{"title":"Excess backfat deposition and restricted feeding in gestating sows: An overview of mechanisms compromising their health and performance, and regulatory effects of functional dietary fibers","authors":"Shenghuang Cai, Yujiao Chen, Yu Liang, Jinping Deng, Guixin Dong, Chengquan Tan","doi":"10.1016/j.aninu.2025.08.012","DOIUrl":"https://doi.org/10.1016/j.aninu.2025.08.012","url":null,"abstract":"","PeriodicalId":8184,"journal":{"name":"Animal Nutrition","volume":"65 1","pages":""},"PeriodicalIF":6.3,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-07DOI: 10.1016/j.aninu.2025.11.005
Dujuan Zheng, Fernando Y. Yamamoto, Yahong Yao, Zhihao Zhou, Qiyou Xu
This study investigated nutritional programming (NP) in largemouth bass (<ce:italic>Micropterus salmoides</ce:italic>) by examining the long-term effects of early soybean meal (SBM) exposure on growth, immunity, and intestinal health. In Phase 1 (fry stage, 28 days), 720 fry (28 days post-hatch, initial body weight 0.17 ± 0.06 g) were divided into two groups (six replicates per group). They were fed either a fishmeal (FM)-based diet (FM1) or 15% SBM diet (SBM1). In Phase 2 (juvenile stage, 56 days), a cross-over feeding trial was conducted, generating four groups (four replicates per group): F1F2 (FM1→FM2,), F1S2 (FM1→25% SBM [SBM2]), S1F2 (SBM1→FM2), and S1S2 (SBM1→SBM2). Phase 1 SBM feeding (SBM1) impaired fry survival, intestinal relative weight, and villus width (<ce:italic>P</ce:italic> < 0.05), and triggered intestinal inflammation and microbial dysbiosis. Compared to the FM1 group, the SBM1 group exhibited downregulated expression of key intestinal health-related genes, including the tight junction protein gene <ce:italic>claudin-1</ce:italic>, the anti-inflammatory factor interleukin-10 (<ce:italic>IL-10</ce:italic>), and lysozyme (<ce:italic>LZM</ce:italic>). In contrast, it upregulated the expression of pro-inflammatory genes, including nuclear factor kappa-B (<ce:italic>NF-κβ</ce:italic>), interleukin-15 (<ce:italic>IL-15</ce:italic>), and interferon gamma 1 (<ce:italic>IFN-γ1</ce:italic>) (<ce:italic>P</ce:italic> < 0.05). In Phase 2, continuous SBM exposure (S1S2 group) impaired growth performance, as evidenced by significantly lower final body weight and a poorer feed conversion ratio (<ce:italic>P</ce:italic> < 0.05), but enhanced hepatic alkaline phosphatase (AKP) and LZM activities (<ce:italic>P</ce:italic> < 0.001). Concurrently, the S1S2 group developed an immunologically tolerant intestinal phenotype, characterized by a significant upregulation (<ce:italic>P</ce:italic> < 0.05) of: 1) regulatory T cell (Treg)-related transcription factors, including forkhead box P3 (<ce:italic>Foxp3</ce:italic>) and Ikaros family zinc finger protein elios (<ce:italic>Helios</ce:italic>); 2) the Treg-associated signaling molecule signal transducer and activator of transcription 5b (<ce:italic>Stat5b</ce:italic>); 3) immunoregulatory cytokines, including transforming growth factor-β (<ce:italic>TGF-β</ce:italic>) and interleukin-10 (<ce:italic>IL-10</ce:italic>); and 4) the immune tolerance-related molecule tumor necrosis factor alpha-induced protein 2 (<ce:italic>TNFAIP2</ce:italic>), without a concomitant increase in the pro-inflammatory cytokine interleukin-15 (<ce:italic>IL-15</ce:italic>). Continuous SBM exposure (S1S2) also improved gut microbiota composition, characterized by increased abundance of Firmicutes and <ce:italic>Streptococcus</ce:italic> and decreased abundance of Proteobacteria. These changes were accompanied by a significant downregulation of the arachidonic acid metabolic pathway (<ce:italic>P</ce:italic> <
{"title":"Nutritional programming through early exposure to soybean meal: Effects on growth performance, intestinal health, metabolism, and microbiota of juvenile largemouth bass (Micropterus salmoides)","authors":"Dujuan Zheng, Fernando Y. Yamamoto, Yahong Yao, Zhihao Zhou, Qiyou Xu","doi":"10.1016/j.aninu.2025.11.005","DOIUrl":"https://doi.org/10.1016/j.aninu.2025.11.005","url":null,"abstract":"This study investigated nutritional programming (NP) in largemouth bass (<ce:italic>Micropterus salmoides</ce:italic>) by examining the long-term effects of early soybean meal (SBM) exposure on growth, immunity, and intestinal health. In Phase 1 (fry stage, 28 days), 720 fry (28 days post-hatch, initial body weight 0.17 ± 0.06 g) were divided into two groups (six replicates per group). They were fed either a fishmeal (FM)-based diet (FM1) or 15% SBM diet (SBM1). In Phase 2 (juvenile stage, 56 days), a cross-over feeding trial was conducted, generating four groups (four replicates per group): F1F2 (FM1→FM2,), F1S2 (FM1→25% SBM [SBM2]), S1F2 (SBM1→FM2), and S1S2 (SBM1→SBM2). Phase 1 SBM feeding (SBM1) impaired fry survival, intestinal relative weight, and villus width (<ce:italic>P</ce:italic> < 0.05), and triggered intestinal inflammation and microbial dysbiosis. Compared to the FM1 group, the SBM1 group exhibited downregulated expression of key intestinal health-related genes, including the tight junction protein gene <ce:italic>claudin-1</ce:italic>, the anti-inflammatory factor interleukin-10 (<ce:italic>IL-10</ce:italic>), and lysozyme (<ce:italic>LZM</ce:italic>). In contrast, it upregulated the expression of pro-inflammatory genes, including nuclear factor kappa-B (<ce:italic>NF-κβ</ce:italic>), interleukin-15 (<ce:italic>IL-15</ce:italic>), and interferon gamma 1 (<ce:italic>IFN-γ1</ce:italic>) (<ce:italic>P</ce:italic> < 0.05). In Phase 2, continuous SBM exposure (S1S2 group) impaired growth performance, as evidenced by significantly lower final body weight and a poorer feed conversion ratio (<ce:italic>P</ce:italic> < 0.05), but enhanced hepatic alkaline phosphatase (AKP) and LZM activities (<ce:italic>P</ce:italic> < 0.001). Concurrently, the S1S2 group developed an immunologically tolerant intestinal phenotype, characterized by a significant upregulation (<ce:italic>P</ce:italic> < 0.05) of: 1) regulatory T cell (Treg)-related transcription factors, including forkhead box P3 (<ce:italic>Foxp3</ce:italic>) and Ikaros family zinc finger protein elios (<ce:italic>Helios</ce:italic>); 2) the Treg-associated signaling molecule signal transducer and activator of transcription 5b (<ce:italic>Stat5b</ce:italic>); 3) immunoregulatory cytokines, including transforming growth factor-β (<ce:italic>TGF-β</ce:italic>) and interleukin-10 (<ce:italic>IL-10</ce:italic>); and 4) the immune tolerance-related molecule tumor necrosis factor alpha-induced protein 2 (<ce:italic>TNFAIP2</ce:italic>), without a concomitant increase in the pro-inflammatory cytokine interleukin-15 (<ce:italic>IL-15</ce:italic>). Continuous SBM exposure (S1S2) also improved gut microbiota composition, characterized by increased abundance of Firmicutes and <ce:italic>Streptococcus</ce:italic> and decreased abundance of Proteobacteria. These changes were accompanied by a significant downregulation of the arachidonic acid metabolic pathway (<ce:italic>P</ce:italic> <","PeriodicalId":8184,"journal":{"name":"Animal Nutrition","volume":"52 1","pages":""},"PeriodicalIF":6.3,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-07DOI: 10.1016/j.aninu.2025.12.002
Honglei Guo, Shudong Liu, Manhua You, Xinbo Zhang, Shugeng Wu, Xinghua Zhao, Wanyu Shi, Ning Ma
Fatty liver hemorrhagic syndrome (FLHS) is a metabolic disease in laying hens. Total flavonoids from <ce:italic>Abrus cantoniensis</ce:italic> (TFAC) comprise multiple bioactive compounds with potential benefits against FLHS. This study aimed to explore the effects and mechanism of TFAC in improving FLHS. Firstly, analysis by liquid chromatography-tandem mass spectrometry identified 20 flavonoid compounds in the TFAC, including vicenin-3 and acacetin. Subsequently, 144 laying hens at 28 weeks of age with similar body weight (1.45 ± 0.03 kg) were randomly divided into six groups (eight replicates per group and three hen per replicate, <ce:italic>n</ce:italic> = 8) : a control group (standard diet), an FLHS model group (high-energy and low-protein diet), three TFAC-supplemented groups (0.25, 0.50, 1.00 g/kg), and a positive control group (1.00 g/kg choline chloride). After a two-week acclimation, the formal experiment lasted four weeks. Total flavonoids from <ce:italic>A</ce:italic>. <ce:italic>cantoniensis</ce:italic> significantly alleviated FLHS-induced alterations by reducing excessive liver weight (<ce:italic>P</ce:italic> < 0.001) and abdominal fat weight (<ce:italic>P</ce:italic> < 0.001), and decreasing hepatic lipid accumulation (triacylglycerol, total cholesterol, free fatty acids; <ce:italic>P</ce:italic> < 0.05) as well as serum lipid levels (triacylglycerol, total cholesterol, aspartate aminotransaminase, alanine aminotransferase, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol; <ce:italic>P</ce:italic> < 0.05). It also enhanced hepatic antioxidant capacity (total antioxidant capacity, superoxide dismutase, glutathione peroxidase; <ce:italic>P</ce:italic> < 0.05) and attenuated inflammation (as shown by decreased levels of interleukin-6, nuclear factor kappa-B, cyclooxygenase-2; <ce:italic>P</ce:italic> < 0.05). Moreover, TFAC regulated cecal metabolites and microbiota, especially increasing Se-Methyl-L-selenocysteine (<ce:italic>P</ce:italic> = 0.043) and probiotic <ce:italic>Akkermansia</ce:italic> (<ce:italic>P</ce:italic> = 0.028), as well as elevating lithocholic acid-3-sulfate (<ce:italic>P</ce:italic> < 0.001) and isodeoxycholic acid (<ce:italic>P</ce:italic> = 0.020). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed that TFAC upregulated farnesoid X receptor (<ce:italic>FXR</ce:italic>; <ce:italic>P</ce:italic> = 0.017) and organic solute transporter-β (<ce:italic>P</ce:italic> = 0.038) in the ileum. Meanwhile, in the liver, <ce:italic>FXR</ce:italic> (<ce:italic>P</ce:italic> = 0.040) and small heterodimer partner (<ce:italic>P</ce:italic> < 0.001) were increased, and fatty acid synthase (<ce:italic>P</ce:italic> = 0.003) was inhibited. In conclusion, this study demonstrated that TFAC ameliorated FLHS through multiple mechanisms, including attenuating hepatic inflammation, enhancing antioxidant capacity, and modulating cecal metabolites and microbio
{"title":"Total flavonoids from Abrus cantoniensis alleviate fatty liver hemorrhagic syndrome in laying hens by regulating inflammation, oxidative stress, and cecal metabolites and microbiota","authors":"Honglei Guo, Shudong Liu, Manhua You, Xinbo Zhang, Shugeng Wu, Xinghua Zhao, Wanyu Shi, Ning Ma","doi":"10.1016/j.aninu.2025.12.002","DOIUrl":"https://doi.org/10.1016/j.aninu.2025.12.002","url":null,"abstract":"Fatty liver hemorrhagic syndrome (FLHS) is a metabolic disease in laying hens. Total flavonoids from <ce:italic>Abrus cantoniensis</ce:italic> (TFAC) comprise multiple bioactive compounds with potential benefits against FLHS. This study aimed to explore the effects and mechanism of TFAC in improving FLHS. Firstly, analysis by liquid chromatography-tandem mass spectrometry identified 20 flavonoid compounds in the TFAC, including vicenin-3 and acacetin. Subsequently, 144 laying hens at 28 weeks of age with similar body weight (1.45 ± 0.03 kg) were randomly divided into six groups (eight replicates per group and three hen per replicate, <ce:italic>n</ce:italic> = 8) : a control group (standard diet), an FLHS model group (high-energy and low-protein diet), three TFAC-supplemented groups (0.25, 0.50, 1.00 g/kg), and a positive control group (1.00 g/kg choline chloride). After a two-week acclimation, the formal experiment lasted four weeks. Total flavonoids from <ce:italic>A</ce:italic>. <ce:italic>cantoniensis</ce:italic> significantly alleviated FLHS-induced alterations by reducing excessive liver weight (<ce:italic>P</ce:italic> < 0.001) and abdominal fat weight (<ce:italic>P</ce:italic> < 0.001), and decreasing hepatic lipid accumulation (triacylglycerol, total cholesterol, free fatty acids; <ce:italic>P</ce:italic> < 0.05) as well as serum lipid levels (triacylglycerol, total cholesterol, aspartate aminotransaminase, alanine aminotransferase, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol; <ce:italic>P</ce:italic> < 0.05). It also enhanced hepatic antioxidant capacity (total antioxidant capacity, superoxide dismutase, glutathione peroxidase; <ce:italic>P</ce:italic> < 0.05) and attenuated inflammation (as shown by decreased levels of interleukin-6, nuclear factor kappa-B, cyclooxygenase-2; <ce:italic>P</ce:italic> < 0.05). Moreover, TFAC regulated cecal metabolites and microbiota, especially increasing Se-Methyl-L-selenocysteine (<ce:italic>P</ce:italic> = 0.043) and probiotic <ce:italic>Akkermansia</ce:italic> (<ce:italic>P</ce:italic> = 0.028), as well as elevating lithocholic acid-3-sulfate (<ce:italic>P</ce:italic> < 0.001) and isodeoxycholic acid (<ce:italic>P</ce:italic> = 0.020). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed that TFAC upregulated farnesoid X receptor (<ce:italic>FXR</ce:italic>; <ce:italic>P</ce:italic> = 0.017) and organic solute transporter-β (<ce:italic>P</ce:italic> = 0.038) in the ileum. Meanwhile, in the liver, <ce:italic>FXR</ce:italic> (<ce:italic>P</ce:italic> = 0.040) and small heterodimer partner (<ce:italic>P</ce:italic> < 0.001) were increased, and fatty acid synthase (<ce:italic>P</ce:italic> = 0.003) was inhibited. In conclusion, this study demonstrated that TFAC ameliorated FLHS through multiple mechanisms, including attenuating hepatic inflammation, enhancing antioxidant capacity, and modulating cecal metabolites and microbio","PeriodicalId":8184,"journal":{"name":"Animal Nutrition","volume":"2 1","pages":""},"PeriodicalIF":6.3,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study employed multi-omics approaches to reveal soybean meal (SBM) -induced alterations in gut microbiota and metabolic disturbances in largemouth bass (<ce:italic>Micropterus salmoides</ce:italic>), providing important insights for aquaculture nutrition. Four isonitrogenous and isolipidic diets, named fishmeal (FM, control), SBM10, SBM30, and SBM50, were formulated by replacing 0%, 10%, 30%, and 50% FM with SBM. A total of 240 healthy largemouth bass (initial weight: 11.00 ± 0.2 g) were randomly assigned into four groups, each in triplicate, with 20 fish per tank. The experiment lasted for 56 days. The results demonstrated an inclusion level-dependent reduction in the final average weight, weight gain rate, and specific growth rate as SBM replacement levels increased, with the SBM50 group showing the lowest values (<ce:italic>P</ce:italic> < 0.05). The plica height, plica width, and the number of goblet cells were significantly lower in the SBM50 group compared to the FM group (<ce:italic>P</ce:italic> < 0.05). Immunohistochemical results revealed decreased mucin 2 content in the SBM50 group compared to the FM group. Lipopolysaccharide content and fluorescein isothiocyanate-dextran (FITC-dextran) absorbance value in the SBM50 group were significantly higher than those in the FM group (<ce:italic>P</ce:italic> < 0.05). The intestinal microbiota analysis showed that, compared to the FM group, the SBM50 group exhibited markedly lower abundances of beneficial genera (<ce:italic>Roseburia</ce:italic> and <ce:italic>Lactococcus</ce:italic>) but higher levels of potential pathogens (<ce:italic>Salmonella</ce:italic> and <ce:italic>Enterobacter</ce:italic>; linear discriminant analysis score > 4.0) (<ce:italic>P</ce:italic> < 0.05). Metabolomic analysis showed significant differences between FM and SBM50 groups, with decreased levels of indolelactic acid, indole-3-butyric acid, and L-glutamine but elevated soyasaponin i, soyasaponin ii, and linoleic acid levels (<ce:italic>P</ce:italic> < 0.05). Transcriptome analysis further revealed significant enrichment of phosphatidylinositol 3-kinase—protein kinase B (PI3K-Akt) and nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway (NF-κB) signaling pathways in the SBM50 group compared with the FM group (<ce:italic>P</ce:italic> < 0.05). Concurrently, key intestinal epithelial barrier genes, including zonula occludens-1 (<ce:italic>zo-1</ce:italic>), <ce:italic>claudin-1</ce:italic>, epithelial cadherin (<ce:italic>E-cadherin</ce:italic>), and myosin heavy chain 10 (<ce:italic>myosin-10</ce:italic>), were markedly downregulated (<ce:italic>P</ce:italic> < 0.05). These results indicate that a substitution level not exceeding 30% did not adversely affect the growth performance of largemouth bass. Higher replacement levels impair growth performance and trigger intestinal inflammation by disrupting gut microbiota homeostasis, altering key metabolites, and comp
{"title":"Multi-omics reveals soybean meal-induced gut microbiota alterations and metabolic disturbances in largemouth bass (Micropterus salmoides): Implications for aquaculture nutrition","authors":"Rongyan Yue, Fengyu Qu, Haiqing Wu, Xiaojie Li, Xinghua Zhou, Yongjun Chen, Shimei Lin, Qinghui Ai, Yuanfa He","doi":"10.1016/j.aninu.2025.12.003","DOIUrl":"https://doi.org/10.1016/j.aninu.2025.12.003","url":null,"abstract":"This study employed multi-omics approaches to reveal soybean meal (SBM) -induced alterations in gut microbiota and metabolic disturbances in largemouth bass (<ce:italic>Micropterus salmoides</ce:italic>), providing important insights for aquaculture nutrition. Four isonitrogenous and isolipidic diets, named fishmeal (FM, control), SBM10, SBM30, and SBM50, were formulated by replacing 0%, 10%, 30%, and 50% FM with SBM. A total of 240 healthy largemouth bass (initial weight: 11.00 ± 0.2 g) were randomly assigned into four groups, each in triplicate, with 20 fish per tank. The experiment lasted for 56 days. The results demonstrated an inclusion level-dependent reduction in the final average weight, weight gain rate, and specific growth rate as SBM replacement levels increased, with the SBM50 group showing the lowest values (<ce:italic>P</ce:italic> < 0.05). The plica height, plica width, and the number of goblet cells were significantly lower in the SBM50 group compared to the FM group (<ce:italic>P</ce:italic> < 0.05). Immunohistochemical results revealed decreased mucin 2 content in the SBM50 group compared to the FM group. Lipopolysaccharide content and fluorescein isothiocyanate-dextran (FITC-dextran) absorbance value in the SBM50 group were significantly higher than those in the FM group (<ce:italic>P</ce:italic> < 0.05). The intestinal microbiota analysis showed that, compared to the FM group, the SBM50 group exhibited markedly lower abundances of beneficial genera (<ce:italic>Roseburia</ce:italic> and <ce:italic>Lactococcus</ce:italic>) but higher levels of potential pathogens (<ce:italic>Salmonella</ce:italic> and <ce:italic>Enterobacter</ce:italic>; linear discriminant analysis score > 4.0) (<ce:italic>P</ce:italic> < 0.05). Metabolomic analysis showed significant differences between FM and SBM50 groups, with decreased levels of indolelactic acid, indole-3-butyric acid, and L-glutamine but elevated soyasaponin i, soyasaponin ii, and linoleic acid levels (<ce:italic>P</ce:italic> < 0.05). Transcriptome analysis further revealed significant enrichment of phosphatidylinositol 3-kinase—protein kinase B (PI3K-Akt) and nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway (NF-κB) signaling pathways in the SBM50 group compared with the FM group (<ce:italic>P</ce:italic> < 0.05). Concurrently, key intestinal epithelial barrier genes, including zonula occludens-1 (<ce:italic>zo-1</ce:italic>), <ce:italic>claudin-1</ce:italic>, epithelial cadherin (<ce:italic>E-cadherin</ce:italic>), and myosin heavy chain 10 (<ce:italic>myosin-10</ce:italic>), were markedly downregulated (<ce:italic>P</ce:italic> < 0.05). These results indicate that a substitution level not exceeding 30% did not adversely affect the growth performance of largemouth bass. Higher replacement levels impair growth performance and trigger intestinal inflammation by disrupting gut microbiota homeostasis, altering key metabolites, and comp","PeriodicalId":8184,"journal":{"name":"Animal Nutrition","volume":"141 1","pages":""},"PeriodicalIF":6.3,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-06DOI: 10.1016/j.aninu.2025.10.004
Wenpeng Wu, Shuyue Wang, Chenyu Xue, Na Dong
{"title":"Role of gut microbiota metabolites in maintaining intestinal health and preventing weaning-associated diarrhea in piglets","authors":"Wenpeng Wu, Shuyue Wang, Chenyu Xue, Na Dong","doi":"10.1016/j.aninu.2025.10.004","DOIUrl":"https://doi.org/10.1016/j.aninu.2025.10.004","url":null,"abstract":"","PeriodicalId":8184,"journal":{"name":"Animal Nutrition","volume":"131 1","pages":""},"PeriodicalIF":6.3,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-06DOI: 10.1016/j.aninu.2025.10.005
Santiago N. Saez-Torillo, Rebecca Danielsson, Tuan Q. Nguyen, Joana Lima, Matthew A. Cleveland, Rainer Roehe, Marina Martínez-Álvaro
Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.
{"title":"Predicting beef diet nutritional composition and intake from rumen metagenomic profiles","authors":"Santiago N. Saez-Torillo, Rebecca Danielsson, Tuan Q. Nguyen, Joana Lima, Matthew A. Cleveland, Rainer Roehe, Marina Martínez-Álvaro","doi":"10.1016/j.aninu.2025.10.005","DOIUrl":"https://doi.org/10.1016/j.aninu.2025.10.005","url":null,"abstract":"Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (<ce:italic>n</ce:italic> = 70) and Charolais crossbred (<ce:italic>n</ce:italic> = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately <ce:italic>postmortem</ce:italic> and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included <ce:italic>Mitsuokella</ce:italic>, <ce:italic>Selenomonas</ce:italic>, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.","PeriodicalId":8184,"journal":{"name":"Animal Nutrition","volume":"259 1","pages":""},"PeriodicalIF":6.3,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145957132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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