Variations of Soybean Meal and Corn Mixed Substrates in Physicochemical Characteristics and Microbiota During Two-Stage Solid-State Fermentation

Formic acid enhances whole-plant mulberry silage fermentation by boosting lactic acid production and inhibiting harmful bacteria

Mulberry has also been regarded as a valuable source of forage for ruminants. This study was developed to investigate the impact of four additives and combinations thereof on fermentation quality and bacterial communities associated with whole-plant mulberry silage. Control fresh material (FM) was left untreated, while other groups were treated with glucose (G, 20 g/kg FM), a mixture of Lactobacillus plantarum and L. buchneri (L, 106 CFU/g FM), formic acid (A, 5 mL/kg FM), salts including sodium benzoate and potassium sorbate (S, 1.5 g/kg FM), a combination of G and L (GL), a combination of G and A (GA), or a combination of G and S (GS), followed by ensiling for 90 days. Dry matter content in the A, S, GA, and GS groups was elevated relative to the other groups (p < 0.01). Relative to the C group, all additives and combinations thereof were associated with reductions in pH and NH3-N content (p < 0.01). The A groups exhibited the lowest pH and NH3-N content at 4.23 and 3.27 g/kg DM, respectively (p < 0.01), whereas the C groups demonstrated the highest values at 4.43 and 4.44 g/kg DM, respectively (p < 0.01). The highest levels of lactic acid were observed in the GA and A groups (70.99 and 69.14 g/kg DM, respectively; p < 0.01), followed by the GL, L, and GS groups (66.88, 64.17 and 63.68 g/kg DM, respectively), with all of these values being higher than those for the C group (53.27 g/kg DM; p < 0.01). Lactobacillus were the predominant bacteria associated with each of these samples, but the overall composition of the bacterial community was significantly impacted by different additives. For example, Lactobacillus levels were higher in the G, A, and GA groups (p < 0.01), while those of Weissella levels were raised in the L, GL, and GS groups (p < 0.01), Pediococcus levels were higher in the A and GA groups (p < 0.01), Enterococcus levels were higher in the G and S groups (p < 0.01), and Lactococcus levels were raised in the S group (p < 0.01). Relative to the C group, a reduction in the levels of undesirable Enterobacter was evident in all groups treated with additives (p < 0.01), with the greatest reductions being evident in the A, S, GA, and GS groups. The additives utilized in this study can thus improve the quality of whole-plant mulberry silage to varying extents through the modification of the associated bacterial community, with A and GA addition achieving the most efficient reductions in pH together with increases in lactic acid content and the suppression of undesirable bacterial growth.

Cellulase with Bacillus velezensis improves physicochemical characteristics, microbiota and metabolites of corn germ meal during two-stage co-fermentation

Corn germ meal (CGM) is one of the major byproducts of corn starch extraction. Although CGM has rich fiber content, it lacks good protein content and amino acid balance, and therefore cannot be fully utilized as animal feed. In this study, we investigated the processing effect of cellulase synergized with Bacillus velezensis on the nutritional value of pretreated CGM (PCGM) in two-stage solid-state fermentation (SSF). High-throughput sequencing technology was used to explore the dynamic changes in microbial diversity. The results showed that compared with four combinations of B. velezensis + Lactiplantibacillus plantarum (PCGM-BL), cellulase + L. plantarum (PCGM-CL),control group (PCGM-CK), and cellulase + B. velezensis + L. plantarum (PCGM-BCL), the fourth combination of PCGM-BCL significantly improved the nutritional characteristics of PCGM. After two-stage SSF (48 h), viable bacterial count and contents of crude protein (CP) and trichloroacetic acid-soluble protein (TCA-SP) all were increased in PCGM-BCL (p < 0.05), while the pH was reduced to 4.38 ± 0.02. In addition, compared with PCGM-BL, the cellulose degradation rate increased from 5.02 to 50.74%, increasing the amounts of short-chain fatty acids (216.61 ± 2.74 to 1727.55 ± 23.00 µg/g) and total amino acids (18.60 to 21.02%) in PCGM-BCL. Furthermore, high-throughput sequencing analysis revealed significant dynamic changes in microbial diversity. In the first stage of PCGM-BCL fermentation, Bacillus was the dominant genus (99.87%), which after 24 h of anaerobic fermentation changed to lactobacillus (37.45%). Kyoto Encylopaedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed that the pathways related to the metabolism of carbohydrates, amino acids, cofactors, and vitamins accounted for more than 10% of the enriched pathways throughout the fermentation period. Concisely, we show that cellulase can effectively improve the nutritional value of PCGM when synergized with B. velezensis in two-stage SSF.

Physicochemical characteristics and microbial community succession during oat silage prepared without or with Lactiplantibacillus plantarum or Lentilactobacillus buchneri

IMPORTANCE

Ensiled whole-plant oats are an important feedstuff for ruminants in large parts of the world. Oat silage is rich in dietary fibers, minerals, vitamins, and phytochemicals beneficial to animal health. The fermentation of oat silage is a complex biochemical process that includes interactions between various microorganisms. The activity of many microbes in silage may cause an extensive breakdown of nutrition and lead to undesirable fermentation. Moreover, it is difficult to make high-quality oat silage because the number of epiphytic lactic acid bacterium microflora was lower than the requirement. Understanding the complex microbial community during the fermentation process and its relationship with community functions is therefore important in the context of developing improved fermentation biotechnology systems. These results suggested that the addition of Lactobacillus plantarum or Lactobacillus buchneri regulated the ensiling performance and microbial community in oat silage by shaping the metabolic pathways.

Compound probiotics producing cellulase could replace cellulase preparations during solid-state fermentation of millet bran

Low-value agricultural by-products can be converted into high-value biological products by fermentation with probiotic strains or by enzymatic hydrolysis. However, the high costs of enzyme preparations significantly limit their applications in fermentation. In this study, the solid-state fermentation of millet bran was performed using a cellulase preparation and compound probiotics producing cellulase (CPPC), respectively. The results showed that both factors effectively destroyed the fiber structure, reduced the crude fiber content by 23.78% and 28.32%, respectively, and significantly increased the contents of beneficial metabolites and microorganisms. Moreover, CPPC could more effectively reduce the anti-nutrient factors and increase the content of anti-inflammatory metabolites. The correlation analysis revealed that Lactiplantibacillus and Issatchenkia had synergistic growth during fermentation. Overall, these results suggested that CPPC could replace cellulase preparation and improve antioxidant properties while reducing anti-nutrient factors of millet bran, thus providing a theoretical reference for the efficient utilization of agricultural by-products.

Enrichment of a Plant Feedstuff Mixture's Nutritional Value through Solid-State Fermentation

Plant feedstuffs are the main ingredients of animal feed. Owing to food-feed competition, increasing the utilization efficiency of these feedstuffs is important for animal nutrition. This can be achieved via solid-state fermentation (SSF). SSF of a plant feedstuff mixture (PFM) (25% rapeseed meal, soybean meal, rice bran, and sunflower meal) by three fungi (Aspergillus ibericus MUM 03.29, Aspergillus niger CECT 2088, and Aspergillus niger CECT 2915) resulted in an increase in protein content by 5%, irrespective of fungi, a reduction in cellulose content by 9 to 11%, and of hemicellulose content by 21 to 34%, relative to unfermented PFM. Enzyme production was measured: the highest cellulase (123.7 U/g), xylanase (431.8 U/g), and beta-glucosidase (117.9 U/g) activity were achieved with A. niger CECT 2088. Principal component analysis showed a positive correlation between all fermented PFMs and enzyme production, protein content, digestibility, and fiber reduction. Bioprocessing of the PFM by SSF increased its nutritional value and digestibility, making it more appealing for animal feeds.

Effect of isolated lactic acid bacteria on the quality and bacterial diversity of native grass silage

Objective

The objective of this study was to isolate lactic acid bacteria (LAB) from native grasses and naturally fermented silages, determine their identity, and assess their effects on silage quality and bacterial communities of the native grasses of three steppe types fermented for 60 days.

Methods

Among the 58 isolated LAB strains, Limosilactobacillus fermentum (BL1) and Latilactobacillus graminis (BL5) were identified using 16S rRNA sequences. Both strains showed normal growth at 15- 45°C temperature, 3-6.5% NaCl concentration, and pH 4-9. Two isolated LAB strains (labeled L1 and L5) and two commercial additives (Lactiplantibacillus plantarum and Lentilactobacillus buchneri; designated as LP and LB, respectively) were added individually to native grasses of three steppe types (meadow steppe, MS; typical steppe, TS; desert steppe, DS), and measured after 60 d of fermentation. The fresh material (FM) of different steppe types was treated with LAB (1 × 10⁵ colony forming units/g fresh weight) or distilled water (control treatment [CK]).

Results

Compared with CK, the LAB treatment showed favorable effects on all three steppe types, i.e., reduced pH and increased water-soluble carbohydrate content, by modulating the microbiota. The lowest pH was found in the L5 treatment of three steppe types, at the same time, the markedly (p < 0.05) elevated acetic acid (AA) concentration was detected in the L1 and LB treatment. The composition of bacterial community in native grass silage shifted from Pantoea agglomerans and Rosenbergiella nectarea to Lentilactobacillus buchneri at the species level. The abundance of Lentilactobacillus buchneri and Lactiplantibacillus plantarum increased significantly in L1, L5, LP, and LB treatments, respectively, compared with CK (p < 0.05).

Conclusion

In summary, the addition of LAB led to the shifted of microbiota and modified the quality of silage, and L. fermentum and L. graminis improved the performance of native grass silage.

Properties investigations of rape stalks fermented by different salt concentration: Effect of volatile compounds and physicochemical indexes

In order to find out the effect of salt concentration on fermented rape stalks, the physicochemical quality and volatile components was investigated using high performance liquid chromatography (HPLC) and headspace solid phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). The results showed that there were abundant kinds of free amino acids (FAAs) in all samples, mainly presenting sweet, umami and bitter taste. Through taste activity value (TAV), His, Glu, and Ala contributed significantly to the taste of the sample. 51 volatile components were identified, of which the relative contents of ketones and alcohols were high. By the relative odor activity value (ROAV) analysis, the main components that had a great impact on the flavor were phenylacetaldehyde, β-Ionone, ethyl palmitate and furanone. Adjusting the appropriate salt concentration for fermentation could improve the comprehensive quality of fermented rape stalks and promote the development and utilization of rape products.

Innovations and developments in single cell protein: Bibliometric review and patents analysis

Background

Global demand for food products derived from alternative proteins and produced through sustainable technological routes is increasing. Evaluation of research progress, main trends and developments in the field are valuable to identify evolutionary nuances.

Methods

In this study, a bibliometric analysis and search of patents on alternative proteins from fermentation processes was carried out using the Web of Science and Derwent World Patents Index^™ databases, using the keywords and Boolean operators "fermentation" AND "single cell protein" OR "single-cell protein." The dataset was processed and graphics generated using the bibliometric software VOSviewer and OriginPro 8.1.

Results

The analysis performed recovered a total of 360 articles, of which 271 were research articles, 49 literature review articles and 40 publications distributed in different categories, such as reprint, proceedings paper, meeting abstract among others. In addition, 397 patents related to the field were identified, with China being the country with the largest number of publications and patents deposits. While this topic is largely interdisciplinary, the majority of work is in the area of Biotechnology Applied Microbiology, which boasts the largest number of publications. The area with the most patent filings is the food sector, with particular emphasis on the fields of biochemistry, beverages, microbiology, enzymology and genetic engineering. Among these patents, 110 are active, with industries or companies being the largest depositors. Keyword analysis revealed that the area of study involving single cell protein has included investigation into types of microorganisms, fermentation, and substrates (showing a strong trend in the use of agro-industrial by-products) as well as optimization of production processes.

Conclusion

This bibliometric analysis provided important information, challenges, and trends on this relevant subject.

Effects of Isolated LAB on Chemical Composition, Fermentation Quality and Bacterial Community of Stipa grandis Silage

This study aimed to screen and identify lactic acid bacteria (LAB) strains from the Stipa grandis and naturally fermented silage, and assess their effects on the silage quality and bacterial community of Stipa grandis after 60 days of the fermentation process. A total of 38 LAB were isolated, and strains ZX301 and YX34 were identified as Lactiplantibacillus plantarum and Pediococcus pentosaceus using 16S rRNA sequences; they can normally grow at 10−30 °C, with a tolerance of pH and NaCl from 3.5 to 8.0 and 3 to 6.5%, respectively. Subsequently, the two isolated LAB and one commercial additive (Lactiplantibacillus plantarum) were added to Stipa grandis for ensiling for 60 days and recorded as the ZX301, YX34, and P treatments. The addition of LAB was added at 1 × 105 colony-forming unit/g of fresh weight, and the same amount of distilled water was sprayed to serve as a control treatment (CK). Compared to the CK treatment, the ZX301 and YX34 treatments exhibited a positive effect on pH reduction. The water-soluble carbohydrate content was significantly (p < 0.05) increased in ZX301, YX34, and P treatments than in CK treatment. At the genus level, the bacterial community in Stipa grandis silage involves a shift from Pantoea to Lactiplantibacillus. Compared to the CK treatment, the ZX301, YX34, and P treatments significantly (p < 0.05) increase the abundance of Pediococcus and Lactiplantibacillus, respectively. Consequently, the results indicated that the addition of LAB reconstructed microbiota and influenced silage quality. The strain ZX301 could improve the ensiling performance in Stipa grandis silage.

Fermentation Characteristics, Microbial Compositions, and Predicted Functional Profiles of Forage Oat Ensiled with Lactiplantibacillus plantarum or Lentilactobacillus buchneri

This study aimed to investigate the effects of lactic acid bacteria (LAB) inoculants on the fermentation quality, microbial compositions, and predicted functional profiles of forage oat. The forage oat was inoculated with distilled water, Lentilactobacillus buchneri (LB), and Lactiplantibacillus plantarum (LP) as the control (CON), LB and LP treatments, respectively, and the addition of Lentilactobacillus buchneri (LB) or Lactiplantibacillus plantarum (LP) resulted in 1 × 106 colony-forming units/g of fresh weight. After 30 days of fermentation, the lowest pH (4.23) and the lowest content of ammoniacal nitrogen (NH3-N) in dry matter (DM, 4.39%) were observed in the LP treatment. Interestingly, there was a significant (p < 0.05) difference in lactic acid (LA) concentration among the three treatments. The LP treatment had the highest lactate concentration (7.49% DM). At the same time, a markedly (p < 0.05) elevated acetic acid (AA) concentration (2.48% DM) was detected in the LB treatment. The Shannon and Chao1 indexes of bacterial and fungal communities in all the silage samples decreased compared to those in the fresh materials (FM). Proteobacteria was the dominant phylum in the FM group and shifted from Proteobacteria to Firmicutes after ensiling. Lactobacillus (64.87%) and Weissella (18.93%) were the predominant genera in the CON, whereas Lactobacillus dominated the fermentation process in the LB (94.65%) and LP (99.60%) treatments. For the fungal community structure, the major genus was Apiotrichum (21.65% and 60.66%) in the FM and CON groups after 30 days of fermentation. Apiotrichum was the most predominant in the LB and LP treatments, accounting for 52.54% and 34.47%, respectively. The genera Lactococcus, Pediococcus, and Weissella were negatively associated with the LA content. The genus Ustilago and Bulleromyces were positively associated with the LA content. These results suggest that the addition of LAB regulated the microbial community in oat silage, which influenced the ensiling products, and LP was more beneficial for decreasing the pH and NH3-N and increasing the LA concentration than LB in forage oat silage.

Diversity of growth performance and rumen microbiota vary with feed types

Diet is a major factor in influencing the growth performance and the microbial community of lambs. This study aimed to investigate how diverse diets influence their growth performance and rumen microbiota. Ninety male lambs were randomly allocated into three groups in a completely randomized design with equal lambs: non-pelleted native grass hay (HA) as the control diet and pelleted native grass hay (GP) and pelleted native grass hay with concentrate (GPC) as experimental diets. The rumen fluid samples of the lambs in the HA, GP, and GPC groups were used to study rumen microbiota diversity through 16S rDNA high-throughput sequencing. In the present study, the final body weight, dry matter intake, and average daily gain differed significantly (p &lt; 0.05) among the HA, GP, and GPC groups. Compared to the HA group, higher final body weight, dry matter intake, and average daily gain were found in the GP group. Similarly, better animal performance was observed in the GPC group than in the GP group. The principal coordinates analysis displayed that the composition of the rumen microbiota in the three groups was distinctly separated from each other. Bacteroidetes and Firmicutes were the dominant members of the community in the HA and GP groups, while Bacteroidetes, Firmicutes, and Proteobacteria became the predominant members in the GPC group. The comparison among these groups showed significant (p &lt; 0.05) differences in Rikenellaceae_RC9_gut_group, Prevotella_1, Ruminococcaceae_NK4A214_group, and Succiniclasticum. These results suggest that the GP and GPC diets are more beneficial for growth performance than the HA diet and also indicate that the rumen microbiota varied in response to different feed types. In conclusion, these results could provide strategies to influence rumen microbiota for better growth and a healthier ecosystem on the Mongolian Plateau and lay the theoretical groundwork for feeding the pelleted native grass diet.

Bacillus amyloliquefaciens 40 regulates piglet performance, antioxidant capacity, immune status and gut microbiota

Probiotics can improve animal growth performance and intestinal health. Bacillus species, Lactobacillus species, Bifidobacterium species, yeast etc. are the common types of probiotics. However, understanding the effects of probiotics on the immune status and gut microbiota of weaning piglets and how the probiotics exert their impact are still limited. This study aimed to investigate the effects of Bacillus amyloliquefaciens 40 (BA40) on the performance, immune status and gut microbiota of piglets. A total of 12 litters of newborn piglets were randomly divided into 3 groups. Piglets in control group were orally dosed with phosphate buffered saline; BA40 group and probiotics group were orally gavaged with resuspension BA40 and a probiotics product, respectively. The results showed that BA40 treatment significantly decreased (P < 0.05) the diarrhea incidence (from d 5 to 40), diamine oxidase, D-lactate, interleukin (IL)-1β and interferon-γ concentrations compared with control group and probiotics group. Meanwhile BA40 dramatically increased the total antioxidant capacity, IL-10 and secretory immunoglobulin-A concentrations in contrast to control group. For the microbial composition, BA40 modulated the microbiota by improving the abundance of Bacteroides, Phascolarctobacterium (producing short-chain fatty acids) and Desulfovibrio and reducing the proliferation of pathogens (Streptococcus, Tyzzerella, Vellionella and paraeggerthella). Meanwhile, a metabolic function prediction explained that carbohydrate metabolism and amino acid metabolism enriched in BA40 group in contrast to control group and probiotics group. For correlation analysis, the results demonstrated that BA40-enriched Phascolarctobacterium and Desulfovibrio provide insights into strategies for elevating the health status and performance of weaned piglets. Altogether, BA40 exerted stronger ability in decreasing diarrhea incidence and improved antioxidant activity, gut barrier function and immune status of piglets than the other treatments. Our study provided the experimental and theoretical basis for the application of BA40 in pig production.

Dynamics of the fermentation quality and microbiota in Ephedra sinica treated native grass silage

AIMS

This study aimed to evaluate the effects of Ephedra sinica on physicochemical characteristics and bacterial community of ensiled native grass by multiple physicochemical analyses combined with high-throughput sequencing.

METHODS AND RESULTS

Treatments were a control treatment with no additive (CON), Ephedra sinica was added at 1% (CEa1), 3% (CEa2) and 5% of the fresh materials (CEa3). Compared to the CON group, the dry matter and water-soluble carbohydrate contents were significantly (p < 0.05) decreased in the CEa1 group. Compared to the CON group, the pH was significantly (p < 0.05) decreased in Ephedra sinica treated silages, and the higher lactic acid content was observed in Ephedra sinica treated silages. At the genus level, the abundance of Enterococcus, Lactobacillus, Pediococcus and Weissella were the predominant member in the CON, CEa1, CEa2 and CEa3 groups, respectively. The abundance of Lactobacillus was significantly (p < 0.05) increased in the CEa1 group and Pediococcus was significantly (p < 0.05) increased in the CEa2 group. According to the 16S rRNA gene-predicted functional profiles, the inoculation of Ephedra sinica accelerated the carbohydrate metabolism.

CONCLUSIONS

In summary, the addition of Ephedra sinica could improve the silage quality of native grass by regulating the bacterial community and the addition of a 1% percentage of fresh materials exhibited the potential possibility in responding to get high-quality native grass silages.

SIGNIFICANCE AND IMPACT OF THE STUDY

The utilization of herbal additives on fermentation quality combined with 16S rRNA gene-predicted functional analyses will contribute to the direction of future research in improving silage quality.

Longitudinal Investigation of the Native Grass Hay from Storage to Market Reveals Mycotoxin-Associated Fungi

This study aimed to characterize the fungal diversity and mycotoxin concentrations of native grass hay in various storage periods. In the present study, the native grass hay samples were collected when stored for 0 d (D0 group), 30 d (D30 group), and 150 d (D150 group), respectively. Here, mycotoxin analyses combined with ITS gene sequence were performed to reveal the changes in response to the storage period. There were notable differences in deoxynivalenol and aflatoxin B1 concentrations among the three groups. Compared to the D150 group, the diversity of the fungal community was higher in the D0 and D30 groups, which indicating the diversity was significantly influenced by the storage period. No significant (p > 0.05) difference was observed among the three groups on the dominant phyla. Interestingly, a significant (p < 0.05) difference was also observed in Chactomella and Aspergillus among the three groups, the abundance of the Chactomella was significantly (p < 0.05) decreased and the abundance of Aspergillus was statistically (p < 0.05) increased in the D150 group. Correlation analysis of the association of fungi with mycotoxin could provide a comprehensive understanding of the structure and function of the fungal community. These results indicated that the good practices of storage are essential for the prevention of mycotoxin. The information contained in the present study is vital for the further development of strategies for hay storage with high quality in the harsh Mongolian Plateau ecosystem.

Dynamics Changes of Microorganisms Community and Fermentation Quality in Soybean Meal Prepared with Lactic Acid Bacteria and Artemisia argyi through Fermentation and Aerobic Exposure Processes

This study evaluated the effects of Lactiplantibacillus plantarum subsp. plantarum ZA3, Artemisia argyi and their combination, on the fermentation characteristics, microbial community, mycotoxins and crude flavonoids content of fermented soybean meal during fermentation (under anaerobic conditions) and aerobic exposure (under aerobic conditions). The results showed that ZA3, Artemisia argyi and ZA3+ Artemisia argyi groups had lower pH values and higher lactic acid concentrations compared with controls, and additives increased the abundance of Lactiplantibacillus and decreased those of Acetobacter and Enterobacter; in particular, Artemisia argyi and ZA3+ Artemisia argyi reduced the abundance of fungi, such as Aspergillus, Pichia, Fusarium, Cladosporium and Xeromyces. Meanwhile, the contents of mycotoxins were lower in treated groups, and even mycotoxins in the control were significantly reduced after 30 d (p < 0.05). Crude flavonoids that were correlated positively with Lactococcus and negatively with Bacillus, Aspergillus, Enterobacter and Kazachstania were significantly higher in the Artemisia argyi and ZA3+ Artemisia argyi groups (p < 0.05).

Microbial Population Succession and Community Diversity and Its Correlation with Fermentation Quality in Soybean Meal Treated with Enterococcus faecalis during Fermentation and Aerobic Exposure

This study assessed the effects of Enterococcus faecalis (E. faecalis) in combination with protease on fermentation characteristics and microbial communities during ensiling and aerobic exposure phases of soybean meal (SBM). In this study, response surface methodology (RSM) was used to optimize the optimal growth conditions of E. faecalis ZZUPF95, which produced protease, and fermented SBM under the optimal fermentation conditions. The fermentation test was divided into four groups as follows: CK (Control check), ZZUPF95, Protease and ZZUPF95+Protease groups. Results showed that the best medium ratio of ZZUPF95 was glucose 1%, peptone 2%, inorganic salt 1.47%; fermentation time 36 h, inoculation amount 10%, ratio of material to water 1:1 is the optimal fermentation scheme; after fermentation and aerobic exposure treatment, ZZUPF95 and ZZUPF95 + Protease group can reduce the pH of feed, improve the content of lactic acid in the fermentation system, and have the effect of inhibiting the reproduction of pathogenic bacteria, increasing the content of crude protein and ether extract, and degrading crude fiber; the microbial community of SBM were changed after fermentation and aerobic exposure. This study explored the changes of fermentation quality of SBM, which has certain theoretical value to improve the fermentation mode and storage of SBM.

Dynamics of defatted rice bran in physicochemical characteristics, microbiota and metabolic functions during two-stage co-fermentation

Defatted rice bran (DFRB) is an inexpensive and easily available agricultural byproduct. Existence of anti-nutritional factors (ANFs), high fiber and low protein content, susceptible to oxidation and rancidity make DFRB currently underutilized. In this study, Bacillus subtilis with high enzyme activities, Saccharomyces cerevisiae with high single-cell proteins concentration and Lactiplantibacillus plantarum with excellent acid secreting capacity were screened to co-fermented DFRB with phytase, and multiple physicochemical analyses combined with high-throughput sequencing were applied to provide insights into the dynamics of the physicochemical characteristics and the complex microbiome during the two-stage co-fermentation of DFRB. The results showed that co-fermentation effectively improved the nutritional value by degrading ANFs (trypsin inhibitors and phytic acid), fiber (acid detergent fiber and neutral detergent fiber) and allergenic protein, and increasing the trichloroacetic acid soluble protein, amino acids and organic acid. In addition, co-fermentation prevented lipid oxidation by enhancing antioxidant activity and reducing the activity of lipase and lipoxygenase. High-throughput sequencing results suggested that co-fermentation optimized microbial community of DFRB by increasing desirable Lactobacillus, Pediococcus, Saccharomyces and Talaromyces and reducing undesirable bacteria (Enterobacter and Pseudomonas) and animal and plant-pathogenic fungi (Blumeria, Alternaria, Fusarium, etc.). Furthermore, high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS) were adopted to predict microbial metabolic functions and metabolic pathways during whole DFRB co-fermentation.