Agricultural and agro-industrial activities result in the production of large quantities of byproducts. These byproducts amount to approximately 998 million tons yearly [18]. They have different types and can be categorized based on their source and composition. One type of agricultural byproduct is field residue, composed of plant parts such as leaves, stalks, seed pods, and culms [19,20,21]. Agricultural byproducts are materials generated in large quantities during the processing of primary agricultural products. These byproducts can include materials from various industries, such as milling, oil, sugar, starch, fruit and vegetable, and fermentation industries. Byproducts from the milling industry, for example, can include bran, byproduct flour, residues from grain cleaning processes, wheat, corn, and rye germ. In addition, husks from certain seeds, such as pea, barley, and buckwheat, can be considered byproducts of the milling industry. These are examples of various byproducts from different industries that can be used in animal feed production. For instance, the residual materials of the oil industry, like cakes obtained from soybean and oil-producing rapeseed, sunflower, and flax products, along with lecithin and fatty acids resulting from the refining of vegetable oils, can be used in the production of animal feed. Similarly, residual materials from the sugar industries and starch industries, including beet pulp, molasses, potato pulp, potato cell juice, and other seed residues after starch extraction, as well as byproducts from the fruit and vegetable industry, such as products that result from the peeling of vegetables, apples, avocados, grapes, pomace, and fruit stones, can also be used in animal feed production. Additionally, byproducts of the fermentation industry, including grain, molasses, soluble potato distillery, brewer’s and wine’s yeast, bacterial and fungal biomass, spent grains, and malt germ in breweries, can be used in animal feed production [19].

Commonly found anti-nutritional factors are presented in Table 1. Anti-nutritional factors (A.N.F.s) are chemical substances in some feed ingredients that can negatively affect animal health, feed conversion, and production. A.N.F.s can impair the uptake, availability, or metabolism of nutrients in an animal and affect feed palatability, voluntary feed intake, and physiological control processes [22,23]. A.N.F.s are classified into two main categories: those impairing protein digestion and utilization (such as tannins, protease inhibitors, and lectins) and those that interfere with the utilization of minerals (such as gossypol, phytates, and glucosinolates). Other A.N.F.s include antivitamins and substances such as alkaloids, cyanogens, mycotoxins, mimosine, saponins, and phytoestrogens [24,25].

Gossypol is a toxic compound found in the cotton plant, with the highest concentration being in the cotton seeds. While cottonseed meals can be used as components of poultry diets, their use is often restricted due to gossypol and their low lysine content [26]. Free gossypol can bind to lysine and reduce its availability, harming growth performance and increasing broilers’ mortality. Therefore, it is essential to carefully consider the use of cottonseed meals in poultry diets and take measures to mitigate the potential adverse effects of gossypol [27,28].

Chitin is a complex carbohydrate that the digestive enzymes of poultry cannot break down. Nutrients in feed ingredients containing chitin can be limited in some products, such as shrimp byproducts, for poultry [29,30,31]. Shrimp byproducts are rich in nutrients, particularly protein, comparable to quality fishmeal, and relatively inexpensive. However, the presence of chitin in shrimp byproducts can be problematic as it binds to proteins and minerals in a way that limits availability [30,32].

Glucosinolates are a group of sulfur-containing phytochemicals commonly found in cruciferous vegetables and vegetables. In R.S.M. (rapeseed meal), the main glucosinolates are glucosamine, glucobrassicin, progoitrin, gluconapoleiferin, and glucobrassicin. These compounds can have positive and negative effects on animal health, depending on their level and the animal species being fed [33,34]. Phytic acid, or myoinositol hexaphosphoric acid, is a compound found in grains, legumes, nuts, and seeds [35]. It is the stored form of phosphorus in these foods. However, phytic acid is considered an anti-nutritional factor since it can form insoluble complexes by binding with proteins and minerals. This interaction can lead to alterations in protein solubility and structure, making them less available for absorption in the gut in both humans and animals [36].

Tannins are polyphenolic compounds with high molecular weights that can be grouped into condensed or hydrolyzable tannins. The majority of tannins in canola are condensed tannins [37]. Tannins can decrease nutrient bioavailability by forming indigestible and bitter-tasting complexes with proteins [38]. Rapeseed meal (R.S.M.) contains anti-nutritional components such as glucosinolates, phytic acid, and fiber, which can limit its nutritional value and palatability. As a result, R.S.M. is used in limited amounts in animal feed [39]. Similarly, rapeseed meal contains nutritionally inhibiting factors, including phytates, glucosinolates, tannins, and crude fibers, which can affect a broiler’s feed utilization [40].

Cyanogenic glycosides (C.G.s) comprise a type of organic compound, containing cyanide, commonly found in various plants such as almonds, wheat, barley, sorghum, cassava, apples, and flaxseed [41]. Linseed meal (F.S.M.) is a novel protein source in animal farming that contains several beneficial nutrients. However, it also contains nutritional inhibitors, such as cyanogenic glycosides, phytic acid (P.A.), and antivitamin B6 (VB6), that can adversely affect animal health and limit the use of F.S.M. in animal nutrition. The antivitamin B6 in F.S.M. is a dipeptide composed of glutamine and proline with a concentration of approximately 177,437 g/g. This antivitamin B6 factor can bind to the enzyme formed after VB6 phosphorylation, which causes the enzyme to lose its physiological role and impairs the utilization and absorption of vitamins by animals, leading to Vitamin B6 insufficiency [42].

Non-starch polysaccharides (N.S.P.s) such as mannan, xylan, and cellulose in poultry feed limit the digestibility of the basal diet. Palm kernel cake (PKC) use in monogastric animal feeds has been limited due to high N.S.P. concentrations and high content of coarse texture, crude fiber, and sandy appearance. It is also stated that PKC comprises 35.2% mannan [43,44]. The indigestible portions comprise N.S.P.s, consisting of mannan (78%), cellulose (12%), arabinoxylans (3%), and water-insoluble glucoxylans (3%) [45]. Because of the adverse effects observed in poultry, palm-kernel-cake dietary intake should not exceed 40% [45,46]. Feedstuffs such as soybeans, wheat, barley, and rapeseed meal contain vast amounts of N.S.P.s, but poultry lacks endogenous N.S.P. hydrolase. The soluble N.S.P. in the feed increases the digestive viscosity of the small intestine broiler and decreases the digestibility of nutrients [47].

Phytate is a compound that serves as the primary storage form of phosphorus in many plants, particularly in bran and seeds. However, phytate can also hinder the absorption of other minerals in addition to phosphorus. Soy meal, a byproduct of soybean oil extraction, is a commonly used animal feed, particularly for poultry. This meal contains a variety of anti-nutritional factors, including protease inhibitors, phytic acid, lectins, saponins, phytoestrogens, and antivitamins [25].

Table 2 presents the role of biological treatments on reducing antinutritional factors from agricultural byproducts. The nutrient availability and digestibility of feed and agro-industrial byproducts can be impaired by the presence of anti-nutritional factors (A.N.F.s) such as hydrocyanic acid, oxalates, phytates, tannins, polyphenols, and saponins [55]. Different methods, such as biological (microbial) processes, have been used to enhance the nutritional quality and decrease the quantities of A.N.F.s. Chemical and mechanical processes are costly and labor-intensive, whereas microbial fermentation is a more affordable and safer alternative for improving the nutrient content of agro-industrial byproducts. The abundance and composition (cellulose, hemicellulose, and lignin) of agro-industrial byproducts make them an attractive option for recycling and fermentation through microbial fermentation as a viable alternative for product management [55]. Solid-state fermentation (S.S.F.) is a type of biological fermentation that involves cultivating microorganisms on humid, compact, insoluble biological ingredients. These materials serve as nutrient bases for the microorganisms to grow, and the process occurs in the absence or near-nonexistence of free-flowing water [32,56].

S.S.F. has been found to reduce A.N.F.s, which are bioactive compounds that affect the bioavailability and bio-digestibility of nutrients in feed, thereby improving the bioavailability and digestibility of nutrients in agro-industrial byproducts [57]. Both filamentous fungi such as Trichoderma reesei, Trichoderma viride, Rhizopus oligosporus, Aspergillus niger, Mucor racemosus, Rhizopus arrhizus, Rhizopus oryzae, Mucor rouxii, Penicillium oxalicum, Penicillium viridicatum, and Fusarium oxysporum as well as yeasts such as Saccharomyces boulardii, Saccharomyces cerevisiae, Candida sphaerica, Candida tropicalis, Candida stellate, and Candida are commonly used in S.S.F. Bacteria such as Bacillus mycoides, Bacillus megatherium, Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus plantarum, and Lactobacillus rhamnosus have also been used in S.S.F. [32,56].

Several studies have demonstrated the effectiveness of S.S.F. in the biological detoxification of and reduction in the quantities of A.N.F.s in agro-industrial byproducts using filamentous fungi, yeast, and bacteria [58]. However, it has been reported that fermentation can also increase the levels of A.N.F.s in feedstuff components, such as glucosinolates in rapeseed meal; lectins and trypsin inhibitors in soybean meal; tannins, hemagglutinins, and prosopin in prosopean meal; and phytate in corn [59,60]. Despite this, some studies have shown that S.S.F. can decrease the levels of A.N.F.s in animal feed. For example, Oboh [48] found S.S.F. using a mixed culture of Lactobacillus spp and Saccharomyces cerevisiae, significantly decreased phytate and cyanide levels in fermented cassava peel compared to not-fermented peel, which contained higher concentrations of these A.N.F.s. In another study, Bacillus subtilis, Candida utilis, and Enterococcus faecalis were found to degrade phytic acid, glucosinolate, and tannin in rapeseed meal under S.S.F., resulting in reductions of 20%, 96%, and 36%, respectively [61]. Overall, S.S.F. is a practical approach to reducing A.N.F. quantities in animal feed production. It can significantly benefit both the animals and the farmers who rely on them for their livelihoods.

Aspergillus niger is known to produce Phytase during fermentation, which releases the protein trapped in rice bran by hydrolyzing the phytic acid and making it easier to digest. Additionally, anti-nutritional factors (A.N.F.s) in animal feed can produce intermediate products that decrease the presence of essential nutrients [62]. However, solid-state fermentation (S.S.F.) treatment with microorganisms can reduce the harmful effects of A.N.F.s. For instance, S.S.F. with Lactobacillus fermentum, Enterococcus faecium, Saccharomyces cerevisiae, and Bacillus subtilis reduced the amount of isothiocyanate in rapeseed meals from 119 to 14 mmol/kg after 30 days [63]. Similarly, other studies have documented a reduction in isothiocyanate levels after S.S.F. [64]. In one study, glucosinolates, isothiocyanate, phytic acid, and tannins were reduced from 41.91 to 23.86 mol/g, 2.48 to 1.10 mg/g, 2.66% to 0.37%, and 1.32% to 0.84%, respectively [65]. The reductions in glucosinolate content may have been due to the utilization of glucose and the sulfur portions of these compounds by microbial enzymes [66,67]. The reduction in phytic acid can be attributed to microbial enzymes such as Phytase produced during S.S.F.

S.S.F. with the bacterial degradation of A.N.F.s in rapeseed flour using the enzyme myrosinase can degrade glucosinolates and release several derivatives [67]. Additionally, in some studies, S.S.F. significantly decreased the amount of free gossypol and A.N.F. Tang et al. [68] found that free gossypol was reduced from 0.82 to 0.21 g/kg in solid fermented cottonseed meal. Similarly, in another study, free gossypol decreased from 90 to 30 mg/kg [69]. The reduction in free gossypol content during S.S.F. may have been due to the binding of free gossypol to proteins or amino acids produced by microorganisms, the degradation of gossypol by microbial enzymes, or both mechanisms.

The fermentation process for shrimp byproducts can be carried out using a stepwise fermentation technique with Bacillus licheniformis, Lactobacillus sp., and yeast in the form of Saccharomyces cerevisiae. Bacillus licheniformis bacteria produce chitinase and protease enzymes with deproteinizing properties that release nitrogen or protein from chitin bonds [30,31]. Saccharomyces cerevisiae is a yeast that produces enzymes such as amylase, lipase, protease, and others that can aid in the digestion process of feed in the digestive organs [70]. After deproteinization and demineralization, proteins and minerals bound to chitin can be broken down, allowing a chicken’s digestive system to digest this protein [70,71]. In a study, the phytate and tannin content of biotransformed peanut shells was also significantly reduced [7]. The decrease in tannin and phytate content in the byproduct material during S.S.F. may have been due to the ability of the test fungi to produce Phytase. Phytase is an enzyme that breaks down phytate, i.e., phosphorus, in many plant-based foods. Conversely, tannins can also be degraded by certain microorganisms or their enzymes during S.S.F.

Table 3 presents the role of microbial fermentation in improving the chemical composition of agricultural byproducts. Biotransforming microorganisms have been shown to enhance chicken feed’s chemical composition and nutritional value [79]. Purwadaria et al. [80] also reported that the fermentation of agricultural byproducts improved their nutritional value. Nutrient bioavailability has been improved using solid-state fermentation (S.S.F.) while reducing anti-nutritional agents. For S.S.F. to increase nutrition, several microbes have been used, primarily Lactobacillus, Bacillus, and Aspergillus strains. Aspergillus can produce enzymes such as hemicellulase, pectinase, protease, lipase, amylase, tannase [81,82], and Phytase [83,84]. The bacterium Lactobacillus produces Phytase, cellulase, xylanase, and glucanase [85]. Bacillus can synthesize cellulase and Phytase [86]. In a study utilizing Aspergillus niger to determine the impact of S.S.F. on the nutrient content of rice bran, Hardini [87] found that the nutrient composition of fermented rice bran had significantly increased. For determining the nutritional value of fermented feed, it is vital to consider the crude protein content, pH level, and the number of bacteria [88].

Lu et al. [89] reported that microbial fermentation increased levels of organic acids (citric, succinic, and butyric), amino acids (Ser, Gly, Cys, Leu, Lys, His, and Arg), crude protein, and levels of neutral and acidic Detergent fibers in soybeans and other flour types. The findings demonstrated that fermentation by microorganisms altered the feed’s chemical makeup and boosted certain nutrients.

Guo et al. [79] showed that microbial fermentation increased the C.P. content of the substrate substantially. This could have been because the relative concentration of other nutrients rises due to the dry matter loss in fermented feed, particularly the loss of carbs. The breakdown of macromolecular proteins, primarily antigenic proteins, may have contributed to the rise in C.P. [90]. The microbial fermentation of S.B.M. eliminates A.N.F.s and increases nutritional value [79,91]. It was noticed that the quantity of glucan, phytic acid, and crude fiber decreased following fermentation with the probiotic agent. This might have been because those antinutrient substances are broken down by similar enzymes, like Phytase and cellulase, that are produced. The crude protein level was doubled in the biotransformed crop residues using endophytic fungi [7]. The rise in crude protein could be attributed to the fungi’s production of mycelial proteins or the fermenting fungus’s growth, breaking down complex polysaccharides into single-cell proteins (S.C.P.) [92].

The extracellular enzymes—amylases, cellulases, xylanases, and pectinases—secreted by fungi to use complex polysaccharides may be the reason for the processed material’s higher protein concentration [93,94]. It was also found that the quantities of total carbohydrates are increased, showing that hexoses are released due to Togninia spp—an example of extracellular protease synthesis [7].

Crude protein in rapeseed meals rose from 37.1% to 58.4% after solid-state fermentation (S.S.F.) with Lactobacillus plantarum and Bacillus subtilis [95]. Similarly, Bacillus subtilis, Candida utilis, and Enterococcus faecalis inoculation increased the crude protein level from 42.11% to 44.63% [61]. The drop in T.S. content and the extra microbial protein produced during S.S.F. were responsible for the rise in crude protein levels. Likewise, S.S.F. caused a decrease in rapeseed meal’s dry matter content (D.M.) [63]. The decrease in the T.S. content could be due to the sugar consumption of the microorganisms. Adding Lactobacillus plantarum and Bacillus subtilis to S.S.F. rapeseed meal improved its crude fat content [95]. A similar result was observed by [64] when Bacillus subtilis and Lactobacillus fermentum were tried out. The increase in fat can be partly attributed to the reduction in the quantity of carbohydrates during S.S.F. In contrast to these studies, the authors of [65] reported that the S.S.F. of rapeseed meals employing Aspergillus niger resulted in lower crude fat. Overall, variations in the solid fermented rapeseed meal’s crude fat content may occur due to factors like oil processing techniques, feed source, and microorganisms utilized.

According to Bidura et al. [53], fermentation increased rice bran’s crude protein content and metabolizable energy. Fermented rice bran has a more excellent crude protein content and ether extract due to Phytase and microbial biomass. Hardini [96] conducted a study using Aspergillus niger to determine the effect of fermentation in the soil on the nutrient content of rice bran and discovered a considerable enhancement of fermented rice bran’s nutritional profile. The nutritional and energy profile of agricultural wastes is improved by fungal bioconversion. Endophytic fungi can convert the selected residues of agriculture into digestible hexoses, considerably increasing the concentration of protein and nitrogen. The most significant amounts of total carbs, total proteins, and digestible lipids are found in biotransformed peanut shell residue [7].

Shrimp waste products treated by fermentation showed increased quality and palatability in rations [82,97]. Haddar et al. [83] and Saleh et al. [31] also reported that the processing of shrimp waste products and olive cake flour using the microorganism Bacillus licheniformis and yeast in the form of Saccharomyces cerevisiae makes protein independent of the limiting factor in the form of chitin, increasing the nutritional value—namely, increasing the protein content in shrimp as a product and improving its palatability.