruit by-products, pomace, functional, and physiological and technological properties of dietary fiber; also, regardless of timeframe, relevant articles were chosen. The figure was created using Biorender.com.

3. Probiotics and Their Benefits

Probiotic strains can be isolated from humans, animals, and the environment; however, it is suggested that the strains used in human nutrition should be isolated from the gut microbiota. Such probiotics are more likely to adapt and proliferate after entering the body, and they may also exhibit greater specificity compared to probiotics isolated from other sources [6,35]. Nevertheless, there is an increasing number of studies evaluating the probiotic potential of bacteria isolated from various fermented foods [36,37,38] or other sources. Rodrigues et al. [39] isolated lactic acid bacteria (LAB) with probiotic potential from apples, bananas, oranges, and grapes. Among the isolates, the most promising LAB strains were identified as L. brevis and other LAB belonging to the former group of Lactobacillus spp., demonstrating the ability to maintain high viable counts and active physiological functions in various plant- and animal-based foods during refrigeration storage. Another study demonstrated that LAB isolated from fresh fruits and vegetables (including tomato, cucumber, strawberry, peach, lettuce, parsley, and cabbage) not only exhibited probiotic properties but also showed significant immunomodulatory activities and produced exopolysaccharides (EPSs) [40]. Bacterial EPSs are regarded as valuable compounds in the food, pharmaceutical, and nutraceutical industries, owing to their health-promoting bioactivities and significant influence on rheological properties [41].

The mechanisms of action underlying the biological effects of probiotics that have entered the body are not completely clear or fully understood; they are usually associated with and explained by their ability to colonize the host intestine or their competitive effects on pathogenic microorganisms [23]. Once in the gut, probiotics adapt and proliferate while inhibiting the growth of undesirable microorganisms, thereby competitively reducing the abundance of pathogenic bacteria [7]. The ability of probiotics to adhere to epithelial cells in the gut is a key feature that facilitates their colonization of the host. Several mechanisms have been proposed to explain this process. One possible mechanism is the hydrophobic interaction between probiotics and the intestinal surface. Additionally, specific proteins, such as mucin and fibronectin-binding proteins, enhance adhesion capacity [42]. Mucins, the production of which may be stimulated by probiotics, can act as a barrier, inhibiting the adhesion of pathogenic bacteria to the intestinal walls [7]. The presence of pili provides another mechanism by which bacteria can attach to the intestinal mucosal surface [42]. The production of EPSs by certain biofilm-forming probiotic LAB has been identified as a potential mechanism for inhibiting the biofilm formation of pathogenic bacteria and preventing their colonization on device surfaces or within susceptible hosts [41]. Probiotics contribute to intestinal immune defense by stimulating the secretion of IgA antibodies, which play a crucial role in binding and neutralizing enteric pathogens. They are also known to exert anti-inflammatory effects in the gut environment, primarily through the suppression of NF-κB activation and downregulation of IL-8, a key chemokine involved in neutrophil recruitment. Furthermore, certain strains have been implicated in modulating visceral sensitivity via interaction with opioid and cannabinoid receptors, offering potential therapeutic benefit in conditions such as irritable bowel syndrome [7].

Probiotics secrete compounds with antimicrobial properties, such as lactic and acetic acids and bacteriocins. Lactic acid-producing probiotic strains may exhibit antibacterial effects by lowering the environmental pH. Pyruvate, obtained during fermentation, can be used in the formation of short-chain fatty acids (SCFAs) by anaerobic microorganisms in the intestine [7]. The specific combination of these properties determines the strain-dependent effects of probiotics [43]. Probiotics, particularly L. paracasei SD1 in combination with L. rhamnosus SD11, have been identified as promising natural sources of butyrate, a SCFA with significant anti-cancer potential. SCFAs, especially butyrate, have garnered attention for their ability to prevent or delay colorectal cancer. Probiotic strains produce varying amounts of SCFAs, which exert anti-cancer effects by inhibiting the growth of pathogens related to colon cancer, such as Fusobacterium nucleatum and Porphyromonas gingivalis. These SCFAs also suppress cancer cell growth, stimulate the production of the anti-inflammatory cytokine IL-10, and promote the production of antimicrobial peptides like human β-defensin-2. Moreover, SCFAs help to reduce pathogen-induced pro-inflammatory cytokines, particularly IL-8. These findings suggest that probiotics may offer a biotherapeutic strategy for preventing or delaying the progression of colon cancer [44].

Probiotics may also function as quorum-quenching (QQ) agents and inhibit growth of other bacteria. Several studies described different mechanisms of quorum sensing inhibition (QSI). Probiotics can secrete bioactive compounds that exhibit potent anti-virulence activity. Cella et al. [45] investigated the effects of bioactive peptides isolated from two strains of LAB against two clinical MRSA (methicillin-resistant Staphylococcus aureus) isolates, demonstrating that naturally produced QQ molecules have the potential to inhibit the growth of multidrug-resistant bacteria. Similarly, Xu et al. [46] reported that EPSs derived from L. coryniformis NA-3 (EPS-NA3) reduced biofilm formation of Bacillus cereus and Salmonella enterica subsp. enterica serovar Typhimurium by approximately 80% and 40%, respectively. Other reported potential QSI agents include lipopeptides (such as fengycin and surfactin), lipoproteins (biosurfactants), organic compounds, cyclic peptides, lipoteichoic acid, exopolysaccharides, bacteriocins (such as reuterin and lactocin), and AHL-lytic enzymes [47]. Some probiotics can potentially affect quorum sensing (QS) signals mediated by acylated homoserine lactones (AHL and HSL) and furanosyl borate diester (also known as autoinducer 2 or AI-2), thereby disrupting biofilm formation in Escherichia coli O157:H7 [48]. Postbiotics may also influence QS signaling in pathogens. Azami et al. [49] demonstrated that postbiotic metabolites from L. casei are capable of attenuating the virulence and inhibiting biofilm development in Pseudomonas aeruginosa. The potential use of probiotics as QQ agents represents a promising therapeutic alternative; however, further studies are required to elucidate the underlying mechanisms of QSI.

The health benefits of probiotics are primarily associated with the digestive tract and maintenance of normal intestinal microflora. These bacteria are used in the treatment of diseases of the digestive tract, such as diarrhea, complications caused by Helicobacter pylori, inflammatory bowel diseases, and irritable bowel syndrome. In addition to beneficial effects on the gut microbiota, probiotics are recognized as valuable in the prevention of many chronic diseases and disorders (e.g., obesity, cardiovascular disease, allergies, etc.), as well as for enhancing the immune system, reducing serum cholesterol and blood pressure, and improving nutrient absorption. Some strains may have anti-carcinogenic effects. The health benefits provided by probiotics depend on their origin, as individual bacterial strains possess distinct properties [4,6,50]. Fei Shen et al. [51] demonstrated in their study that the novel probiotic L. plantarum T34 alleviates constipation by enhancing gut transit in a mouse model. Another study revealed L. brevis RAMULAB52, isolated from fermented papaya, exhibits promising probiotic properties and potential therapeutic effects for diabetes. This novel strain also showed resistance to gastrointestinal conditions, along with antibacterial and antioxidant activities, strong adhesion to various cell types, and significant inhibition of target enzymes [52]. Alard et al. [53] reported in their study that the administration of B. longum PI10, both alone and in combination with B. animalis subsp. lactis LA804 and L. gasseri LA806, resulted in reduced body weight gain and alleviated obesity-related metabolic dysfunction and inflammation. These protective effects were linked to alterations in hypothalamic gene expression, particularly leptin and its receptor, as well as changes in gut microbiota composition and bile acid profiles. Several other studies [54,55] also demonstrated the immunomodulatory potential of probiotics and postbiotics. To evaluate this potential, selected isolates were tested for their ability to induce cytokine production in ex vivo-cultured murine spleen cells.

The most commonly used probiotics in food production are LAB belonging to the former group of Lactobacillus spp., and less commonly, probiotics belonging to the genus of Bifidobacterium. When developing new probiotic-enriched products, one of the most important factors is the selection of appropriate cultures.

4. Criteria for Probiotic Selection

The properties and environmental resistance of probiotics are dependent on the specific strain used. The viability of probiotics in food products must be maintained throughout their shelf life. However, certain conditions such as acidity, water activity, concentrations of salt, sugar, sweeteners, aromatic compounds, flavorings, and dyes, and oxygen, temperature, and food processing methods can have a negative effect on bacterial viability [42,50]. Elevated oxygen levels and high redox potential generally have detrimental effects on anaerobic bacteria [56]. It is recommended that the concentration of probiotics in food exceed 10⁶ CFU/g. It is also recommended to consume approximately 100 g per day of probiotic-containing products to deliver around 10⁹ viable cells to the gut [6,50]. Therefore, the selection of probiotic strains should take into account the product characteristics, processing and storage conditions, and the intended health benefits for the consumer.

In 2002, the FAO and WHO published the Guidelines for the Evaluation of Probiotics in Food, establishing standardized criteria for assessing the safety and health benefits of probiotics intended for use in food products. These guidelines also provided a systematic framework for the selection of probiotic strains. It is well-established that probiotic strains incorporated into food must be accurately identified, as their health effects are strain-specific. In vitro tests are commonly performed to evaluate the resistance of probiotic bacteria to the acidic conditions of digestion and to bile acids. Additional important characteristics include the ability to adhere to the intestinal epithelium, to inhibit the adhesion of pathogenic microorganisms, to exhibit antimicrobial activity, and to produce bile salt hydrolase [57]. When evaluating the safety of strains classified as probiotics, toxicity or pathogenicity tests are often performed by studying the hemolytic activity of bacteria and sensitivity to antibiotics [6,58,59].

In order for probiotics to provide benefits to the consumer, it is important that the bacteria remain viable not only in the product, but also after entering the digestive tract. Probiotics administered to the gastrointestinal tract may experience a decrease in viability of 10⁶–10⁸ CFU/g [56]. In the digestive tract, bacteria encounter various stressors, with gastric acidity (pH 1.5–4.0) being a major challenge. Therefore, probiotic strains must exhibit resistance to low pH conditions to ensure their survival and functionality. In vitro assays that simulate gastric acidity are commonly employed to assess probiotic tolerance. These methods involve incubation in acidified media (e.g., MRS broth or buffer at pH 2.0–3.0 for 1–4 h) or exposure to simulated gastric juice (pH 2.0–3.0 with pepsin). Additionally, more advanced digestive tract models can be utilized to provide a comprehensive evaluation of probiotic survival and performance under gastrointestinal conditions [42]. Bacteria belonging to the former group of Lactobacillus spp., which are usually isolated from traditional fermented products, are typically more resistant to low pH, and therefore they are frequently used in the food industry [50]. The viability of probiotics can be significantly affected in the small intestine due to the presence of bile acids, bile salts, and pancreatic enzymes. Bile acids play a crucial role in lipid digestion, while bile salts are secreted into the duodenum to facilitate emulsification. Moreover, as essential digestive surfactants, bile acids aid in lipid solubilization. However, these compounds also exhibit antimicrobial properties, which can negatively impact probiotic survival and functionality in the gastrointestinal environment [42].

A comprehensive evaluation of probiotics should include an assessment of their antioxidant capacity, cytotoxic effects, and the antimicrobial activity of their metabolites. Antioxidant properties can enhance the functional value of probiotic products, while cytotoxicity may contribute to the inhibition of cancer cell development [35]. The antioxidant activity of bacteria is associated with their cell surface compounds, such as extracellular polysaccharides, lipoic acid, and specific enzymes [60,61]. In contrast, the cytotoxic effects are mainly attributed to probiotic-derived metabolites such as SCFAs, bacteriocins, and other bioactive compounds. These metabolites can selectively induce apoptosis (programmed cell death) and cause cell cycle arrest in cancer cells, thereby suppressing tumor growth without damaging normal healthy cells. This selective cytotoxicity varies between probiotic strains and depends on the nature and concentration of the metabolites they produce [62,63].

The formation of substances with antimicrobial effects (acids and bacteriocins) during fermentation is an important property of probiotics that helps protect the host from pathogens, but suboptimal antimicrobial activity can also have a negative effect on the user, disrupting the healthy intestinal microbiota [6]. When probiotics are used in the production of fermented products, their metabolic products can have a significant impact on sensory properties. The acids released may not always be acceptable, depending on the types and concentrations of acids formed [50]. Probiotics exhibiting antimicrobial activity have potential applications as biocontrol agents in the food industry [64]. Rastogi et al. [65] isolated probiotic bacteria from the feces of exclusively breastfed infants, demonstrating antagonistic activity against multidrug-resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which pose a significant challenge to public health systems worldwide.

EPSs synthesized by probiotic bacteria have gained significant attention due to their diverse functional properties and potential applications in the food and health industries. The molecular characteristics, such as chain length and molecular weight, of EPSs have been reported to influence their biological activities, including antimicrobial properties. Larger EPS molecules enhance viscosity by transitioning from double-helical structures to macroscopic gels, thereby improving antimicrobial activity through viscosity-related biological mechanisms [41]. Janani Murugu and Rajnish Narayanan [66] reported that EPS produced by L. amylovorus MTCC 8129 exhibits antioxidant properties and emulsifying capacity, indicating its potential utility in food formulation and processing applications.

Recent studies have highlighted the potential of combining probiotics with natural food co-components to improve both the nutritional quality and technological functionality of functional products [27,28,33,67,68,69]. In this context, fruit and berry pomace—a by-product of juice processing—has gained interest due to its high content of phenolic compounds, vitamins, and prebiotic DF [67,70,71,72,73,74]. The following section reviews the physiological and technological properties of DF derived from fruit and berry pomace, which may contribute to the design of value-added probiotic-enriched products.

5. Physiological and Technological Properties of Dietary Fiber from Fruit/Berry Processing By-Products

5.1. Physiological Effects of Dietary Fiber from Fruit and Berry Processing By-Products

DFs are associated with positive health effects for consumers by helping to reduce the risk of hypertension, obesity, diabetes, coronary heart disease, stroke, and certain gastrointestinal disorders [10]. DFs can be categorized based on their source, chemical composition, water solubility, fermentability, or physiological effects. However, the most common classification distinguishes DFs by their water solubility—soluble dietary fiber (SDF) and insoluble dietary fiber (IDF) [32]. Nevertheless, this binary classification has been increasingly criticized for oversimplifying the structural and functional diversity of DFs, as it does not account for key characteristics such as fermentability, viscosity, water-holding capacity, or interaction with the food matrix—factors essential for understanding their physiological functions and health effects [75].

It is recommended that adults consume approximately 25–35 g of DF per day, of which 6 g should consist of SDF. Some studies show that additional intake of 10 g of DF can reduce the risk of mortality from coronary heart disease by up to 35% [10,11,12]. According to the 2023 Nordic Nutrition Recommendations, the recommended daily intake of DF is 25–35 g for adults, with specific guidance suggesting around 28–35 g for men and 25–31 g for women [76]. Adequate DF intake, particularly from fruits and vegetables, is widely recognized as a key component of a healthy diet, contributing not only to the reduction of cardiovascular disease risk, but also to the prevention of other chronic conditions [77]. Recent large-scale cohort studies have further demonstrated that higher consumption of total DF, SDF, and IDF is associated with significantly lower risks of all-cause, cardiovascular, and cancer-related mortality, emphasizing the importance of diverse fiber types to promote long-term health [78].

SDF and IDF exhibit distinct physiological effects (

Table 1. Functional, physiological, and technological properties of DF typically found in fruit and berry by-products.

DF Type	Physiological Properties	Technological Properties	Impact on Probiotics	References
Pectin	Lowers cholesterol, delays gastric emptying, improves glucose metabolism, stimulates bile acid excretion	High water-holding capacity, forms thermoreversible gels	Highly fermentable by gut microbes; enhances SCFA production and growth of Bifidobacterium and Lactobacillus in vitro	[32,75,76,81,82,83,84,85]
Inulin	Promotes mineral absorption, improves lipid metabolism, relieves constipation	Low viscosity, fat replacement, freeze–thaw stable	Highly fermentable; strong bifidogenic effect with increased SCFA production	[75,81,82,83,84,86,87]
Cellulose	Increases fecal bulk, reduces transit time, acts as a laxative	Insoluble, low water-holding capacity, texture modifier	Poorly fermentable; passes to colon largely intact, supporting microbial diversity indirectly	[81,82,84,87]
Hemicellulose	Supports bowel regularity, partial fermentation yields SCFAs	Moderate water-holding, viscosity development, could be used as a viscosity-increasing and stabilizing agent	Supports diverse microbiota via SCFA production	[81,82,84,88]
Lignin	Provides fecal bulking, reduces transit time, antioxidant activity	High oil-holding, textural integrity	Non-fermentable; negligible impact on probiotic bacteria	[76,81,84]
Oligosaccharides	Enhanced mineral absorption, reduced caloric density, improves gut barrier function	High solubility, low viscosity, sweetness enhancement	Strong prebiotic effect; selectively stimulates bifidobacteria	[75,76,81,82,83,84]

). SDF, which includes β-glucan, pectin, various gums, arabinoxylans, and inulin, is associated with cholesterol-lowering and prebiotic activity. It has a high water absorption capacity and form gels that slow gastric emptying and nutrient absorption. In contrast, IDFs—such as cellulose, hemicellulose, chitosan, and lignin—accelerate gastrointestinal transit and increase fecal bulk, as they are poorly fermented by colonic microbiota. IDFs also have the ability to adsorb carcinogens, mutagens, and toxins, thereby potentially preventing their harmful effects on the body. Both SDF and IDF contribute to carbohydrate metabolism regulation and may support body weight management in consumers [79,80]. The DF content in fruit and berry pomace typically includes pectin, lignin, cellulose, hemicellulose, and inulin [13]. The proportions of these components depend on the type of fruit or berry, the processing method, and the efficiency of the technological process.

Another important property of DF is its prebiotic activity. Prebiotics are defined as selectively fermentable substances that induce specific changes in the composition and/or activity of the gastrointestinal microbiota, which have a beneficial effect on the health of the consumer [89]. The consumption of prebiotic-containing foods can promote gut health by stimulating the growth and activity of beneficial bacteria, such as bifidobacteria and other LAB, while also enhancing resistance to pathogenic microorganisms. Prebiotics are selectively utilized by probiotic microorganisms in the colon, whereas pathogenic bacteria are generally unable to utilize them. To be classified as prebiotics, substances must fulfill the following criteria: (i) resistance to digestion and absorption in the stomach and small intestine; (ii) selective utilization by beneficial colonic microbiota; and (iii) production of beneficial physiological effects upon fermentation [90]. Although various fermentable carbohydrates have been identified as potential prebiotics, the most extensively studied and documented in human health are non-digestible oligosaccharides, particularly fructans and galactans. Additionally, plant-derived polyphenols may also fulfil the criteria for prebiotic activity; however, further investigation in the target host is needed. Notably, approximately 90–95% of ingested polyphenols are not absorbed in the small intestine, allowing them to reach the colon where they may exert bioactive and microbiota-modulating effects. Furthermore, a wide array of compounds—including conjugated linoleic acid, phenolics, phytochemicals, diverse types of DFs, polyunsaturated fatty acids, human milk oligosaccharides, and other oligosaccharides—have been shown to possess prebiotic potential, although their mechanisms and host-specific effects require further elucidation [89].

5.2. Technological Properties of Dietary Fiber from Fruit/Berry Processing By-Products

SDF and IDF, isolated from different sources, have not only different physiological properties, but also technological properties, depending on the carbohydrate composition. When evaluating the technological properties of DF, it is important to understand the properties of the main components of DF and their behavior in food systems. Cellulose is an important and widespread component of plant cells, which, together with other polysaccharides (such as hemicellulose, lignin, and pectin), performs a structural function. Cellulose is a homopolysaccharide composed of β-glucopyranose units linked by β-1,4-O-glycosidic bonds [79]. It is insoluble in dilute solutions of acids or bases, but has a high water-holding capacity [32]. Hemicellulose, on the other hand, is a heteropolysaccharide that can be composed of glucose, galactose, xylose, arabinose, mannose, and glucuronic acid. It is mainly found in plant cell walls [79]. Compared to cellulose, hemicellulose has a more complex structure. Hemicellulose can have different types of side chains attached to the main chain, which gives it a more complex structure. Hemicellulose is insoluble in water and dilute acids, but soluble in dilute bases [32]. This polysaccharide can be used in the food industry as a viscosity-increasing and stabilizing agent [88]. Lignin is a three-dimensional amorphous aromatic polymer of phenolic compounds that binds cellulose and hemicellulose fibers and provides rigidity to plants in nature. Lignin is insoluble in water; its molecules are resistant to both chemical and enzymatic degradation. It is also resistant to bacterial degradation [32].

Pectin is another important and widely distributed carbohydrate in plants. It consists of a complex mixture of polysaccharides primarily composed of galacturonic acid residues linked by α-(1→4) glycosidic bonds. In the pectin polymer chain, some of the branches are connected through α-L-(1→2) rhamnose residues, which form external side chains containing mannose, glucose, galactose, and xylose. Pectin exhibits excellent gel-forming ability; however, its incorporation into food products is limited by its potential effect on sensory properties [32]. Pectin is mainly located in the middle lamella and primary cell walls of plant tissues [79]. Apple and citrus pomace are among the main commercial sources of pectin. The functional and technological properties of pectin are closely associated with its molecular structure. Therefore, during pectin extraction, attention must be paid not only to the yield but also to the extraction method, as it determines key characteristics such as molecular weight and degree of esterification [91].

Inulin is a plant-derived polysaccharide composed of fructose units linked by β-(2→1)-D-fructosyl-fructose bonds. Its functional properties are largely dependent on its degree of polymerization and branching. Inulin possesses prebiotic activity and can serve as a fat replacer and texture modifier in various food applications [32].

The inclusion of DF in food production can change its consistency, texture, and sensory properties. The behavior of DF in interaction with water depends largely on the source of the raw material, which determines its chemical composition—particularly the ratio and amount of SDF and IDF, as well as on the microstructure and processing conditions of the material. These properties are further influenced by the characteristics of the food matrix into which the DF is incorporated, including pH, ionic charge, and the presence of other constituents such as starches and sugars. The most commonly evaluated functional attributes include water retention capacity, swelling capacity, and solubility index [32]. Water retention capacity is defined as the amount of water retained per gram of material under specific conditions, including time, temperature, and centrifugation speed. Swelling capacity is assessed by immersing the DF in water for a set period and measuring the change in volume [31]. In contrast, the solubility index is associated with the polysaccharide structure of the material and may vary depending on temperature [30]. DF also has oil-holding capacity, defined as the amount of oil retained after mixing, incubation, and centrifugation. This capacity is influenced by the chemical structure of the polysaccharides, surface properties of the particles, overall charge, and hydrophilicity of the DF material [31].

DF also has the ability to form gels and increase the viscosity of products. Viscosity is related to the water retention capacity and swelling capacity properties of polysaccharides and depends on their chemical composition. For instance, SDFs such as β-glucans and galactomannans exhibit notable thickening properties, whereas compounds like carboxymethylcellulose and pectin are known for their gel-forming abilities [31]. The gelation capacity of DF is primarily linked to its water retention capacity [32]. Furthermore, numerous types of DF can function as fat replacers due to their foam- and emulsion-stabilizing properties and their ability to form viscous solutions, enhancing the texture and mouthfeel in reduced-fat products [31].

5.3. Impact of Modification on the Prebiotic and Technological Properties of By-Products

Fruit processing residues are considered to be valuable prebiotic candidates due to their abundant content of DFs—such as oligosaccharides and resistant polysaccharides including hemicellulose, cellulose, lignin, and pectin—as well as a wide range of phytochemicals, including phenolic compounds, flavonoids, and carotenoids [26]. DFs may enhance the tolerance of probiotics to gastric digestion and improve their viability following heat shock, highlighting the potential of fruit and berry pomace as an effective probiotic carrier [25]. However, their prebiotic potential is strongly influenced by their structural and compositional characteristics. Vásquez et al. [92] reported that the efficacy of pectin oligosaccharides as prebiotics is influenced by factors such as molecular size, monosaccharide composition, and degree of esterification, all of which affect their interactions with the gut microbiota.

Several modification methods can be applied to improve the technological and functional properties of pomace or DFs. Different extraction techniques impact the yield and characteristics of the resulting compounds and enable modulation of their properties [93]. The most commonly used modification methods are physical, chemical, and biological. Combined methods are also employed, typically involving both physical and biological techniques (e.g., ultrasonication coupled with enzymatic hydrolysis or microwave treatment combined with enzymatic hydrolysis) [24]. Multiple studies have demonstrated that novel, eco-friendly physical techniques such as extrusion [94,95], ultrasound [96,97,98], microwave [93,99], ultrafine grinding [100], and high-pressure [101] processing not only enhance the functional and technological properties of pomace-derived fibers but also improve their prebiotic potential. Among these, ultrasound and microwave treatments have been extensively investigated for their capacity to alter polysaccharide structure and enhance functional properties. Ultrasonication affects the extraction yield, composition, and molecular weight (MW) of prebiotic compounds, depending on the raw material used. Ultrasound-assisted extraction has been shown to efficiently increase polysaccharide yield while reducing the MW of high-MW polysaccharides without altering their primary structure, as observed in Rosa roxburghii Tratt pomace. The polysaccharides obtained after ultrasound treatment contained galacturonic acid, galactose, glucose, arabinose, rhamnose, and glucuronic acid in varying ratios, with the decreased molecular weight significantly contributing to the modulation of the pomace’s prebiotic potential [96]. Similarly, Bachari et al. reported that ultrasonic treatment improved pectin extracted from pomegranate peel by enhancing its total phenol content, antioxidant activity, and α-amylase inhibition, while significantly decreasing the MW, particle size, and degree of esterification. These modifications contributed to pectin’s ability to effectively promote the growth of Bifidobacterium longum and L. casei, indicating enhanced prebiotic potential [98]. Polysaccharides extracted ultrasonically from date pomace exhibited notable antioxidant activity and inhibitory effects on α-amylase, α-glucosidase, and angiotensin-converting enzyme, as well as strong antiproliferative activity against Caco-2 and MCF-7 cancer cell lines. Additionally, they demonstrated broad-spectrum antimicrobial properties, enhanced the abundance of beneficial gut microbiota during in vitro fermentations, and positively modulated gut metabolic pathways, promoting the production of major SCFAs [97]. Microwave treatment affected pomace-derived fibers by inducing structural loosening, disrupting covalent and noncovalent bonds among hemicellulose, cellulose, and other components. This resulted in increased SDF due to the release of bound compounds such as lignin and pectin, which influenced fiber fermentability and SCFA production [99]. Bamigbade et al. [102] isolated high-MW bioactive heteropolysaccharides from date pomace by employing microwave-assisted extraction with deep eutectic solvents. These polysaccharides exhibited potent antioxidant, antidiabetic, antihypertensive, anti-cancer, and antimicrobial activities. Furthermore, they displayed prebiotic activity by stimulating the proliferation of beneficial probiotic bacteria and colonic microbiota.

Application of ultrafine grinding disrupts chemical bonds within the fiber matrix, leading to reduced crystallinity and decreased thermal stability. Analysis of SDFs derived from grapefruit peel confirmed the preservation of characteristic polysaccharide spectral patterns and a cellulose I-type crystalline structure. This modification also increased the pectin content in the SDFs, which may enhance their functional properties. Furthermore, the treated fibers exhibited the potential to promote bacterial growth and stimulate probiotic strains to increase SCFA production [100]. In another study, Wang et al. [101] demonstrated that ultra-high-pressure treatment of IDF enhanced the prebiotic potential of Rosa roxburghii Tratt.

Extrusion, a thermo-mechanical method, appears effective in modifying DF fermentability. Tejada-Ortigoza et al. [94] reported a reduction of multibranched sugars in fruit peels after extrusion, and the applied treatment enhanced fermentability, leading to increased SCFA production [94]. In another study, extrusion of orange pomace improved in vitro glucose diffusion, inhibited α-amylase activity, enhanced cholesterol and bile acid binding capacity, and increased total SCFA production [95].

Chemical treatment involves the use of chemical reagents such as acids and alkalis. By adjusting reagent concentrations, temperature, and reaction time, IDF content can be reduced and SDF content increased [24]. Alkaline hydrolysis disrupts the linkages among hemicellulose and cellulose microfibers, impacting the microstructure of IDF of grape pomace [103]. Kang et al. [104] extracted pectic polysaccharides from pumpkin pulp using alkaline KOH, obtaining low-MW, low-degree-of-esterification fractions rich in RG-I regions and diverse monosaccharides, which effectively promoted the proliferation of probiotic strains and enhanced production of the lactic, acetic, and propionic acids.

Biological methods can be more environmentally friendly than other approaches and include enzymatic hydrolysis and microbial fermentation. Enzymatic modification employs enzyme preparations that hydrolyze DF [24]. The composition of enzymes influences the resulting DF structure and its techno-functional properties. Enzymatic hydrolysis typically operates at low temperatures without significant pressure changes. The enzyme preparations used are substrate-specific. This method avoids chemical contamination, making it more suitable for food applications. Commonly used enzymes include xylanases, cellulases, and lignin oxidases [24]. Hydrolysis of cellulose and hemicellulose increases SDF content and enhances hydrogen bonding, which improves hydration properties. The techno-functional properties of treated pomace depend on both the amount and quality of the SDF produced [30,105]. A guava purée by-product treated with cellulase showed a shift from high to low MW distribution, along with improved prebiotic activity [106]. Similarly, enzymatically hydrolyzed Asian pear pomace, treated with cellulase and β-glucanase from T. reesei, demonstrated prebiotic potential and anti-inflammatory effects. It also enhanced cytokine production by modulating the NF-κB pathway [107]. Prebiotic activity of enzymatically modified pomace depends on several factors: enzyme composition, primary pomace composition, and the structure of the resulting saccharide fractions. For example, Vásquez et al. [92] obtained three pectin oligosaccharide fractions from enzymatically treated pisco grape pomace. The <3 kDa fraction, rich in galacturonic acid and glucose, exhibited the highest prebiotic index. In another study, enzymatic treatment of pumpkin pulp with Pectinex^® Ultra SP-L yielded a pectic polysaccharide fraction that stimulated probiotic growth and acetate production. This fraction contained α-1,4-linked GalA and α-1,2-linked rhamnose residues, indicating the presence of both homogalacturonan and RG-I domains [108].

Combined methods, such as ultrasonic and enzymatic treatment, have also demonstrated increased prebiotic potential. Li et al. [109] reported that ultrasonic–enzymatic modification of litchi pomace resulted in a higher SDF content, along with a significant increase in arabinose levels and apparent viscosity. The modified SDF exhibited functional properties such as enhanced radical scavenging activity and stimulation of probiotic bacterial growth. In another study, the combined application of alkaline hydrogen peroxide and xylanase to citrus fibers significantly increased SDF content, altered monosaccharide composition, and improved porosity and specific surface area, without modifying the core chemical structure [110].

Different technological treatments applied to agro-food by-products produce diverse effects on their functional and technological characteristics. While considerable attention has been devoted to optimizing extraction efficiency and enhancing physicochemical properties, the in vivo prebiotic potential of these modified fractions remains largely underexplored. A more comprehensive understanding—linking structural modifications to gut microbiota modulation—is essential to fully validate their health-promoting applications and support their integration into functional food systems.

6. Berry and Fruit By-Products for Application with Probiotics in Functional Foods

The combined application of DF and probiotics—particularly through the use of fruit and berry pomace—results in a synergistic synbiotic effect that enhances both the nutritional and functional properties of food products. This interaction promotes probiotic viability and activity, while DFs act as prebiotics, supporting gut health through the production of beneficial metabolites. Such integration enables the development of innovative functional foods with improved health benefits and technological performance (Figure 1). Berry and fruit pomace, rich in DF and bioactive compounds, enhances the antioxidant and nutritional value of foods. It also acts as a prebiotic, supporting the growth and activity of probiotics. The combined use of fruit and berry by-products with probiotics in food production has been evaluated in several studies (Table 2). Pomace and probiotic strains from the former group of Lactobacillus spp. are commonly used in dairy products such as yogurt, while their application in plant-based foods remains less explored. As shown in Table 2, incorporating fruit and berry pomace and probiotic strains into food products enhances nutritional quality by increasing total phenolic content and antioxidant activity. These by-products also support the viability of various probiotic strains, improve textural properties, and reduce undesirable effects such as syneresis in yogurt. In addition, many studies report improved sensory characteristics, indicating strong consumer acceptance.

DFs from berry and fruit by-products can differentially influence probiotic viability and metabolite production, depending on their origin and composition. This synergistic combination facilitates the fermentation process, during which probiotic bacteria produce SCFAs, such as acetate, propionate, and butyrate. These metabolites contribute to intestinal homeostasis by lowering luminal pH, inhibiting pathogenic bacteria, and strengthening the gut epithelial barrier. Moreover, SCFAs play a key role in host metabolic regulation, thereby supporting the health-promoting potential of probiotic-enriched functional foods [111]. According to a study by Rivas et al., fibers from different sources exhibit distinct effects on probiotic activity. Grape stem fiber showed the strongest stimulation of LAB growth, while pomegranate peel fiber not only supported LAB growth but also resulted in the highest SCFA production [112]. For example, in another study, fermentation of a soymilk beverage supplemented with passion fruit pomace increased folic acid content. In contrast, fermentation of jabuticaba pomace with L. acidophilus, L. casei, and B. animalis subsp. lactis resulted in higher SCFA production [113,114]. Likewise, cranberry oligosaccharides, including arabino-xyloglucan and pectic rhamnogalacturonan I, were found to support the growth of strains from the former group of Lactobacillus spp. All strains produced lactic, acetic, propionic, and, in some cases, butyric acids. These oligosaccharide structures, combined with the metabolic capacity of certain strains from the former group of Lactobacillus to utilize them for SCFA production, highlight their promising potential as synbiotic ingredients in functional food development [115].

Beyond SCFA formation, probiotic fermentation of various pomaces induces biochemical changes that enhance antioxidant capacity and other functional attributes relevant to food applications. For example, fermenting blueberry pomace with L. rhamnosus GG and L. plantarum-1 significantly increased the levels of organic acids, such as lactic and acetic acids. Fermentation also elevated the active compound levels and antioxidant capacity in blueberry pomace. Additionally, the fermented pomace exhibited excellent cholesterol clearance after 24 h under three cholate concentrations and demonstrated strong anti-fatigue properties [116]. Similarly, fermentation of apple pomace with L. rhamnosus L08—a strain characterized by high cell membrane-associated β-glucosidase activity—significantly modified the phenolic profile. Quercitrin and phlorizin levels were reduced, while quercetin, phloretin, gallic acid, epicatechin, caffeic acid, and ferulic acid levels increased. This biotransformation led to enhanced antioxidant activity, indicating that LAB fermentation effectively improves the bioactivity of phenolic compounds in apple pomace. These findings support its potential as a valuable and economically beneficial by-product for the food industry [117]. Yogurts fortified with mango and banana peel powders exhibited higher total phenolic content and antioxidant activity during storage compared to non-fortified samples. They also contained prebiotic oligosaccharides, which enhanced LAB survival over 28 days, making them effective synbiotic matrices [20]. Pomace application affects not only health benefits but also the technological attributes of food products. Lee et al. [118] reported that supplementing fermented milk with Mandarin Melon Berry (Cudrania tricuspidata) powder slightly improved lactic acid fermentation and enhanced the color of the product, making it darker, redder, and more appealing. Higher concentrations of C. tricuspidata powder increased phenolic and flavonoid content, thereby boosting antioxidant and antimutagenic activities.

Recent research has increasingly focused on the functional role of fruit and berry pomace in supporting probiotic viability and activity. Beyond their well-known content of DF and antioxidants, these by-products have demonstrated the potential to modulate microbial dynamics in food systems and during gastrointestinal transit. For example, Saskatoon berry pomace extract has been identified as a promising source of antioxidants. Its co-encapsulation with probiotics through spray drying was shown to produce a powder with diverse functional properties suitable for applications in the food and pharmaceutical industries [27]. Similarly, various fruit and berry by-products have been found to contain prebiotic compounds. The chemical composition, functional properties, and prebiotic potential of apple, banana, and mango peel powders have been investigated. Studies show that supplementation with 2% peel powder effectively supports the growth of L. rhamnosus, L. casei, and B. lactis in both individual and mixed cultures [67]. In addition to promoting probiotic growth, some pomaces have shown selective antimicrobial activity against foodborne pathogens. For instance, Aditya et al. [119] demonstrated that chokeberry pomace exhibited an antagonistic effect against E. coli O157:H7, while it did not affect strains from the former group of Lactobacillus spp. or other gut microflora. However, not all pomaces act selectively. Certain types have been observed to support the growth of both beneficial and harmful bacteria. Therefore, their classification as prebiotics is not universal, and their application in food fermentation may be constrained by microbiological contamination risks [33]. Nevertheless, components derived from pomace—such as DF or phenolic compounds—have shown the ability to enhance probiotic viability and improve the overall functional quality of food products [120].

The integration of pomace and probiotics into food systems presents promising opportunities to enhance nutritional, functional, and sensory properties. However, current knowledge of their molecular interactions and synergistic effects is still limited. Future research should focus on elucidating these mechanisms, optimizing fermentation processes, and conducting comprehensive in vivo evaluations to fully realize their potential as innovative functional food ingredients.

Table 2. Foods supplemented with by-products and probiotic strains, particularly those from the former group of Lactobacillus spp. and other bacteria strains.

Food Product	By-Products	Microorganisms	Outcomes	Reference
Fermented goat milk	Grape pomace extract	L. acidophilus LA-5, L. rhamnosus HN001	↑ Total phenolic compound content; ↑ viability of L. acidophilus; ↑ sensory scores of flavor, color, and overall acceptability	[121]
Fermented skim milk		Str. thermophilus TA040, L. acidophilus LAC4	↑ Total phenolic compound content; ↑ viability of Str. thermophilus and L. acidophilus	[120]
Yogurt	Grape pomace	L. acidophilus, B. bifidum	↑ Total phenolic compound content; ↑ antioxidant activity; ↓ syneresis; ↑ viable cell counts	[72]
Fermented grape juice		L. casei subsp. rhamnosus ATCC 7469	↑ Growth of LAB population	[122]
Low-fat symbiotic yogurt gel		L. acidophilus LA-5, B. bifidum BB-12	↑ Viable cell counts; ↓ syneresis; ↑ steady and dynamic rheological properties; ↑ firmness; ↑ overall acceptability	[71]
Yogurt	Apple pomace	L. acidophilus, Str. thermophilus, B. bifidum	↑ Total phenolic compound content; ↑ antioxidant activity; ↓ syneresis of enriched yogurts; ↓ colon cancer cells’ viability	[123]
Cheese		Lac. lactis LL16	↑ Viability of Lac. lactis LL16; ↑ overall sensory acceptance	[124]
Fermented soy drink		Loigalactobacillus bifermentans MIUG BL-16	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ viable cell counts	[74]
Gummy supplements		L. plantarum LUHS135, L. paracasei LUHS244	↑ Total phenolic compound content; ↑ antioxidant activity	[125]
Yogurt	Orange pomace	Str. thermophilus, L. acidophilus, L. bulgaricus	↓ Syneresis; ↓ firmness; ↑ consistency index	[126]
Ice cream	Fruit (grape, apricot, and apple) and grain (rice, corn, sunflower, and barley)-based by-products	L. acidophilus ATCC 4357D-5, B. animalis subsp. lactis ATCC 27536	↑ Survival of the probiotic strains	[127]
Milk	Peach pomace fiber	L. acidophilus, B. animalis subsp. lactis	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ titratable acidity; ↓ pH	[128]
Fermented soymilk	Passion fruit by-products	Str. thermophilus TH-4, L. acidophilus LA-5, L. rhamnosus LGG, L. fermentum PCC, and L. reuteri RC-14, Str. thermophilus ST-M6 and TA-40	↑ Folate content; ↑ growth of probiotics	[114]
Millet probiotic beverage	Pineapple pomace	L. rhamnosus LGG	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ sensory score	[129]
Petit suisse cheese	Blueberry pomace	Lac. lactis subsp. cremoris, Lac. lactis subsp. lactis, Lac. lactis subsp. lactis biovar. diacetylactis, Leuc. mesenteroides subsp. cremoris, Leuc. pseudomesenteroides, L. acidophilus LA5, B. animalis subsp. lactis BB12	↑ Fiber content; ↑ total phenolic compound content; ↑ antioxidant activity; ↑ sensory score	[130]
Ice cream	Passion fruit peel	L. acidophilus TISTR 2365	↑ Growth of probiotics; ↑ overrun value; ↑ sensory score; ↓ melting rate; ↓ pH; ↓ color intensity	[131]
Butter spread product	Soluble DF extracted from cranberry and sea buckthorn berry pomace	L. reuteri 182, L. paracasei subsp. paracasei ATCC® BAA-52, L. plantarum F1	↑ Viscosity; ↑ probiotic viability	[132]
Low-fat yogurt	Sour cherry pomace pectin-derived oligosaccharides	L. acidophilus DSM 20079	↑ Acidity; ↑ viscosity; ↑ probiotic viability; ↓ pH; ↓ syneresis; ↑ sensory properties; ↑ antioxidant activity	[22]
Yogurt	Carrot waste extract	L. plantarum	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ survival of the probiotic strains	[133]
Yogurt	Wolfberry DF	L. casei CGMCC1.5956, L. plantarum subsp. plantarum CGMCC 1.5953	↓ Syneresis; ↑ acidity; ↑ sensory properties; ↑ viscosity	[21]
Yogurt	Orange, mandarin, and lemon pomaces	L. acidophilus LA-5, B. animalis subsp. lactis BB12, Str. thermophilus	↑ Acidity; ↑ growth of probiotics; ↑ stability and enhanced texture; ↑ sensorial quality; ↑ antioxidant activity	[134]
Yogurt	Mango peel powder and banana peel powder	L. casei 431®, L. rhamnosus LGG®, B. subsp. lactis Bb-12®	↑ Viable cell counts; ↑ fat, ash, and protein contents; ↑ total phenolic contents; ↑ antioxidant activity; ↑ sugar contents; ↑ titratable acidity; ↓ pH	[20]

↑—indicates an increase in the indicator compared with the control sample; ↓—indicates a decrease in the indicator compared with the control sample.

Table 2. Foods supplemented with by-products and probiotic strains, particularly those from the former group of Lactobacillus spp. and other bacteria strains.

Food Product	By-Products	Microorganisms	Outcomes	Reference
Fermented goat milk	Grape pomace extract	L. acidophilus LA-5, L. rhamnosus HN001	↑ Total phenolic compound content; ↑ viability of L. acidophilus; ↑ sensory scores of flavor, color, and overall acceptability	[121]
Fermented skim milk		Str. thermophilus TA040, L. acidophilus LAC4	↑ Total phenolic compound content; ↑ viability of Str. thermophilus and L. acidophilus	[120]
Yogurt	Grape pomace	L. acidophilus, B. bifidum	↑ Total phenolic compound content; ↑ antioxidant activity; ↓ syneresis; ↑ viable cell counts	[72]
Fermented grape juice		L. casei subsp. rhamnosus ATCC 7469	↑ Growth of LAB population	[122]
Low-fat symbiotic yogurt gel		L. acidophilus LA-5, B. bifidum BB-12	↑ Viable cell counts; ↓ syneresis; ↑ steady and dynamic rheological properties; ↑ firmness; ↑ overall acceptability	[71]
Yogurt	Apple pomace	L. acidophilus, Str. thermophilus, B. bifidum	↑ Total phenolic compound content; ↑ antioxidant activity; ↓ syneresis of enriched yogurts; ↓ colon cancer cells’ viability	[123]
Cheese		Lac. lactis LL16	↑ Viability of Lac. lactis LL16; ↑ overall sensory acceptance	[124]
Fermented soy drink		Loigalactobacillus bifermentans MIUG BL-16	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ viable cell counts	[74]
Gummy supplements		L. plantarum LUHS135, L. paracasei LUHS244	↑ Total phenolic compound content; ↑ antioxidant activity	[125]
Yogurt	Orange pomace	Str. thermophilus, L. acidophilus, L. bulgaricus	↓ Syneresis; ↓ firmness; ↑ consistency index	[126]
Ice cream	Fruit (grape, apricot, and apple) and grain (rice, corn, sunflower, and barley)-based by-products	L. acidophilus ATCC 4357D-5, B. animalis subsp. lactis ATCC 27536	↑ Survival of the probiotic strains	[127]
Milk	Peach pomace fiber	L. acidophilus, B. animalis subsp. lactis	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ titratable acidity; ↓ pH	[128]
Fermented soymilk	Passion fruit by-products	Str. thermophilus TH-4, L. acidophilus LA-5, L. rhamnosus LGG, L. fermentum PCC, and L. reuteri RC-14, Str. thermophilus ST-M6 and TA-40	↑ Folate content; ↑ growth of probiotics	[114]
Millet probiotic beverage	Pineapple pomace	L. rhamnosus LGG	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ sensory score	[129]
Petit suisse cheese	Blueberry pomace	Lac. lactis subsp. cremoris, Lac. lactis subsp. lactis, Lac. lactis subsp. lactis biovar. diacetylactis, Leuc. mesenteroides subsp. cremoris, Leuc. pseudomesenteroides, L. acidophilus LA5, B. animalis subsp. lactis BB12	↑ Fiber content; ↑ total phenolic compound content; ↑ antioxidant activity; ↑ sensory score	[130]
Ice cream	Passion fruit peel	L. acidophilus TISTR 2365	↑ Growth of probiotics; ↑ overrun value; ↑ sensory score; ↓ melting rate; ↓ pH; ↓ color intensity	[131]
Butter spread product	Soluble DF extracted from cranberry and sea buckthorn berry pomace	L. reuteri 182, L. paracasei subsp. paracasei ATCC® BAA-52, L. plantarum F1	↑ Viscosity; ↑ probiotic viability	[132]
Low-fat yogurt	Sour cherry pomace pectin-derived oligosaccharides	L. acidophilus DSM 20079	↑ Acidity; ↑ viscosity; ↑ probiotic viability; ↓ pH; ↓ syneresis; ↑ sensory properties; ↑ antioxidant activity	[22]
Yogurt	Carrot waste extract	L. plantarum	↑ Total phenolic compound content; ↑ antioxidant activity; ↑ survival of the probiotic strains	[133]
Yogurt	Wolfberry DF	L. casei CGMCC1.5956, L. plantarum subsp. plantarum CGMCC 1.5953	↓ Syneresis; ↑ acidity; ↑ sensory properties; ↑ viscosity	[21]
Yogurt	Orange, mandarin, and lemon pomaces	L. acidophilus LA-5, B. animalis subsp. lactis BB12, Str. thermophilus	↑ Acidity; ↑ growth of probiotics; ↑ stability and enhanced texture; ↑ sensorial quality; ↑ antioxidant activity	[134]
Yogurt	Mango peel powder and banana peel powder	L. casei 431®, L. rhamnosus LGG®, B. subsp. lactis Bb-12®	↑ Viable cell counts; ↑ fat, ash, and protein contents; ↑ total phenolic contents; ↑ antioxidant activity; ↑ sugar contents; ↑ titratable acidity; ↓ pH	[20]

↑—indicates an increase in the indicator compared with the control sample; ↓—indicates a decrease in the indicator compared with the control sample.

7. Regulatory Overview of Pomace and Probiotics in Food Products

The incorporation of DF derived from fruit and berry pomace into food products has attracted increasing scientific interest due to its potential to enhance both nutritional quality and sustainability. Such utilization not only improves the functional and physiological properties of foods but also supports waste valorization strategies, aligning with the European Union (EU)’s circular economy goals. Regulation (EC) No 1924/2006 establishes a legal framework for nutrition and health claims in the EU and allows the labeling of products as a “source of fiber” or “high fiber” if they meet specific DF content thresholds [135]. These regulatory provisions enable food manufacturers to communicate added nutritional value through approved claims, thus reinforcing the relevance of pomace-derived DF in the development of value-added food products.

While the health benefits of DFs are well recognized, their physiological effects depend on various factors, including the source, chemical composition, soluble-to-insoluble fiber ratio, and the amount incorporated into the product [79,80]. Although there is growing interest in valorizing agro-food by-products, significant regulatory gaps persist regarding their specific safety risks. Therefore, integrating such by-products into the food chain requires a comprehensive safety assessment alongside the application of appropriate upcycling technologies prior to commercialization. In the EU, any material not historically consumed to a significant degree before 15 May 1997 must undergo novel-food authorization under Regulation (EU) 2015/2283. When by-products are used as food additives, they fall under Regulation (EC) No 1333/2008; when employed as processing aids—such as enzymes—they are governed by Regulation (EC) No 1332/2008. All authorized additives carry an E-number and must satisfy the purity and microbiological criteria set out in Regulation (EU) No 231/2012. Although novel foods, additives, and enzymes share a unified risk-assessment framework—encompassing hazard identification, exposure assessment, and risk characterization—each category is subject to distinct dossier requirements including compositional, toxicological, and manufacturing data. The European Food Safety Authority (EFSA)’s rigorous, transparent scientific review process not only safeguards consumer health but also underpins a regulatory environment that encourages sustainable innovation in food production [136,137].

However, current EU food safety legislation does not explicitly cover many food processing by-products, including pomace, peels, spent grains, whey, and oilseed cakes. Existing frameworks, such as Regulation (EC) No 1881/2006 on maximum contaminant levels, Regulation (EC) No 2073/2005 on microbiological criteria, and Regulation (EU) 2018/62 on pesticide residues, largely exclude these by-product fractions, leaving potential chemical and microbiological risks insufficiently addressed. In the absence of specific regulatory guidance, the implementation of private food safety standards tailored to by-product valorization has emerged as a practical solution. These voluntary schemes, already applied in various segments of the food industry, incorporate targeted risk assessments and safety criteria, thereby supporting the safe and sustainable integration of agro-food residues into food systems. Over time, such practices may contribute to the development of a formal regulatory framework [136,137].

Despite the increasing scientific and commercial interest in probiotics, their regulatory status remains fragmented across jurisdictions. Within the EU, probiotics are regulated under general food law (Regulation (EC) No 178/2002/EC and Directive 2000/13/EU), with safety evaluations guided by the EFSA Qualified Presumption of Safety (QPS) framework. Currently, 22 bacterial species—primarily strains from the former group of Lactobacillus spp. and Bifidobacterium—hold QPS status, which exempts them from pre-market safety assessments. However, novel strains must still demonstrate safety, including the absence of transferable antibiotic resistance and limited metabolic activity in the upper gastrointestinal tract. Under Regulation (EC) No 1924/2006 on nutrition and health claims, terms such as “probiotic” or “contains probiotics” are classified as health claims and therefore prohibited unless specifically authorized. To date, only the claim related to live yogurt’s ability to improve lactose digestion has been approved. Member States exhibit varying degrees of regulatory tolerance regarding the use of the term “probiotic” on product labeling, with countries such as Denmark, Italy, the Czech Republic, the Netherlands, Spain, and France implementing national approaches [138,139,140].

In the United States, probiotics lack a statutory definition but fall under certain categories—food, dietary supplement, drug, or live biotherapeutic products—depending on their intended use and claims. The U.S. Food and Drug Administration (FDA) oversees their incorporation via two main pathways: Generally Recognized as Safe (GRAS) affirmation for ingredients with established safety, and Food Additive Petitions for technological agents. New dietary ingredients, including novel probiotic strains, require a pre-market safety notification submitted at least 75 days prior to introduction into interstate commerce, in accordance with current draft guidance. Probiotic claims fall into four categories: nutrient content, structure/function, health, and qualified health claims. Structure/function claims (e.g., “promotes digestion”) do not require pre-approval but must avoid implying disease treatment or prevention. In contrast, health and qualified health claims require either FDA authorization or substantiation through “significant scientific agreement” [138,140,141].

8. Conclusions and Future Perspectives

The market for probiotic-enriched foods is expanding globally. For probiotics to deliver health benefits to consumers, they must maintain viability throughout the product’s shelf life, survive gastrointestinal conditions, and effectively adhere to intestinal epithelial cells. Additional selection criteria include antioxidant activity, cytotoxicity, production of antimicrobial metabolites, and exopolysaccharide synthesis.

However, probiotic functionality is highly strain-specific, and the precise mechanisms underlying their beneficial effects remain incompletely understood. Further research is needed to elucidate these mechanisms.

Several studies have explored the use of probiotics in combination with various types of pomaces as dietary fiber sources, although plant-based applications remain less studied. Fermentation of pomace by strains from the former group of Lactobacillus spp. can enhance the production of short-chain fatty acids and antimicrobial compounds such as organic acids and bacteriocins.

Pomace is recognized as a promising source of antioxidants and prebiotics, capable of promoting the growth of beneficial lactic acid bacteria while inhibiting spoilage microorganisms. However, certain types of pomaces may also support the growth of pathogenic bacteria, highlighting the need for thorough evaluation of their composition and prebiotic activity. Safety concerns related to bacterial contamination during food production must also be carefully addressed.

Processing of agro-food by-products can alter their functional properties; however, in vivo evidence regarding the prebiotic effects of such modified fractions is limited. Establishing clear correlations between structural changes and gut microbiota responses is critical to harness their potential in functional foods. Future investigations should prioritize the integration of probiotics and pomace—or their individual components—into plant-based food matrices. Evaluating the impact of various pomace types on probiotic viability during production, storage, and digestion is essential for the development of novel, high-value-added nutritional products.

Combinations of pomace and probiotics offer a versatile platform for the development of functional foods with enhanced health benefits and improved sensory attributes. Nevertheless, the molecular mechanisms governing their interactions remain insufficiently understood and warrant further investigation.

Moreover, future research and innovation must address existing regulatory gaps at the European Union and international levels, as current food safety legislation lacks specific guidelines on the assessment, permissible contaminant limits, and microbiological risks associated with the inclusion of processing by-products like pomace in food products. In vivo validation of health claims is imperative to confirm the biological relevance of in vitro findings and to understand the long-term effects on human health. Continued research into the molecular mechanisms of probiotic–prebiotic interactions and their effects on gut microbiota composition, immune modulation, and disease prevention is essential for advancing the field.