The genus Bacillus provides important microbial cell factories for bioactive metabolite production in agricultural biomanufacturing, yet optimization of metabolic regulation and fermentation processes still relies heavily on costly trial-and-error. This creates a need for models that can synthesize domain knowledge and support rational intervention design. However, strain performance data and process parameters are typically proprietary, restricting the practical use of cloud-based general-purpose large language models. Here, we present BaciCausalLM, a lightweight, domain-specific large language model for Bacillus-based biomanufacturing that can be deployed on local hardware. We integrate literature, patents, and private datasets to construct a supervised fine-tuning corpus, a domain benchmark, and a dedicated evaluation set for metabolic network regulation. Starting from Qwen3-32B, BaciCausalLM was adapted using QLoRA and supports single-GPU inference on desktop-class hardware (≤32 GB) under 4-bit quantization. BaciCausalLM achieved 94.4% accuracy on the domain-general benchmark and a Cohen's κ of 0.770 on the metabolic intervention–outcome reasoning task. In this task, explicit causal-chain reasoning reduced false-positive improvement recommendations for experimentally no-improvement interventions from 25.9% to 14.8%. In closed-loop wet-lab validation, model-guided optimization increased the maximum iturin A titer to 1442.0 mg L−1 while keeping the final-stage median unit cost below the base-model stage. In a cross-task brevicidine application, zero-shot medium generation followed by feedback-guided optimization increased the peak titer to 337.93 mg L−1. Collectively, BaciCausalLM provides a local decision-support framework that fuses domain knowledge with causal reasoning, enabling accelerated iterative optimization in agricultural microbial biomanufacturing.

Intensive swine production causes nutrient losses and enhanced gaseous emissions during manure management, which disrupts nutrient cycling within agricultural systems and threatens agroecosystem sustainability. Prior research has typically examined feeding and manure management as isolated processes, failing to integrate these two components to improve system performance, and this gap limits the design of integrated agricultural systems. Here, we implemented a low-protein balanced diet (LPBD) system and compared it with a high-protein traditional diet (HPTD) to evaluate impacts on swine growth performance and nutrient-use efficiency, followed by sawdust co-composting of the resulting manures. System responses were quantified through integrated monitoring of nutrient excretion, compost physicochemical properties, and gaseous emissions, together with metagenomic profiling of microbial communities and functional genes and subsequent path modeling to resolve key interaction pathways across the feed–compost agricultural system. We found that LPBD improved C/N digestion synchronization, reduced protein/energy excretion, and maintained swine productivity, while markedly decreased CO2, CH4, N2O and NH3 emissions during composting. Metagenomics indicated that LPBD enriched N-cycling genes (nirK, nosZ, nifH) and restructured CAZyme repertoires and microbial communities, patterns consistent with lower NH3 emissions and enhanced carbon cycling. Path modeling further indicated that diet-driven shifts in compost composition altered environmental factors and indirectly regulated gas emissions via enzymatic and genetic pathways. Overall, this integrated feed–compost strategy links livestock nutrition with environmental management, enhances nutrient cycling efficiency at the agroecosystem level, and provides a basis for sustainable, low-emission circular livestock systems.

β-Carotene exhibits distinct biological effects that enhance reproductive performance in mammals; however, the mechanisms underlying these effects remain poorly understood. This study aimed to evaluate the effect of β-carotene on ovarian development in replacement gilts and to investigate its potential mechanisms. A total of 20 gilts, aged 130 d, were randomly assigned to control group or β-carotene group (β-C group, diet containing 10 mg/kg of β-carotene). Each group consisted of 10 replicates, with one gilt per replicate, over a 60-d trial. β-Carotene significantly increased the number of follicles measuring 2–5 mm in diameter, elevated estradiol concentrations in both blood and follicular fluid of replacement gilts (P < 0.05). Compared to the control group, the β-C group exhibited a significant increase in β-carotene concentration within ovarian follicular fluid (P < 0.05). Transcriptomic analysis of GCs revealed that β-carotene could significantly upregulated the expression of Forkhead Box L2 (FOXL2). When β-carotene and its metabolic product were administered to granulosa cells (GCs), validation of differentially expressed genes in the transcriptome suggests the possibility that β-carotene, rather than its metabolic product, is responsible for the upregulation of FOXL2 in ovarian GCs, which subsequently may regulate StAR and enhance estradiol synthesis. Furthermore, β-carotene is likely to promote lipolysis, providing essential substrates for estradiol and adenosine triphosphate (ATP) production. Concurrently, β-carotene appears to increase the activity of the antioxidant enzymes superoxide dismutase 1 (SOD1) and glutathione peroxidase 4 (GPX4) in gilts, thereby reducing reactive oxygen species (ROS) (P < 0.05) and maintaining redox balance. Our findings suggest that β-carotene could promote lipolysis, activate the FOXL2-StAR pathway to increase estradiol synthesis in GCs, and alleviate oxidative stress, thereby contributing to follicle development.

The systematic exploration of novel bioactive compounds with superior functional properties is critical for driving innovations in agriculture, healthcare, and related fields, thereby becoming essential for advancing sustainable biotechnological solutions. Nonprotein amino acids (NPAAs), functional amino acids not incorporated into proteins, exhibit unique physiological activities and provide distinctive advantages in nutritional enhancement, functional product formulation, and food/feed processing. These attributes challenge the conventional perception of proteins as mere nutritional carriers, positioning NPAAs as promising bioproducts for biosynthesis and functional applications in agriculture, food, and medicine. This review summarizes the classification of the available NPAAs based on their synthetic substrates for the first time and then outlines their diverse functional roles. A comprehensive analysis of recent advances in biosynthetic pathways, engineering strategies, and production level demonstrates their primary research progress in the laboratory phase. The further sustainable biomanufacturing of NPAAs is hampered by several challenges, including poorly elucidated biosynthetic mechanisms, limited robustness and low productivity of microbial strains, and difficulties in scaling up production for industrial applications. Addressing these bottlenecks will require innovative strategies and technologies to facilitate the translation of NPAA production from bench to industry. This review offers valuable insights into the potential of NPAAs in the development of next-generation bioproducts of nutrition, immune regulation, antioxidant defense, and intestinal homeostasis maintenance, suggesting a promising direction for microbial production of high-performance bioactive molecules in agricultural synthetic biomanufacturing.

Diarrheal diseases, such as yellow dysentery and white dysentery caused by pathogens or viruses, in newborn piglets lead to substantial economic losses in the swine industry worldwide. Gut microbiota dysbiosis is frequently observed in diarrheic piglets and is thought to play a role in disease pathogenesis, although causal relationships remain to be established. However, developing reliable microbiome-based diagnostic tools still poses a significant challenge. This study aimed to develop a diagnostic model for piglet diarrhea by integrating core microbiota analysis with machine learning. Fecal samples from diarrheic and healthy piglets were subjected to metagenomic sequencing to characterize archaeal, bacterial, and fungal communities. We identified diarrhea-associated bacterial biomarkers via LEfSe, DESeq2, and microbial cooccurrence network analysis. These microbial features were used to construct and compare multiple machine learning classifiers. Our results revealed significant disparities in the structure and diversity of the gut microbiota between diarrheic and healthy piglets, with the bacterial community showing the most notable changes. Among the models developed, the decision tree classifier based on bacterial genus-level features achieved the highest prediction accuracy of 91.18%. Furthermore, a simplified model utilizing a panel of 18 core bacterial genera also demonstrated high efficacy, with a support vector machine model achieving 88.24% accuracy. In independent validation using our internal dataset, the random forest model exhibited the best generalizability and stability. This study establishes a robust, microbiota-based diagnostic model for diarrhea in neonatal piglets, highlighting the potential of machine learning in leveraging microbiome data for disease classification and health management in livestock production.

High fat diet (HFD) is widely utilized in aquaculture to promote growth and feed protein retention, but overconsumption of fat will induce systemic metabolic disorders of fish accompanied by impaired intestinal health and lower pathogen resistance. Indole-3-propionic acid (IPA) has been widely reported to enhance intestinal health in mammals. Our previous study has proven that IPA alleviated lipid metabolism disorder and lipotoxic liver injury in Nile tilapia (Oreochromis niloticus). However, it remains unclear whether IPA can sustain fish intestinal health. In this study, 540 Nile tilapia (2.53 ± 0.02 g) were allotted in 6 groups with 3 tanks each and fed with control diet or high-fat diet supplemented with different levels of IPA (0, 20, 40, 80, 160 mg/kg) respectively. After 8 weeks, it was observed that 80 mg/kg IPA proved the most beneficial for decreasing intestinal myeloperoxidase (MPO) enzyme activity and improving the survival rate of Nile tilapia infected with Aeromonas hydrophila. Dietary IPA restored intestinal barrier integrity impaired by HFD and increased the genes expression of tight junctional proteins (tjps), such as zona occludens 1 (zo-1) and occludin. The results showed that dietary IPA effectively mitigated HFD caused intestinal oxidative stress, manifesting as lower levels of reactive oxygen species (ROS) and malondialdehyde (MDA) and higher activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px). Dietary IPA promoted the gene and protein expression of aryl hydrocarbon receptor (Ahr) in intestine. Further investigation suggested that IPA could activate Ahr and affect nuclear factor-E2-related factor 2 (NRF2) signaling to reduce oxidative stress. Moreover, IPA might suppress enteritis by inhibiting the Ahr-mediated nuclear factor kappa light-chain-enhancer of activated B (NF-κB) signaling pathway. These findings indicated that IPA has the potential to improve intestinal health and pathogen resistance in HFD-fed fish, offering crucial insights for the application of innovative additives in aquatic feeds.

The escalating global antimicrobial resistance crisis underscores the urgent need for novel antibiotics. Here, Paenibacillus elgii 219 is identified as an efficient producer of octapeptins (B2, B3, A1 and B1) by nuclear magnetic resonance and tandem mass spectrometry. These octapeptins exhibited broad-spectrum antibacterial activity, high stability under extreme pH, temperature, and enzymatic conditions, and without cytotoxicity. These promising bioactivity and stability profiles, underscore the need to optimize methods to increase octapeptins yields to unlock their application prospects. Initial fermentation optimization markedly augmented the total octapeptins yield by 32-fold, achieving 1.0 g/L; Atmospheric and room temperature plasma mutagenesis and chromogenic screening picked a superior mutant with a 75 % higher octapeptins titer (1.7 g/L), as confirmed by transcriptomic analysis. Targeted knockout of glycosyltransferases GTp4383 and GTp5312 reduced broth viscosity and increased the total octapeptins titer to 2.3 g/L, and further scaled up to 3.94 g/L in fed-batch fermentation. This integrated approach establishes a scalable platform for high-yield octapeptins production, highlighting its potential as a next-generation anti-resistance agent.

Preweaning piglet diarrhea not only compromises animal health but also causes significant economic losses to the swine industry; however, the underlying molecular mechanisms remain poorly understood. Here, we use a preweaning piglet model to systematically explore the underlying risk features of pre-weaning diarrhea risk through multi-omics integration analysis. We identified thousands of differentially expressed genes, proteins, and metabolites. Key findings include: (1) activation of the complement cascade but downregulation of complement receptors; (2) increased chemokine production with reduced receptor expression; (3) overexpression of mitochondrial ribosomal proteins (MRPs) and NADH: ubiquinone oxidoreductase (NDUF), suggesting mitochondrial dysfunction; (4) aberrant activation of neuroactive ligand-receptor pathways; and (5) accumulation of undigested polypeptides in the jejunum due to reduced peptidase activity and amino acid transporter expression, indicating disrupted protein digestion and absorption. These findings provide critical insights and a valuable resource for addressing the underlying mechanisms of preweaning disease challenges in newborns.

BackgroundWhile the livestock industry actively seeks alternatives to antibiotics, residual low-dose exposures continue to drive the spread of antibiotic resistance genes (ARGs). Icariin, a plant-derived compound, is recognized for improving poultry growth and immunity. However, it remains unclear how this compound influences the environmental persistence of ARGs, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) during the vulnerable recovery phase after antibiotic withdrawal.ResultsWe designed a two-phase feeding trial with laying hens, using longitudinal metagenomic sequencing to track post-withdrawal resistance dynamics. Following initial exposure to a low-dose antibiotic mixture that established a baseline of elevated resistance, hens received either a basal diet, an icariin-supplemented diet, or a copper sulfate-supplemented diet. The data indicate that icariin supplementation consistently reduced the burdens of both ARGs and MGEs. It also suppressed the potential for HGT and restricted the diversity of microbial hosts harboring these resistance elements. Conversely, copper sulfate-a traditional metal-based additive-exacerbated resistance risks by expanding both the abundance and the host range of ARGs and MGEs. Across all treatments, the population of Escherichia and the prevalent ARG subtype bacA correlated strongly with total resistance loads, tracking the overall resistome burden.ConclusionsCompared to conventional copper sulfate treatments, icariin facilitates a safer ecological recovery in the poultry gut by actively lowering ARG and MGE reservoirs after antibiotic withdrawal. These genomic insights, combined with its known physiological benefits, support icariin as a sustainable feed additive. Furthermore, the Escherichia-bacA correlation provides a reliable, streamlined indicator for monitoring resistance risks in farm environments. However, as these findings rely on short-term fecal metagenomic tracking, further validation through multi-environment studies is warranted.

β-carotene is widely used in food processing and animal feed industries. However, metabolic stress is a primary factor limiting cell growth and β-carotene production in Escherichia coli. To alleviate cellular growth stress, we improved cell membrane tolerance to β-carotene with the cell growth rate increased by 41.22 %, and enhanced β-carotene production (286.57 mg/L). To further enhance the supply of β-carotene precursors, 16 genetic targets were modified for strengthening the metabolic flux of the acetyl-CoA, isopentenyl pyrophosphate/dimethylallyl diphosphate (IPP/DMAPP), farnesyl diphosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) nodes, which led to 619.79 mg/L β-carotene. Thereafter, dynamic regulation of mvaE enabled simultaneous control of acetyl-CoA entry into the MVA pathway and mevalonate synthesis, which raised β-carotene titer and cell growth by 45.75 % and 11.43 %, respectively. Finally, a novel "Transient-state" continuous fermentation was developed, which effectively increased the β-carotene production to 3.93 g/L (54.5 mg/g DCW), with an average productivity of 81.9 mg/L/h. This study presents an effective strategy for improving the biosynthesis of hydrophobic natural compounds, offering a scalable approach for industrial production and wider applications in microbial metabolic engineering.

Microcin J25 (MccJ25) has received substantial attention as a potential solution to the global threat of infection caused by antibiotic-resistant bacteria. However, the industrial fermentation of MccJ25 faces production bottlenecks. It is imperative to further explore the production optimization strategies for MccJ25 to formulate comprehensive approaches for its industrial-scale production and other downstream applications. Here, Fe²⁺ in tap water was identified as a critical inhibitor of MccJ25 biosynthesis, selectively repressing mcjA transcription, which was reversible via 2,2′-bipyridine-mediated chelation. To decouple production from growth phase dependency and Fe²⁺ interference, we engineered Escherichia coli BL21 cells by performing two genetic modifications. First, we replaced the native mcjA promoter with a constitutive promoter (PQ) to allow its mid-log phase expression. Second, we replaced the native mcjBCD promoter with a medium-strength variant (P2223) that delayed production kinetics without affecting final yields. However, the genomic integration of mcjD alleviated plasmid-borne toxicity, increasing the expression timing and doubling the yield to 240 mg/L. Finally, we computationally optimized the mcjA ribosome-binding site (RBS) to enhance translation efficiency. RBS optimization revealed that a moderate translation initiation efficiency (550,584 arbitrary units [au]) maximized production, whereas excessive efficiency (2,019,712 au) impaired growth and output. These interventions synergistically increased the MccJ25 titer 10-fold, reaching 430 mg/L in batch culture. Our findings establish a robust platform for MccJ25 overproduction, highlighting promoter engineering and translational tuning as pivotal strategies for antimicrobial peptide biosynthesis. This study provides insights for overcoming metabolic constraints in microbial fermentation, advancing the development of peptide-based therapeutics against multidrug-resistant pathogens.

Sows and piglets face heightened oxidative stress during gestation and lactation, yet strategies to simultaneously mitigate these challenges remain underexplored. This study investigated the effects of β-carotene and superoxide dismutase (SOD) supplementation on 140 Landrace × Yorkshire sows (parity 3–5) randomly assigned to (1) a control; (2) long-term low-dose treatment (25 mg/kg β-carotene, 4 mg/kg SOD, or both) throughout gestation–lactation; or (3) short-term high-dose treatment (100 mg/kg β-carotene, 14 mg/kg SOD, or both) administered 7 days pre/post-weaning and farrowing. Our data indicate that the antioxidants enhanced the productive performance of both sows and piglets, with the most pronounced effect observed in the long-term, low-dose combined administration of β-carotene and SOD. The composite antioxidants significantly improved the systemic antioxidant capacity in sows, while concurrently reducing the cortisol and lipopolysaccharide concentrations in the serum. This enhancement contributed to elevations in serum progesterone and prolactin levels at day 40 of gestation and farrowing, respectively, ultimately increasing the number of weaned piglets and decreasing the backfat loss. In addition, the compound antioxidants improved the serum antioxidant indices of piglets, increased the growth hormone concentrations, and improved the litter weight gain. Mechanistically, the placental upregulation of CAT, GPX1, and GLUT3, alongside Claudin1, Occludin, and ZO-1 expression, underpinned improved nutrient transport and barrier function. These findings demonstrate that β-carotene and SOD synergistically transfer antioxidant capacity via placental and colostrum pathways, offering a viable strategy for integrated sow–piglet management.

ABSTRACT Paenibacillus species have attracted much attention as a promising cell factory that can yield a variety of bioactive peptides and functional exopolysaccharides. Improving the production capacity of Paenibacillus through genetic engineering is crucial for the development of bioactive natural products. This study systematically evaluated the effects of electroporation transformation parameters on the introduction of DNA into Paenibacillus elgii 219, which was isolated from soil and preserved in our lab. The transformation efficiency was improved to 1.25 × 10 6 transformants/μg DNA by optimizing factors including the growth and recovery media content, the growth stages of P. elgii 219, electric field strength, electroporation buffer composition, cell wall weakening, and DNA quality. The results represent the highest transformation efficiency reported thus far for Paenibacillus . This work further established a group II intron-based gene editing system suitable for P. elgii 219 for the first time. As expected, plasmid pDX4383 was successfully transferred into P. elgii 219, and a putative glycosyltransferase gene was deleted, thereby eliminating flocculent precipitation during fermentation. Taken together, this study demonstrates that the electroporation-mediated transformation of exogenous DNA combined with group II intron-based gene editing provides an effective approach for the genetic engineering of Paenibacillus bacteria. IMPORTANCE The establishment of an efficient plasmid DNA transformation protocol for P. elgii 219 has established a robust foundation for further in-depth investigations into its physiological and metabolic processes. Additionally, the successful advancement of group II intron-mediated gene editing technology imbues P. elgii 219 with the potential to serve as a highly efficient cell factory. These accomplishments furnish novel perspectives and references for the exploration of other Paenibacillus species in environmental contexts and the development of their products with economic value.

BACKGROUND:Placenta is highly susceptible to oxidative stress during pregnancy, which is a major cause of abnormal vascular development, fetal growth restriction and preterm birth. Methionine exhibits remarkable efficacy in promoting embryonic development and pregnancy outcomes, yet the role of methionine in placental antioxidant capacity and angiogenesis remains unclear. METHODS:Pregnant rats and porcine iliac artery endothelial cells (PIECs) were used in our study. Pregnant rats were fed with methionine supplementation or methionine free diet. PIECs were treated with methionine, ROS inducer, VEGFR1 inhibitor, CTNNB1 knockdown or overexpressing. RESULTS:Our findings revealed that dietary methionine supplementation significantly increased the levels of glutathione, while reducing the levels of malondialdehyde in rat placentae. Moreover, experiments from PIECs treatment with ROS inducer, VEGFR1 inhibitor, knockdown or overexpressing of CTNNB1 revealed that methionine regulated angiogenesis in the placenta by modulating ROS levels and the CTNNB1 signaling pathway. Mechanistically, methionine enhanced the transsulfuration metabolism in placental vascular cells, leading to the production of the antioxidant glutathione and a reduction in ROS levels, followed by activating the WNT3A/CTNNB1 signaling pathway. CTNNB1 bind to PIGF, which promoted the phosphorylation of VEGFR1, thereby enhancing angiogenesis. CONCLUSIONS:This study elucidated that methionine promoted placental angiogenesis through the ROS-WNT3A/CTNNB1-PIGF-VEGFR1 axis, providing new therapeutic targets for pregnancy complications.

Zinc plays a crucial role in the gut barrier function and are widely used for the prevention of bowel disease. However, the mechanism via which zinc supplementation exerts this regulatory effect is unclear. The present study identifies and characterizes the zinc-responsive activation of AKT and demonstrates its function in alleviating gut barrier dysfunction. Mechanistically, zinc increased intracellular SAM production, a methyl donor, by promoting the activation of the metallochaperone ZNG1-METAP1 complex. Subsequently, zinc facilitates methylation (symmetrical dimethylarginine, SDMA) of AKT at residues R391 and R15, which is facilitated by PRMT5. The AKTSDMA modification promotes AKT translocation from the cytoplasm to the plasma membrane and its interaction with mTORC2, ultimately promoting AKT activation and cell proliferation. Notably, histidine has an antagonistic effect on zinc-induced the AKT activation, cell proliferation, and gut barrier improvement by chelating zinc. These results demonstrate that zinc activates AKT and alleviates gut barrier dysfunction by inducing activation of the ZNG1-METAP1-PRMT5-AKTSDMA pathway, and highlight that limiting histidine intake may have effective therapeutic potential for bowel diseases such as Crohn's disease and Ulcerative colitis.

Endometrial receptivity and maternal-fetal immune tolerance are two crucial processes for a successful pregnancy. However, the molecular mechanisms of nutrition involved are largely unexplored. Here, we showed that maternal methionine supply significantly improved pregnancy outcomes, which was closely related to interleukin-5 (IL-5) concentration. Mechanistically, methionine induced embryonic IL-5 secretion, which enhanced the conversion of CD4+ T cells to IL-5+ Th2 cells in the uterus, thereby improving maternal-fetal immune tolerance. Meanwhile, methionine-mediated IL-5 secretion activated the nuclear factor κB (NF-κB) pathway and enhanced integrin αvβ3 expression in endometrial cells, which improved endometrial receptivity. Further, methionine strongly influenced the DNA methylation and transcription levels of the transcription factor eomesodermin (Eomes), which bound directly to the IL-5 promoter region and inhibited IL-5 transcription. Methionine modulated IL-5 transcription, maternal-fetal immune tolerance, and endometrial receptivity via its effects on Eomes. This study reveals the crucial functions of methionine and IL-5 and offers a potential nutritional strategy for successful pregnancy.

Growing concerns over foodborne pathogens and limitations of chemical preservatives have intensified the search for natural antimicrobial alternatives. Soil-dwelling Bacillus-like microorganisms have emerged as a potential gold mine for the discovery of natural bioactive peptides. Therefore, in this study, we isolated the Brevibacillus laterosporus strain 811, which specifically inhibits the growth of Enterobacteriaceae pathogens. The antimicrobial peptide in the isolate was purified and identified as brevicidine. In vitro activity assays were used to confirm the excellent antibacterial activity of brevicidine against foodborne pathogens such as Escherichia coli (E. coli) and Salmonella. Brevicidine exhibited high stability, low hemolytic activity, minimal cytotoxicity, and no induction of bacterial resistance. In a mouse model challenged with a cocktail of E. coli and Salmonella, brevicidine pretreatment significantly mitigated weight loss and diarrhea severity, while improving survival rates. Mechanistically, brevicidine prevented infection-induced decrease in tight junction proteins and microbial dysbiosis, thereby preserving intestinal mucosal morphology and ameliorating barrier function impairment and inflammation. Notably, brevicidine enriched the beneficial taxa Lactobacillus and Akkermansia. The strong antimicrobial efficacy, safety, and stability of brevicidine both in vitro and in vivo highlight its potential as a natural antimicrobial agent and food preservative, providing an effective alternative for controlling foodborne pathogens and enhancing food safety.

The objective of this study is to investigate the digestion and metabolism characteristics of amino acids and glucose in energy and protein feeds, and to establish regression equations to accurately predict their release rates in vivo based on the in vitro digestion characteristics of the feedstuffs. A total of 9 energy feedstuffs and 19 protein feedstuffs were selected for in vitro digestion simulation experiments. Additionally, four representative energy and protein feeds were then chosen for the portal vein, femoral artery, and femoral vein blood cannulation experiments in growing pigs. The results showed that among the nine energy feedstuffs tested, wheat bran presented the highest degree of digestion, followed by wheat, whereas potato had the lowest degree of digestion. The digestibility of starch at different time points in vitro was linearly correlated with the crude fiber content, total starch content, and ratio of amylose to amylopectin (R2 = 0.61~0.96). Among the 19 protein feedstuffs tested, peas released the highest total amount of amino acids, followed by sugar beet meal. The in vivo digestibility and metabolism trial in cannulated pigs showed that the total amino acid release was linearly correlated with the in vitro amino acid release rates, dry matter, crude protein, neutral detergent fiber, crude fat, and total energy of the feedstuffs (R2 = 0.93~0.99).

Crude protein, as a traditional standard for characterizing dietary nitrogen content, fails to reflect protein bioavailability. Digestible protein (DP) emphasizes the importance of total available proteins and offers better adaptability in low-protein diversified diets. The objective of this study was to establish and validate the digestible protein (DP) requirement for 80–110 kg finishing pigs (Duroc × Yorkshire × Landrace). In Experiment 1, 450 pigs were fed diets with graded DP levels (8.82–11.26%). Linear and quadratic regression models identified 9.55% DP as the optimal level, optimizing average daily gain and feed efficiency (R2 ≥ 0.94). Experiment 2 validated this requirement using three diet treatments and 270 pigs: high-protein traditional, low-protein traditional, and low-protein diversified. No significant differences were observed in growth performance, carcass traits, or meat quality among diets, confirming the robustness of 9.55% DP across formulations. Plasma urea nitrogen and total amino acids increased linearly with DP (p < 0.05), while hepatic transcriptomics revealed immune and metabolic partial impairments in high-protein traditional diet pigs, which may be linked to nitrogen overload. Muscle tissues from different treatment groups showed minimal transcriptional differences, emphasizing efficient protein utilization when amino acid requirements are met. This study demonstrates that 9.55% DP, combined with balanced amino acids, supports productivity in both traditional and diversified diets, reducing reliance on resource-intensive feed ingredients. These findings advocate for DP as a precise metric in swine production, thereby promoting sustainable development.

The Diqing Tibetan (TP) pig is an roughage tolerance breed that inhabits an area with the highest altitude distribution in the world and can be maintained on a diet containing 90% forage material in confined production systems. Our results showed that TP pigs had a strong capability for high-efficiency utilization of arabinose and xylose. Metagenomic analysis revealed that the secretion of carbohydrate esterases was mainly undertaken by fecal strains of Microbacterium, Alistipes, Acinetobacter, and Faecalibacterium, while Microbacterium, Prevotella, Turicibacter, Lactobacillus, Clostridium and Streptococcus were responsible for most of the secretion of glycoside hydrolases. Then, a brand new species, which was named Microbacterium sp. Qiao 01 was captured and appeared to have the highest fiber utilization ability in vitro, degrading 36.54% of the neutral detergent fiber in corn stover. Our results provide strong evidence that efficient utilization of dietary fiber by TP pigs is due to the emergence of highly specialized microbial strategies in the gut. Microorganisms showed preferences and a clear division of labor in the degradation process of dietary fiber. This study has great practical significance for improving the utilization efficiency of livestock feed and alleviating the tension of food insecurity.