The etymology of the term fermentation comes from the Latin verb “fevere”, which means “to boil”. Fermentation is one of the oldest known food processing methods and its history stretches back to the Neolithic period, as indicated by archaeological findings of clay tools for cheese making. Its unique ability to enhance the sensory properties of raw materials and preserve the developed product has been recognized throughout human history as miscellaneous fermented products are part of the culinary and cultural heritage of many countries globally ^[1][2][1,2]. This biotechnological method includes several subcategories based on primary metabolites produced: (a) alcoholic fermentation, conducted by yeasts, with ethanol and CO₂ as the primary products; (b) acetic fermentation, conducted by bacteria of the genera Acetobacter with acetic acid as the primary product; (c) lactic fermentation, where lactic acid bacteria (LAB) are the fermenting microorganisms and lactic acid is the main metabolic product; and (d) ammonia or alkali fermentation of proteinaceous substrates by different Bacillus and Fungi species, with ammonia being released and giving the food a strong ammoniacal smell [3]. Their common aspect, from a biochemical point of view, is that microorganisms use their metabolic pathways to derive energy from organic compounds in the absence of exogenous oxidizing agents. Under this scope, any raw material containing organic compounds could be fermented by the microorganisms which possess the required enzymatic systems for degradation of the respective carbon sources. Recently, fermentation technology has been brought to the forefront again since it provides a solid background for the development of safe products with unique nutritional and functional attributes.

2. Nutritional Aspects of Cereal-Based Fermented Foods

2.1. Impact on Food Safety and Shelf-Life Extension

Fermenting microorganisms employed to generate new products with improved sensorial and nutritional qualities often produces various metabolites that inhibit the growth of spoilage and/or pathogenic bacteria. These metabolites include organic acids such as lactic acid, propionic acid, acetic acid, etc. that decrease the initial pH value, creating an acidic environment in the food matrix and therefore extending the shelf-life of the fermented product ^[4][7]. Furthermore, ethanol and hydrogen peroxide, which are strong inhibitory factors for microbial growth, as well as other secondary metabolites that can act as antimicrobial compounds, are produced by some LAB and yeast species. These metabolites can be effective in controlling fungal growth and mycotoxins production in grain matrices; the latter is of great importance for cereal derived products, raising public health concern since exposure to mycotoxins may cause adverse health effects to humans ^[5][14]. Lactobacillus and Pediococcus strains, possessing antimicrobial activities, were tested regarding their efficiency to reduce mycotoxin production from Fusarium as well as to restrain the growth of other mycotoxigenic fungi during malting of wheat grains (used for beverages and bakery products). LAB reduced the fusarium toxins (deoxynivalenol-vomitoxin-, T-2, HT-2, and zearalenone) by up to 75%, depending on the strain. Antifungal activity was also observed from LAB metabolites (especially from acetic acid and secondarily from lactic acid) ^[6][15]. Naturally fermented sorghum, used to produce whole grain Ting (an African traditional food), was compared to similar products fermented with the addition of Lactobacillus fermentum strains as starter cultures. The content of mycotoxins (found in the whole grain of sorghum raw material) was decreased in all fermented samples. More specifically, L. fermentum FUA 3321 reduced the studied mycotoxins by up to 98% ^[7][16]. Moreover, traditional fermentation processes reduced the mycotoxin content of kunu-zaki and pito (two popular traditional cereal-based African beverages) by 59% and 99%, respectively ^[8][17]. The antifungal properties of various Lactobacillus strains have been tested in-situ to evaluate their effectiveness to improve the quality and safety of fermented cereal products. It is believed that the antifungal effect of LAB is the result of synergistic interactions among numerous metabolites, including fatty acids, peptides, and organic acids ^[9][18]. Antimicrobial peptides, bacteriocins, are produced by LAB and are partially related to the extended shelf-life of fermented products ^[10][19]. M’hir et al. ^[11][20] reviewed the enterococci strains that were isolated from fermented cereal products and their potential usage as starter cultures according to their technological, functional, and safety characteristics. The antimicrobial activity of 63 LAB isolates from a spontaneously fermented beverage (ogi) was explored. Pediococcus sp. strain OF101 showed the highest antibacterial activity against several tested food pathogens (Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecium, and Escherichia coli) ^[12][21]. Likewise, Chinese fermented foods, including sweet fermented rice, homemade sourdough, and koji, were the samples from which 132 LAB isolates were obtained. All isolates exhibited antimicrobial activity and reduced the five indicator pathogens (E. coli ATCC 25922, Salmonella enteritidis ATCC13076, Salmonella typhimurium ATCC14028, L. monocytogenes EGD-e, and S. aureus ATCC29213) by 2–4 log CFU/mL ^[13][22]. Consumption of traditional fermented cereal products in Africa resulted in reduced diarrhea outbreaks in children by 40% and improvement in well-being ^[4][7]. These findings indicate that isolated microbial strains from indigenous products may be used as starter cultures for standardized production of the respective cereal-based fermented product after their evaluation for technological and probiotic properties ^[9][18] or as sources to isolate metabolites and use them as pure antimicrobial agents ^[14][6].

2.2. Enhancement in Nutritive Value and Compositional Changes of Fermented Cereal Products

2.2.1. Protein and Carbohydrate Digestibility

Protein digestibility depends on the protein structure and the presence of antinutrient factors (protease inhibitors, phytases) that bind with them as well as other parameters such as pH, temperature, and ionic strength, all of which are directly related to proteolytic activities. Fermentation may affect these factors and parameters and thereby contribute to a more effective digestibility of plant proteins ^[15][23]. Proteins need to be broken down to amino acids or even small peptides to enter the human bloodstream after their absorption by the enterocytes of the small intestine, otherwise they reach the large intestine where they are fermented by the gut microorganisms, giving rise to the formation of amines and short-chain fatty acids. These fermentation products elicit various biological reactions via different receptors and mechanisms, including signal transduction involving biogenic amines as neurotransmitters and modulation of inflammatory responses ^[16][24].

2.2.2. Dietary Fiber Modification

According to the American Association of Cereal Chemists (AACC), dietary fibers (DFs) are plant carbohydrates that are resistant to hydrolysis by human enzymes but can be fermented by microorganisms in the large intestine. They are classified in soluble and insoluble DFs and their ratio in food products plays a significant role in both health implications and physical–technological properties ^[17][41]. Cereals contain various DFs, which chemically and compositionally differ depending on the type of cereal and grain tissue in which they are found. The main components of DFs of cereals are non-starch polysaccharides, i.e., arabinoxylans, β-glucans, cellulose, resistant starch, fructans, and lignin, which are a phenolic polymer and often exist in composite structures with other small molecular weight bioactives, e.g., simple phenolics, minerals ^[18][42]. During fermentation of cereals, the pH is decreased due to the production of organic acids (mainly lactic and acetic) and this may result in the activation of various enzymes, either endogenous of the grains or bacterial. The enzymatic activity is responsible for biopolymer degradation, leading to grain softening (cell wall degradation) and improvement of the sensory and physiological characteristics of the fermented product ^[19][43].

2.2.3. Vitamins

Vitamins play a crucial role in proper metabolic functions and therefore, their daily intake is essential since they cannot be synthesized at adequate amounts (or at all) in the human body. These essential micronutrients are divided into two sub-categories according to their solubility: a) the water-soluble vitamin C and the group of B vitamins (thiamin-B1, riboflavin-B2, niacin-B3, pantothenic acid-B5, pyridoxine-B6, biotin, folic acid, cobalamin-B12), and b) the fat-soluble vitamins A, D, E, and K ^[20][50]. Although cereals contain specific vitamins, fermentation with LAB or yeast strains can increase their vitamin content ^[4][21][7,8]. The ability of LAB to produce vitamins is strain-specific and these microorganisms could be used as starter or added cultures to fortify naturally fermented products for targeted nutritional and quality improvement. Such a fortification is of great importance for specific population groups that follow special types of dietary regimes, either by choice (e.g., vegans) or due to cultural habits, religious beliefs, and lack of other available food sources (developing countries). It is worth mentioning that in some African countries, porridges made of cereals can complement breastfeeding ^[22][23][51,52]. Biofortification in vitamins of fermented cereal products has been attempted by a few researchers ^[24][53]. For example, the incorporation of Lactococcus lactis N8 and Saccharomyces boulardii SAA655 in idli batter (an Indian steamed cake made from rice and legumes) increased the riboflavin and folate content by 40–90% ^[25][54]. Sourdough bread and pasta (with a pre-fermentation step) that were fermented by two L. plantarum strains showed a threefold and twofold increment, respectively, in their vitamin B2 content. The used strains were isolated from durum wheat flour and have been characterized as riboflavin-overproducing microorganisms according to in vitro tests with synthetic media ^[26][55]. More recently, Bationo et al. ^[23][52] reported that processing steps like debranning, soaking, and wet-milling may cause a decrease in cereals’ folate content by up to 60%, while on the contrary, fermentation increased folate’s concentration by up to 27%. Various fermented cereal-based foods were studied (fritters, dumplings, porridges, and gelatinized doughs, made from sorghum, corn, or pearl millet) and their estimated folate bioaccessibility ranged from 23% to 81% using an in vitro digestion model. According to Chaves-Lopez et al. ^[27][31], spontaneous maize fermentation may enhance the concentrations of nutritional compounds (thiamine, folate, riboflavin, total carotenoids, vitamin C, and vitamin E), but further preparation steps of the traditional foods result in significant decrements of each important nutrient.

2.2.4. Phenolic Components

Phenolic components, which are secondary plant metabolites, are also found in notable amounts in cereals ^[28][60]. The metabolic pathways (shikimate, phenylpropanoid) for their biosynthesis involve many biomolecules like acetyl CoA, malonyl CoA, pyruvate, acetate, and some amino acids (phenylalanine and tyrosine) ^[7][16]. Their beneficial properties in human health (anti-diabetic, anti-cancer, anti-inflammatory, anti-microbial, anti-oxidant, as well as neuro-, cardio-, and hepato-protective function) are attributed to their ideal chemical structure, which promotes electron transfer or hydrogen donation from the hydroxyl groups of their aromatic ring and thereby exhibit free radical scavenging activities and metal-chelating potential ^[28][29][30][60,62,63]. Phenolic components need to be in a soluble form to enter the human blood circulation system and bring about their antioxidant properties. Phenolics in cereals can be found as free and soluble, conjugated and soluble (bound with sugars and sterols), and non-soluble, which are usually linked to polymers like arabinoxylans and lignin ^[30][31][63,64]. Increases of cereals’ phenolic content can be achieved by size reduction of the particles, germination, addition of hydrolytic enzymes, and fermentation ^[30][63]. Fermentation is reported to also enhance the antioxidant activity of the phenolic fraction ^[32][65]. The conditions during fermentation (temperature, final pH value, duration), microorganisms involved, as well as the type of cereal and the grain tissue employed play an important role in the outcome concerning the release of the bound phenolics ^[29][33][34][62,66,67].

2.3. Cereal-Based Fermented Foods as Probiotic Carriers

Nowadays, the market value of functional foods and beverages is growing with an average rate of 8.6% globally ^[35][77], leading the related industries to a quest of alternative and novel products to meet the consumers’ needs, stay competitive, and ensure their future survival in the globalized functional foods arena. Probiotics have been associated with dairy products for many years, but milk presents many drawbacks as a raw material according to the new trends of the food sector. From an environmental point of view, production of dairy products is generally considered among the possesses that have the greatest burdens based on life cycle assessment analysis ^[36][78]. In addition, lactose intolerance and allergies related to milk proteins concern the vast majority of the world’s population and is an issue that producers should take seriously when developing functional dairy products. Other shortcomings of dairy product matrices include the high cholesterol and fat content, cultural and strict religious beliefs of specific populations that prohibit the consumption of such foods, new diet trends, like veganism, in developed countries, as well as limited access or storage capability of dairy products in developing countries ^[35][37][38][77,79,80]. Other products that may also serve as probiotic carriers are meat, fish, chocolate, vegetables, fruit, and cereals. For the purposes of the present Creview, cereal-based products will be further discussed in this context.

2.4. Prebiotic Potential of Cereal-Based Fermented Foods

The most recent and refined definition of prebiotics was published by The International Scientific Association for Probiotics and Prebiotics (ISAPP) in an expert consensus document. The new definition expands the meaning of prebiotics from non-digestible oligosaccharides of food origin to “a substrate that is selectively utilized by host micro-organisms conferring a health benefit” ^[39][91]. In addition, the site of the host organism, where the beneficial bacteria may be located, is not limited to the human lower gastrointestinal tract (GIT), but also includes other targets such as skin, the whole GIT including the upperparts and mouth, as well as the urogenital tract ^[40][92]. Consequently, besides carbohydrates, other compounds could be considered to exert prebiotic effects, such as micronutrients (inorganic compounds), peptides, phenolics, and fatty acids ^[41][93].

2.5. Reduction of Antinutrients and Allergens

Besides valuable nutrient compounds, cereals contain a notable number of components that are considered anti-nutritional factors (ANFs). These components include phytic acid/phytate (myoinositol-1,2,3,4,5,6-hexakis dihydrogen phosphate), tannins, and polyphenols ^[42][25]. Phytate or phytic acid is a secondary metabolite, found mainly in the aleurone layer and pericarp (wheat, rice) or in the endosperm (maize) of cereals, serving as their phosphorus repository. The content of phytate in cereals varies between 0.18 g to almost 6.5 g per 100 g product (dw) ^[43][111]. The presence of phytic acid plays a crucial role in the nutritional value of the food in which it is found as it has the ability to hinder enzymatic activity (trypsin and beta-galactosidase) and form chelates with metal ions, i.e., iron, magnesium, calcium, and zinc, thus reducing their bioavailability ^[44][112]. Likewise, tannins and polyphenols have a strong negative effect on protein digestibility since their hydroxyl groups form complexes with the carbonyl group of proteins. As a result, proteins precipitate, proteases are inhibited, and thereby, amino acid deprivation is realized when a diet is based on cereal products rich on polyphenols, which is the case in most developing countries or for people following a vegan dietary pattern ^[4][15][7,23]. Prolonged periods of these nutritional deficiencies may also lead to osteoporosis, iron deficiency anemia, and impairments of physical growth ^[45][113].

3. Effect of Cereal-Based Fermented Foods’ Components on Gut Microbiota

Gut microbiota contributes to a wide spectrum of human health aspects. These numerous and variable microbial species (bacteria, viruses, archaea, eukaryotes) may reach 10¹⁴ cells in the gut and their composition can be affected by genetic factors, lifestyle, diet, stress, diseases, and the use of pharmaceutical products ^[46][47][48][131,132,133]. A beneficial, stable, and well-balanced composition is crucial for the maintenance of immune equilibrium, the integrity of the gut epithelial cells, and inflammation prevention. Dysbiosis of the gut ecosystem is associated with intestine related diseases like IBS, skin inflammation (psoriasis, atopic dermatitis), cardiovascular diseases, cancer, obesity, mental health, arthritis, and type II diabetes [2]. Currently, the available intervention studies regarding fermented cereal-based products focus on the impacts of sourdough bread on specific GI diseases as bread is one of the most consumed products around the globe ^[49][134]. Therefore, there are no published data yet on the ways that cereal-based fermented foods may act on human gut microbiota and the possible modifications that they may cause on the species’ dynamics. On account of this, scientific evidence of specific food components and their impact on human gut microbial consortium will be shortly discussed herein. Fermented products in general and cereal-based foods in particular are characterized by an abundance of ingredients that reach the GI tract and are accessible by the gut microorganisms of the host. These ingredients include macronutrients such as carbohydrates and proteins, micronutrients like vitamins, phenolic compounds, and minerals, but also bacterial components from the fermentation cultures, biogenic metabolites (organic acids, biogenic amines, etc.), or even live microorganisms (probiotics) that interact with the human microflora located in the gut ^[50][135]. The daily intake of fermented food and beverages ranges between 5% and 40% depending on the geographic area. Viable bacteria from fermented foods along with foodborne microbes from other food sources may reach up to 1.0% of the commensal gut microbiota (10¹⁰ to 10¹¹ ingested bacteria per day). These transient microorganisms are eliminated through feces, but can also adhere to the GI tract and eventually alter the gut microbial composition ^[2][46][2,131]. Fermented foods enrich the diverse intestinal microbiome, mainly with gram-positive bacteria belonging to the Firmicutes and Actinobacteria phyla, such as Lactobacilli, Lactococci, Streptococci, Enterococci, Carnobacteria, Bifidobacteria, Brevibacteria, and Propionibacteria, and some yeast and fungi species (Saccharomyces, Kluyveromyces, Debaryomyces, Penicilium, etc). Subsequently, dietary habits may exhibit a strong effect on intestinal bacterial dynamics through the consumption of various viable microorganisms. The latter could have an inhibitory or stimulating effect on the gut autochthonous species ^[2][51][2,136]. Dietary choices may also alter the microbial balances in the gut, as is evident from data obtained from clinical studies testing various diets (western, plant-based, meat-based, Mediterranean, vegan, and vegetarian) ^[52][137]. Animal-based diets (low fiber content and high animal protein and fat) seem to decrease the population of Firmicutes and on the contrary, increase bile-tolerant species (Alistipes, Bilophila, and Bacteroides) ^[51][136]. Likewise, gluten-free diets increased the numbers of Enterobacteriaceae, i.e., E.coli and other potentially pathogenic bacteria ^[53][138]. Conversely, diets based on plant-based foods (vegan, vegetarian) or balanced diets (Mediterranean) were linked with higher counts on “beneficial” bacteria (Lactobacillus sps. and Bifidobacterium sps.) ^[54][139]. It should also be mentioned that these diets include elevated daily intakes of fibers, a better ratio of mono- and poly-unsaturated to saturated fatty acids (compared to animal food-based diets), and a variety of antioxidant compounds ^[52][137].