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Review

Fermentation of Organic Wastes for Feed Protein Production: Focus on Agricultural Residues and Industrial By-Products Tied to Agriculture

by
Dan He
1,2,* and
Can Cui
2
1
Fisheries College, Ocean University of China, Qingdao 266003, China
2
College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China
*
Author to whom correspondence should be addressed.
Fermentation 2025, 11(9), 528; https://doi.org/10.3390/fermentation11090528
Submission received: 5 August 2025 / Revised: 5 September 2025 / Accepted: 8 September 2025 / Published: 10 September 2025
(This article belongs to the Special Issue Valorisation of Agro-Industrial By-Products Through Fermentation or Eco-Friendly Techniques)
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Abstract

Global population growth and dietary transition have intensified demand for livestock and aquaculture products, thereby escalating demand for high-quality animal feed. Conventional protein sources, including soybean meal and fishmeal, face severe supply constraints driven by intense competition for arable land, worsening water scarcity, overexploitation of fishery resources, and rising production costs. These challenges are especially pronounced within agricultural systems. Evidence demonstrates that converting agriculturally derived organic wastes and agri-industrial by-products into feed protein can simultaneously alleviate these pressures, address agricultural waste disposal challenges, and reduce the carbon footprint associated with agricultural production. This review synthesizes fermentation processes for generating feed protein from agricultural organic wastes by employing functionally adapted microorganisms or microbial consortia. This distinguishes it from prior studies, which focused solely on single waste streams or individual microbial strains. It aims to advance feed protein production through an integrated approach that unites agricultural organic wastes, microorganisms, and fermentation processes, thereby promoting resource-oriented utilization of agricultural organic wastes and providing actionable solutions to alleviate feed protein scarcity.

1. Introduction

Sustained global population growth, along with rising living standards, has steadily increased demand for livestock and aquatic products [1,2]. This trend has spurred large-scale expansion in the aquaculture and livestock sectors, thereby driving further growth in feed demand. Protein is a critical nutrient in animal feed, as it fundamentally influences animal growth, development, reproduction, and productivity [3]. However, conventional feed protein sources such as soybean meal and fishmeal face pronounced supply constraints, and this imbalance has directly hindered the stable expansion of the breeding industry, particularly in agricultural production systems. To address this challenge, studies have confirmed that converting agriculture-derived organic wastes and agri-industrial by-products into feed protein is a feasible solution [4,5].
Notably, this aforementioned conversion aligns with the biorefinery concept, a sustainable bio-based production model that transforms biomass (e.g., agricultural organic wastes) into multiple high-value products rather than a single output [6]. Among available conversion methods, fermentation has emerged as a promising technical route, with numerous studies exploring its application in converting diverse organic wastes into feed protein [7]. The underlying mechanism relies on the ability of microorganisms, specifically bacteria, yeast, and fungi, to assimilate nutrients (e.g., carbon sources) in organic waste, synthesize proteins through their own metabolism, and accumulate biomass in the waste matrix. This process thus represents a key pathway for protein conversion via fermentation technology [8]. Notably, microbial protein produced via this fermentation process exhibits nutritional equivalence to conventional sources such as fishmeal and soybean meal [9,10]. This nutritional parity provides a critical rationale for its potential as a substitute for conventional protein sources, directly meeting the growing demand for sustainable alternatives in animal feed. Furthermore, fermentation significantly improves the palatability and digestibility of the resulting feed protein, making it more suitable for animal consumption and highlighting the advantages of using fermentation to produce feed protein through organic waste valorization [11,12].
Against this aforementioned backdrop, this narrative review summarizes recent research since 2021 on fermentative conversion of agricultural organic waste into feed protein. The literature analyzed in this review was retrieved from the Web of Science database using the keywords “organic waste”, “fermentation”, and “feed protein”. This review identifies agriculturally relevant organic waste streams utilizable by bacteria and fungi, assesses their application in corresponding waste matrices, and synthesizes the associated fermentation processes. Its objective is to expedite the practical implementation of fermentation technology for converting organic waste into feed protein in agricultural production systems.

2. Fermentation of Agricultural Organic Wastes into Feed Protein

The massive generation of agricultural organic waste now poses a threat to global agricultural sustainability and food security [13]. Such waste, including crop straw and agricultural processing by-products, occupies land resources and poses risks of environmental pollution. However, converting these organic wastes into high-protein feed via fermentation facilitates resource recycling within agricultural systems and effectively reduces carbon footprints, thereby promoting the development of green, low-carbon agriculture [14]. As a bioconversion method, fermentation degrades indigestible macromolecules (e.g., cellulose) into small molecules, enhances nutritional value, increases protein content, and renders these wastes as high-quality raw materials for animal feed [15]. Current technologies for fermentative feed protein production mainly include solid-state fermentation (SSF) and liquid fermentation, with SSF being particularly prominent for agricultural wastes given its suitability for high-solids heterogeneous residues [16]. A comprehensive review of recent studies indicates that a wide range of agricultural residues, including cotton residue, corn stover, wheat straw, honeysuckle residues, chrysanthemum waste, lotus seedpod, cottonseed shells, bagasse, peanut vine, rice straw, cauliflower wastes, macadamia green peel, tea residue, fresh sweet corn processing by-products, peanut meal, wheat bran, palm kernel cake, corncob, and citrus pomace, can be successfully valorized via this fermentation mode [17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36]. Microorganisms involved in this valorization act via mechanisms such as lignocellulose degradation and small-molecule sugar utilization to convert wastes into feed protein, thereby providing a visual framework for understanding substrate–microbe synergies (Figure 1).
To elaborate on the fermentation processes detailed in Table 1, a comparative assessment across agricultural waste categories reveals clear trade-offs between protein yield, processing time, strain complexity, and substrate availability. Fungal monocultures achieve the highest protein gains when applied to high-lignocellulose crop straws, including wheat straw, corn stover, and rice straw. SSF of wheat straw with Inonotus obliquus for 15 d increases crude protein (CP) by approximately 132% [17]. White-rot fungi supplemented with molasses or glucose enhance CP in corn stover and rice straw, respectively, over 14 d, offering low strain complexity and reliance on abundant straw substrates [18]. Composite systems incorporating microbes plus enzymes display variable efficacy. A consortium of Candida utilis, Lactobacillus plantarum, and non-starch polysaccharide enzymes raises CP content in corn stover by 11.8% and in wheat straw by 86.7% after 30 d, combining low strain complexity with continued compatibility with straw substrates [19]. Mixed-straw systems, such as ensiled corn stover and peanut vine (mixed at a 3:1 ratio) inoculated with Lactobacillus plantarum and Enterococcus faecalis followed by compaction at 450–600 kg/m3, increase CP by 2.46–2.78%, supporting farm-scale applicability [20]. Agricultural processing by-products exhibit substrate-specific trends. Cotton residue fermented with bacterial monocultures of Paenibacillus sp. F4 and Cohnella xylanilytica T5 elevates true protein by 89.44–96.90%, demonstrating low complexity and moderate substrate availability [21]. Citrus pomace co-fermentation with Bacillus amyloliquefaciens BF2 and Candida utilis GIM 2.9 achieves a 40.01% CP gain, outperforming Aspergillus niger monoculture at 27.22% [22,23]. Macadamia green peel co-fermentation with Limosilactobacillus fermentum ZC529 plus cellulase increases CP by 8.80%, illustrating enzyme–microbe synergy on a niche substrate [24]. Tea processing by-products blended with wheat bran and fermented with Lactiplantibacillus plantarum and Bacillus licheniformis yield a 2.38% relative CP gain over 5 d, complementing the 34.48% gain observed in chrysanthemum waste using mixed cultures [25,26]. Starch and oilseed by-products benefit from staged or composite approaches. Peanut meal (PNM) subjected to two-stage fermentation with Bacillus velezensis LB-Y-1 followed by Pediococcus acidilactici LC-9-1 increases CP by 6.70% [27]. Enzymatically hydrolyzed palm kernel cake fermented with Saccharomyces cerevisiae reaches 27.31% CP [28]. Sweet corn by-products comprising corn husks, corn cobs, and broken corn kernels mixed with wheat bran at a 9:1 or with millet hull at an 8:2 ratio and ensiled with Lactobacillus plantarum LP1 at 5 × 106 CFU/g for 45 d at 20–25 °C achieve CP gains of 7.87% and 11.75%, respectively [29], building on the 5.33% gain observed in cauliflower waste fermented with Lactobacillus plantarum [30]. Lignocellulosic by-products require pretreatment. Corncob subjected to sulfuric acid pretreatment plus enzymatic hydrolysis and fermented with Rhodotorula glutinis As2.703 yields 74.77 g protein/kg substrate, surpassing the 16.8% CP gain reported for sugarcane bagasse using a mixed microbial consortium and enzymes with 0.5% urea (DM basis) [31,32]. Wheat bran, after being co-cultured with Aspergillus niger and Trichoderma reesei followed by hydrolysis, exhibits a 48.08% increase in CP content [33]. Notably, the resulting CP-enriched residual biomass (i.e., fermented wheat bran) also has increased sugar and fat contents, and its nutritional properties are significantly improved. For instance, the energy content for ruminants is elevated from 9.69 to 12.52 MJ/kg. These improvements thus make it a high-quality alternative feed source for ruminants.
Critical evaluation reveals both strengths and unresolved gaps in these strategies. Fungal systems excel at lignocellulose degradation. Inonotus obliquus and white-rot fungi not only elevate CP but also improve essential amino acid profiles and in vitro digestibility, mitigating limitations inherent to high fiber waste [17,18]. The Aspergillus niger and Trichoderma reesei combination further confirms fungal capacity to release lignocellulosic carbon for protein synthesis [33]. Bacterial and composite systems provide dual functionality. Aspergillus oryzae TM-1 degrades 78.7% of gossypol in cottonseed hulls while increasing CP from 12.5% to 15.5% [34]. Limosilactobacillus fermentum ZC529 plus cellulase decreases anti-nutrients in macadamia green peel and raises CP [24]. Staged systems such as the two-stage bacterial fermentation of peanut meal optimize nutrient use [27]. Economic viability remains unquantified. Molasses or glucose supplements for white-rot fungi and enzymes in composite systems improve yields but add costs, and no techno-economic analysis (TEA) balances inputs and outputs [18,19,24]. Furthermore, it is recommended to refer to reported research findings on wheat straw [17], including data on digestibility and amino acids, and to expand the dimensions of protein quality assessment in the process of feed protein development.
Key limitations hinder industrial translation, beginning with substrate heterogeneity. Costly substrate-specific pretreatments such as sulfuric acid for corncob generate inhibitors including furfural and compromise process stability [31]. Scale-up challenges also persist. Laboratory success relies on pure microbial consortia, for example, the co-culture of Bacillus amyloliquefaciens BF2 and Candida utilis GIM 2.9, which efficiently ferments citrus pomace to enhance nutritional quality [22]. However, scaling to industrial bioreactors (e.g., 1000 L) faces performance attenuation; for instance, the total sugar concentration in wheat bran hydrolysate decreases from 32.3 g/L (25 L lab scale) to 24.4 g/L (1000 L industrial scale) due to non-geometrically similar reactor configurations and reduced oxygen transfer efficiency [22,33]. Additionally, SSF processes, even in controlled lab-scale systems (e.g., 250 mL flasks), require strict control of humidity (70%) and temperature (30 °C) to maintain product uniformity; scaling SSF introduces challenges in maintaining consistent microenvironments, which can compromise the stability of key nutrients such as those in citrus pomace [22]. Safety and regulatory gaps further constrain its application. Currently, there is no consensus on safe post-fermentation thresholds for anti-nutrients (e.g., gossypol in cottonseed hulls) [34], nor on standardized parameters such as inoculum size and moisture content. For instance, Aspergillus niger, widely used in wheat bran fermentation [33], is a well-established strain in the food and feed industry; however, the lack of unified standards for its process parameters still limits large-scale application. Tailored operating conditions including medium-low temperatures of 20–25 °C, carbon source supplementation, and inoculum optimization are essential to limit nutrient loss during fermentation [18,35,36]. Overcoming these limitations through substrate-agnostic pretreatment, integration of TEA, and establishment of safety standards will unlock the potential of fermentation for sustainable agricultural waste to feed conversion.

3. Fermentation of Agri-Industrial By-Products into Feed Protein

Agri-industrial by-products, arising from raw material processing and brewing, present major environmental challenges yet offer substantial resource recovery potential. Alcohol production, including Baijiu (Chinese liquor) and beer manufacturing, generates over 100 million tonnes of distillers’ grains annually. Typical examples include Chinese distillers’ grains (CDGs) and distillers dried grains with solubles (DDGS). This volume positions these residues as a primary focus for protein enhancement research [37,38,39]. Beyond brewing, olive pomace (OP) from olive oil extraction and oilseed meals such as defatted cottonseed meal (DCSM) add millions of tonnes of waste each year, necessitating sustainable treatment strategies comparable to those applied to distillers’ grains [40]. Microbial fermentation has emerged as a pivotal technology that both elevates the nutritional value of these by-products for feed protein and enables circular resource use within agricultural value chains.
Figure 2 illustrates microbial substrate interactions and Table 2 classifies major agri-industrial by-products with their corresponding fermentation technologies [41,42,43,44,45,46,47,48,49,50,51,52,53]. These technologies cover fermentation modes, microbial strains, and operational parameters. The information in Table 2 systematically clarifies how these components drive feed protein synthesis. Practical applications highlight the need for substrate-specific strategies. Organic waste liquid such as wasted date molasses (WDM) and corn steep liquor (CSL) are suitable for liquid fermentation to produce protein, achieving CP contents of 54.30% and 70.18%, respectively [41,42]. Fiber-dense substrates such as OP and DCSM require fungal or consortium approaches. Fermentation of olive pomace with oyster mushroom (Pleurotus ostreatus) raises crude protein from 61.4 g/kg DM to 79.9 g/kg DM and improves ruminal in vitro organic matter degradability from 182 g/kg DM to 361 g/kg DM, while mitigating environmental concerns associated with OP waste disposal [43]. A consortium of Saccharomyces cerevisiae, Enterococcus faecium, and Lactiplantibacillus plantarum boosts DCSM protein by 1.14-fold [44]. Collectively, these processes yield CP increases of 14.6% to 96.3% and confirm fermentation’s role in valorizing agri-industrial wastes [41,42,43,44,45,46,47,48,49,50,51,52,53]. SSF has evolved into a versatile platform for converting by-products such as DDGS, brewer’s spent grain (BSG), and DCSM into high-quality protein sources. Strategies differ markedly in performance and applicability according to substrate properties and desired outcomes. Thermophilic SSF exemplifies substrate-adaptive processing. Bacillus licheniformis CPB2 fermenting BSG-soybean meal co-substrates exploits inherent moisture of 80.98% to eliminate added water and achieves a 338.43% peptide increase within 24 h [45]. Conversely, fungal monocultures such as Aspergillus niger on DDGS with corncob mixtures deliver superior CP gains of 96.3% but require 7 d incubation [46]. Mixed microbial consortia and multi-stage processes offer additional flexibility. A 4-strain probiotic consortium fermenting distillers’ grains from Chinese Baijiu brewing enhances CP by 31.25% and reduces crude fiber content by 33.20%, whereas similar treatment of Chinese distillers’ grains yields a 23.61% CP increase and a 22.31% fiber reduction [47,48]. A two-stage protocol for BSG ammoniation, enzymatic hydrolysis, and fermentation balances a single-cell protein yield of 310 g/kg BSG with the co-production of prebiotic arabinoxylo-oligosaccharides at 80 g/kg but extends pretreatment to 26 h [49]. SSF also addresses enhancement concerns linked to OP disposal [43]. Substrate usability further differentiates strategies. Exploitation of inherent traits such as low anti-nutrient content in DCSM minimizes cost, whereas supplementation with beef extract for olive cake enhances performance yet restricts economic viability [50]. Despite strengths, current strategies face three critical barriers to industrial translation. Methodological inconsistencies, laboratory-scale bias, and strain selection constraints limit progress. Reliance on the Kjeldahl method for CP quantification overestimates nutritional value by including non-protein nitrogen such as residual ammonia from BSG ammoniation and fungal chitin in OP fermentation. Few studies measure true protein via Bradford assay or in vivo digestibility, impeding cross-study comparisons. Laboratory-scale bias persists as most validations employ shake flasks or 7 L bioreactors. Data on scale-up challenges such as heat and moisture gradients in 400 g tray reactors and oxygen transfer for aerobic fungi remain scarce. Even when cellulase yields improve 55% at larger scales, industrial-critical metrics such as uniformity and contamination rates are unreported. Strain selection presents further constraints. Thermophilic bacteria grow rapidly but lack ligninolytic enzymes, restricting use on high-lignin substrates such as corncob. Addressing these gaps requires targeted innovations. Standardizing nutritional assessment through true protein quantification, amino acid bioavailability via pig or rumen in vitro models, and functional properties such as peptide antioxidant activity will align data with feed safety regulations. Validating scale-up technologies at pilot scales of 100 kg or more using continuous SSF reactors with automated moisture and oxygen control and vacuum drying for post-processing is essential. Modifying Aspergillus ibericus tray reactors with perforated trays to enhance aeration exemplifies scalable design [51]. Developing synthetic consortia such as Candida utilis combined with Aspergillus niger that integrate yeast rapid carbon utilization with fungal lignocellulolytic activity can optimize the nutritional quality of the DDGS–corncob mixture, with the optimal fermentation time determined as 10.5 d [52]. Tailoring strategies to regional by-product streams such as cassava residue in Southeast Asia and OP in the Mediterranean and adopting low-cost nitrogen sources such as poultry manure instead of beef extract for olive cake must be accompanied by life-cycle assessment (LCA) to quantify environmental impacts [43,53]. These advances will enable SSF to serve as a cornerstone of circular agriculture by reducing waste, lowering feed costs, and mitigating industrial environmental footprints.
WDM and CSL are high-sugar agri-industrial by-products that adopt distinct microbial strategies for protein production. Liquid fermentation of wasted date molasses with Hanseniaspora guilliermondii JQ690237 and Issatchenkia orientalis JQ690240 yields protein contents of 53% and 54.30%, respectively [41]. These yeasts exploit 73.12% reducing sugar to generate 700 g dry biomass/kg WDM within 48 h, yet the medium requires exogenous nitrogen supplements such as peptone or NH4Cl because intrinsic protein is low. CSL supports high-yield mycoprotein at 70.18% crude protein via liquid fermentation with Rhizopus microsporus var. oligosporus [42]. This fungus benefits from the balanced nutrients of CSL, is classified as a Biosafety Level 1 organism, holds Generally Recognized as Safe status, and produces no mycotoxin, aligning with its traditional application in tempeh. These attributes indicate that, after optimization, the mycoprotein can serve as a safe and sustainable alternative for animal feed and potentially for human food, while CSL can act as a sole medium. Growth of filamentous fungi extends fermentation to 96 h. Both systems exhibit critical limitations. First, reliance on the Kjeldahl method inflates protein values by including non-protein nitrogen such as residual ammonia in WDM and chitin or RNA in mycoprotein, without quantifying true protein or amino acid bioavailability. Second, scale-up data are absent for tray bioreactors used with WDM and for expanding the 14 L airlift system for CSL beyond 1000 L. Third, economic viability remains unvalidated through TEA or life-cycle assessment (LCA). Fourth, strain-specific constraints persist; WDM yeasts lack lignin-degrading enzymes and contain low methionine, whereas R. microsporus is mesophilic and slow-growing. Overcoming these barriers requires standardized nutritional evaluation, pilot-scale validation of at least 100 kg with integrated TEA and LCA, and targeted strain engineering such as expressing ligninase in yeasts and enhancing thermotolerance in R. microsporus. These measures will advance the industrial applicability of WDM and CSL fermentation systems for circular agriculture.

4. Others

Beyond conventional agricultural and agri-industrial by-products, plant-derived residues and leaf vegetable by-products represent two categories of underutilized agriculture-associated organic substrates that have shown promise as feedstocks for microbial fermentation-based feed protein production. SSF dominates processing for these materials owing to its compatibility with high lignocellulose recalcitrance and elevated moisture and organic matter contents, while also minimizing water use and promoting microbial colonization of heterogeneous matrices. Caragana korshinskii Kom. (CKK) waste exemplifies lignocellulosic residues [54]. A validated two-phase strategy comprises 30 d of Lactiplantibacillus plantarum LP1 fermentation followed by 30 d of SSF with the white-rot fungus Irpex lacteus F17, both conducted at 28 °C. Bacteria acidification suppresses pathogens and the fungal phase degrades lignocellulose, releasing fermentable sugars and increasing CP by 39.2%. Leaf vegetable waste such as cabbage waste is treated by single-phase SSF using a consortium of Saccharomyces cerevisiae, Bacillus subtilis, and Lactiplantibacillus plantarum with 15% soybean meal, 15% corn flour, and 15% wheat bran as supplements. Incubation at 30 °C for 15 d enables the microbial consortium to utilize both simple and complex carbohydrates, which not only stabilizes protein yield but also results in a relative increase of over 20% in CP [55]. These studies demonstrate that tailored microbial consortia and process designs can valorize uncommon agricultural wastes and broaden the scope of sustainable feed protein production.
The two fermentation systems outlined above represent distinct paradigms optimized for their respective substrates and exhibit clear contrasts in phase design, microbial interactions, and process outcomes. The two-phase strategy developed for CKK waste, a lignocellulose-rich forestry by-product, elevates CP by 39.2% and simultaneously reduces lignin, total phenols, and tannic acid by 24.4%, 52.2%, and 51.4%, respectively. This performance is achieved through a sequential mechanism in which an initial probiotic-dominant microenvironment with 95.7% probiotic abundance suppresses pathogens such as Aspergillus and Nocardiopsis, followed by lignin degradation mediated by I. lacteus F17. For cabbage waste, a moisture-rich and readily degradable substrate, a single-phase protocol operating at 30 °C for 15 d with 62% moisture and no pH adjustment employs the same yeast–bacteria consortium. This system delivers a 29.5% increase in CP by day 5 and generates favorable sensory and safety indices including 63.4 g/kg dry matter (DM) lactic acid and 66.3 g/kg DM ethanol, and a Flieg’s score of 87. A trade-off between performance and practicality is evident. The two-phase CKK system offers superior nutrient enhancement and anti-nutritional reduction but demands double the processing time and more elaborate control, whereas the single-phase cabbage system prioritizes speed and simplicity at the expense of slightly lower CP gains. Both feeds comply with safety standards, with mycotoxin levels in CKK-derived feed within GB 13078-2017 [56] limits and ammonia-N below 5% in cabbage-derived feed together with effective pathogen inhibition. Nonetheless, three critical limitations hinder industrial translation. First, substrate specificity is pronounced. Extension of the two-phase strategy to other forestry residues such as pine needles, which contain high resin acids, will require adjusted consortia or alkali pretreatment, while the single-phase protocol necessitates dewatering when handing drier vegetable by-products such as carrot pomace. Second, economic viability remains unverified. Both systems depend on expensive pure inocula and temperature control, further undermining feasibility. Third, long-term safety concerns persist, including unevaluated risks of mycotoxin re-synthesis during storage, accumulation of microbial metabolites (such as biogenic amines produced by S. cerevisiae), and absence of data on microbial community stability across repeated batches—all of these factors are essential for maintaining consistent feed quality at industrial scale.

5. Conclusions and Perspectives

Microbial fermentation employing bacteria and fungi has become central to converting agricultural and agri-industrial organic wastes into feed protein. The dominant bacteria are Gram-positive bacteria, including those from the families Bacillaceae, Lactobacillaceae, Enterococcaceae, Pediococcaceae, and Cellulomonadaceae. Lactic acid bacteria such as Lactobacillus plantarum and Lactiplantibacillus plantarum together with Bacillus species including Bacillus amyloliquefaciens and Bacillus subtilis drive substrate degradation through robust metabolism and abundant extracellular enzymes, effectively processing residues and by-products. Fungi comprise Ascomycete yeasts such as Candida utilis and Saccharomyces cerevisiae, molds such as Aspergillus oryzae and Aspergillus niger, Basidiomycete white-rot fungi such as Phanerochaete chrysosporium and Irpex lacteus F17, and edible species such as Pleurotus ostreatus. These organisms transform complex substrates by secreting cellulases, ligninases, and other enzymes while accumulating microbial protein. Applications therefore favor SSF complemented by liquid fermentation, using single-strain or multi-strain systems. This alignment of process and organism ensures efficient waste decomposition and elevated protein synthesis, providing an economically viable route for agricultural waste valorization and sustainable feed protein production.
While current research focuses on the protein enrichment of agricultural residues and industrial by-products tied to agriculture via microbial fermentation, increasing crude protein content alone cannot guarantee an improvement in feed value. Effective utilization also depends on palatability and the bioavailability of essential nutrients. Consequently, future research should pursue four integrated priorities. First, screen and engineer microorganisms that not only synthesize protein efficiently across diverse substrates but also enhance nutrient bioavailability and mitigate anti-nutritional factors that impair palatability. Second, combine solid-state and submerged fermentation to exploit complementary strengths while deploying precision control systems for real-time regulation of pH, temperature, and dissolved oxygen to secure uniform protein content and quality attributes. Third, investigate microbe–substrate interactions that modify palatability, for example, by degrading bitter phenolics, and improve mineral and amino acid availability to guide process optimization. Fourth, validate these advances through comprehensive nutritional, sensory, and safety assessments under pilot and industrial conditions. Such a holistic approach will establish fermentation as a cornerstone of circular agriculture by reducing reliance on conventional protein sources, enhancing nutrient cycling, and delivering feed ingredients that satisfy both nutritional and sensory criteria, thereby supporting global food security.

Author Contributions

Conceptualization, D.H. and C.C.; investigation, C.C.; writing—original draft preparation, writing—review and editing, visualization, supervision, project administration, and funding acquisition, D.H. All authors have read and agreed to the published version of the manuscript.

Funding

This work was financially supported by the Qingdao Postdoctoral Project Grant (No. QDBSH20240102037) and Heilongjiang Province Education Department Fundamental Scientific Research Funds (No. 145209320).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

No new data were created or analyzed in this study. Data sharing is not applicable to this article.

Conflicts of Interest

The authors declare no conflicts of interest.

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Fermentation 11 00528 g001
Figure 1. Schematic illustration of the conversion of diverse agricultural organic wastes into feed protein through fermentation by specific bacteria and fungi. Distinct categories of agricultural organic wastes, namely, crop straws, fruit shells and peels, processing by-products, and residues, are fermented by corresponding microorganisms to produce feed protein.
Figure 1. Schematic illustration of the conversion of diverse agricultural organic wastes into feed protein through fermentation by specific bacteria and fungi. Distinct categories of agricultural organic wastes, namely, crop straws, fruit shells and peels, processing by-products, and residues, are fermented by corresponding microorganisms to produce feed protein.
Fermentation 11 00528 g001
Fermentation 11 00528 g002
Figure 2. Schematic illustration of the conversion of diverse agri-industrial by-products into feed protein via fermentation using specific bacteria, fungi, and molds. Distinct categories of agricultural organic wastes, namely, high-concentration organic waste liquid, fruit shells and seed meals/cakes, distillers’ grains, as well as root, tuber, and legume by-products, are fermented by corresponding microorganisms to produce feed protein.
Figure 2. Schematic illustration of the conversion of diverse agri-industrial by-products into feed protein via fermentation using specific bacteria, fungi, and molds. Distinct categories of agricultural organic wastes, namely, high-concentration organic waste liquid, fruit shells and seed meals/cakes, distillers’ grains, as well as root, tuber, and legume by-products, are fermented by corresponding microorganisms to produce feed protein.
Fermentation 11 00528 g002
Table 1. Operational conditions and crude protein enhancement of diverse agricultural organic waste.
Table 1. Operational conditions and crude protein enhancement of diverse agricultural organic waste.
Agricultural Organic WasteFermentation StrainFermentation Conditions and ProcessRef.
Wheat strawInonotus obliquusSubstrate–moisture ratio 2:1, inoculum 10% (v/w), pH 7.4, (NH4)2SO4 1%, MgSO4·7H2O 0.03%, KH2PO4 0.011%, Tween-80 0.4%, corn starch 10%, 15 d, 26 °C.[17]
Corn straw; rice strawWhite rot fungi
(Phanerochaete chrysosporium)		Corn straw: 25 g + 15 mL distilled water (3% molasses, 0.1% urea, 10% fungus inoculum, 2 × 108 CFU/mL), 28 °C, 14 d.
Rice straw: 25 g + 15 mL distilled water (3% glucose, 0.1% urea, 10% fungus inoculum, 2 × 108 CFU/mL), 28 °C, 14 d.		[18]
Corn stover;
wheat straw		Candida utilis,
Lactobacillus plantarum		Mixed inoculum (25% Candida utilis, 25% Lactobacillus plantarum, 25% cellulase, 25% laccase) at 0.3% (w/w), 25 ± 2 °C, 30 d.[19]
Corn straw and peanut vineLactobacillus plantarum, Enterococcus faecalisSubstrate ratio (corn straw:peanut vine) = 3:1; inoculum (5 × 105 CFU/g Lactobacillus plantarum + 5 × 105 CFU/g Enterococcus faecalis), 25 °C, 60 d, 450 to 600 kg/m3.[20]
Cotton residuePaenibacillus sp. F4,
Cohnella xylanilytica T5		T5 group: 30 °C, 6 d, substrate-to-water ratio 1:0.6, 25% inoculum, 20% corn flour, 1.5% urea.
F4 group: 33 °C, 6 days, substrate-to-water ratio 1:0.9, 25% inoculum, 20% corn flour, 1.5% urea addition.		[21]
Citrus pomaceBacillus amyloli-quefaciens BF2, Candida utilis GIM 2.9Substrate: 80% citrus pomace + 20% corn gluten (w/w); inoculum: Bacillus amyloli-quefaciens BF2:Candida utilis GIM 2.9 = 1:1, 30 °C, 21% (v/w), 5 d.[22]
Citrus pomaceAspergillus nigerSubstrate: citrus pomace:rice bran = 8:2 (mass), moisture 60%; inoculum: 2% (4.0 × 107 spores), 200 g/substrate flask, aerobic fermentation at 28–30 °C for 7 d.[23]
Macadamia green peelHomologous lactic acid bacterium strain ZC5290.9% cellulase, 4% fermentation inoculant, anaerobic fermentation at (30 ± 2)°C for 7 d.[24]
Tea residueLactiplantibacillus plantarum, Bacillus licheniformisSubstrate: tea residue:wheat bran = 7:3, inoculum: L. plantarum:B. licheniformis = 1:1, 34 °C, 5 d.[25]
Chrysanthemum wastePediococcus cellaris,
Candida tropicalis,
Bacillus amyloliquefaciens		Substrate: chrysanthemum waste:cornmeal = 9:1; inoculum: Pediococcus cellaris:Candida tropicalis:Bacillus amyloliquefaciens = 2:2:1 (6% inoculum), 10 d, 29 ± 0.5 °C.[26]
Peanut mealBacillus velezensis LB-Y-1, Pediococcus acidilactici LC-9-1Stage 1: Inoculate Bacillus velezensis LB-Y-1 (6.0 × 109 CFU/kg, moisture 37.0%), quasi-aerobic at 38 °C for 54 h (remix q4h).
Stage 2: Inoculate Pediococcus acidilactici LC-9-1 (2.0 × 109 CFU/kg moisture 40.0%), quasi-anaerobic in PE bag at 37 °C for 18 h.		[27]
Palm kernel cakeSaccharomyces cerevisiaeEnzymolysis: feed–water ratio 1:5, β-mannanase 800 U/g, 55 °C, 72 h, initial pH 4.0.
Fermentation: feed–water ratio 1:1.0, inoculation 0.7 × 108 cells/g, 30 °C, complex enzymes 4%, molasses 6%, ammonium sulfate 1%, 48 h.		[28]
Fresh sweet corn processing by-productLactobacillus plantarum LP1Substrate ratio: by-product:wheat bran = 9:1 (SWB),
by-product:millet hull = 8:2 (SMH),
45 d, inoculum 5 × 106 CFU/g fresh weight, 20–25 °C.		[29]
Cauliflower wastesLactobacillus plantarum1 kg cauliflower wastes inoculated with 100 mL L. plantarum (6 × 106 cfu/kg), 35 °C, 30 d.[30]
CorncobRhodotorula glutinis As2.703Pretreatment: 10 g corncob + 30 mL 1.5 wt% H2SO4, 130 °C/1 h; enzymatic hydrolysis: 10% (w/w) cellulase, 50 °C, 180 rpm, 72 h.
Fermentation: 10% (v/v) inoculum in 2 L fermenter, 30 °C, pH 6.0, aeration 4 vvm, 400 rpm, 200 μL antifoams at 12 h.		[31]
BagasseSaccharomyces cerevisiae, Aspergillus niger,
Aspergillus oryzae, Lactobacillus		Inoculum ratio (Saccharomyces cerevisiae:Aspergillus niger:Aspergillus oryzae:Lactobacillus = 2:1:1:1 (≥4 × 108 CFU/g, ≥2 × 108 CFU/g, ≥2 × 108 CFU/g, 2 × 108 CFU/g, respectively), 0.1% cellulase, 0.1% xylanase, 0.5% (g/g) urea (DM basis), aerobic followed by anaerobic fermentation, 20–30 °C, 96 h.[32]
Wheat branAspergillus niger,
Trichoderma reesei		1.0 g/L Aspergillus niger, 0.2 g/L Trichoderma reesei, 30 °C, pH 4.5; followed by hydrolysis at 50 °C.[33]
Cottonseed shellsAspergillus oryzae TM-120 g cottonseed hulls + 16 mL H2O (pH 7) in 500 mL flask, autoclaved (121 °C, 20 min), inoculated with 10% spore suspension (107 CFU/mL), 30 °C, 4 d[34]
Honeysuckle residuesLactic acid bacteria (LAB) inoculants: Pediococcus pentosaceus PC2-1(F2), Lentilactobacillus buchneri (formerly Lactobacillus buchneri) PC-C1Inoculants (1.0 × 109 CFU/kg fresh material, distilled water-diluted), anaerobic fermented indoors at room temperature for 14 d.[35]
Lotus seedpodLactobacillus plantarum CAU-a214, CAV-M6Acid degradation: 5% edible vinegar 1:1 (w/v), 32 °C, 7 d.
Fermentation: 1% corn flour, 1% molasses, 0.1% cellulase, 0.1% L. plantarum CAU-a214 and CAV-M6 (10 × 109 CFU/g), 10% distilled water, 32 °C, 21 d.		[36]
Table 2. Operational conditions, and crude protein enhancement of diverse agri-industrial by-products.
Table 2. Operational conditions, and crude protein enhancement of diverse agri-industrial by-products.
Agri-Industrial By-ProductFermentation StrainFermentation Conditions and ProcessRef.
Wasted date molassesHanseniaspora guilliermondii JQ690237, Issatchenkia orientalis JQ690240100 mL 20% wasted date molasses solution, 5 mL inoculum (108 cell/mL), 25 °C, 150 rpm, 72 h.[41]
Corn steep liquorRhizopus microsporus var. oligosporus20% (v/v) corn steep liquor dilution, 2 mL inoculum (McFarland scale tube #5), 25 °C, 0.5 vvm, 96 h.[42]
Olive pomaceOyster mushrooms50% inoculum (w/w), 20–25 °C, 35 d[43]
Defatted cottonseed mealSaccharomyces cerevisiae,
Enterococcus faecium, Lactiplantibacillus plantarum		Inoculum: Saccharomyces cerevisiae/Enterococcus faecium/
Lactiplantibacillus plantarum (109 CFU/mL, ratio 1:0.5, v/m), 5 d, 28 °C.		[44]
Brewer’s spent grainBacillus licheniformis CPB2Brewer’s spent grain:soybean meal = 1:1, 12.50% inoculum, 50 °C, 24 h.[45]
Distillers’ dried grains with solublesAspergillus niger10 g distillers’ dried grains with solubles + 10 g corncob + 40 g water, 10% inoculum (v/w, 107–108 CFU/mL), 30 °C, 7 d.[46]
Distillers’ grainsLactobacillus casei, Bacillus subtilis, Saccharomyces cerevisiae,
Aspergillus oryzae		Inoculum: Aspergillus oryzae:Saccharomyces cerevisiae:Lactobacillus casei:Bacillus subtilis = 1:1:1:1 (10% of substrate), compound enzyme: 0.1% of substrate.
Substrate: 45% distillers’ grains, 45% wheat bran, 5% corn, 3% soybean meal, 2% molasses; 31.8 °C, 7 d.		[47]
Chinese distillers’ grainsCandida utilis, Trichoderma viride, Bacillus subtilis, Lactobacillus caseiInoculum: Candida utilis, Bacillus subtilis, Lactobacillus casei (equal volumes, OD600 = 2), Trichoderma viride (equal mycelia suspension), 12% inoculum, 34 °C, 12 d.[48]
Brewer’s spent grainTrichosporon cutaneumAmmoniation pretreatment: 11% ammonia dosage (w/w), 63 °C, 26 h.
Enzymatic hydrolysis: 10% solid loading (w/v), pH 4.8, 50 °C, 150 rpm; fermentation: 1 mL seed (OD600 = 2) in 20 mL hydrolysate, 30 °C, 200 rpm.		[49]
Olive cakeAspergillus oryzaeBeef extract medium, pH 6, 3% inoculum, 28 °C incubation for 14 d.[50]
Brewer’s spent grainAspergillus ibericusInoculated with spore suspension (2 × 106 spores/g dry BSG), aerobic fermentation at 25 °C for 7 d.[51]
Corncob and distillers’ dried grains with solublesAspergillus niger, Candida utilisDistillers’ dried grains with solubles:corncob = 8:1, 15.0% inoculum (v/w), 30 °C, material-to-water ratio 0.4, Aspergillus niger:Candida utilis = 1.2:1 (v/v), 10.5 d.[52]
Cassava; soybean residuesPleurotus ostreatus mycelium100 g substrate (80% cassava + 20% soybean residues), 5 mL colony solution, 25–28 °C, 9 d (colony covers plate, 120 mm).[53]
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He, D.; Cui, C. Fermentation of Organic Wastes for Feed Protein Production: Focus on Agricultural Residues and Industrial By-Products Tied to Agriculture. Fermentation 2025, 11, 528. https://doi.org/10.3390/fermentation11090528

AMA Style

He D, Cui C. Fermentation of Organic Wastes for Feed Protein Production: Focus on Agricultural Residues and Industrial By-Products Tied to Agriculture. Fermentation. 2025; 11(9):528. https://doi.org/10.3390/fermentation11090528

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He, Dan, and Can Cui. 2025. "Fermentation of Organic Wastes for Feed Protein Production: Focus on Agricultural Residues and Industrial By-Products Tied to Agriculture" Fermentation 11, no. 9: 528. https://doi.org/10.3390/fermentation11090528

APA Style

He, D., & Cui, C. (2025). Fermentation of Organic Wastes for Feed Protein Production: Focus on Agricultural Residues and Industrial By-Products Tied to Agriculture. Fermentation, 11(9), 528. https://doi.org/10.3390/fermentation11090528

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