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Keywords = rumen microbes

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17 pages, 847 KB  
Article
Supplementation of Rosemary Extract Improves Lactation Performance and Rumen Function in Dairy Buffaloes Under Hot Weather
by Yinghui Li, Chenglong Li, Hanxing Yao, Pingting Liu, Mengwei Li, Xingguo Huang and Chengjian Yang
Animals 2026, 16(2), 216; https://doi.org/10.3390/ani16020216 (registering DOI) - 11 Jan 2026
Abstract
Rosemary extract (RE), rich in carnosic and rosmarinic acid, which have antibacterial/antioxidant/anti-inflammatory effects, is a potential natural feed supplement for heat-stressed dairy buffaloes. This study systematically evaluated dietary RE effects on dairy buffaloes during hot weather. Twenty Mediterranean dairy buffaloes were randomly allocated [...] Read more.
Rosemary extract (RE), rich in carnosic and rosmarinic acid, which have antibacterial/antioxidant/anti-inflammatory effects, is a potential natural feed supplement for heat-stressed dairy buffaloes. This study systematically evaluated dietary RE effects on dairy buffaloes during hot weather. Twenty Mediterranean dairy buffaloes were randomly allocated into two groups for a 35-day trial: the control (CON) group receiving a basal diet, and the RE group receiving the same basal diet supplemented with 20 g/d of RE. Results showed RE tended to reduce buffalo body surface temperature; increased milk production, 4% fat-corrected milk, milk protein, lactose, and solids-not-fat; and optimized milk fatty acid profiles. In regard to blood, the RE group exhibited higher catalase activity, total antioxidant capacity, and concentrations of immunoglobulin A and M, together with lower concentrations of the pro-inflammatory cytokines interleukin-1β and tumor necrosis factor-α. Additionally, RE markedly elevated concentrations of total volatile fatty acid, acetate, propionate, and butyrate; improved microbial α-diversity indices (Sobs and Ace); and increased the abundances of Rikenellaceae_RC9_gut_group and Butyrivibrio spp., as well as the enrichment of multiple genera belonging to the family Lachnospiraceae. In conclusion, supplementing the diet of heat-stressed dairy buffaloes with 20 g/d of RE improves milk production and composition-related performance by optimizing the rumen ecosystem and enhancing systemic health status, with these effects observed as short-term responses under the conditions of the present study. Full article
(This article belongs to the Special Issue Use of Agro-Industrial Co-Products in Animal Nutrition)
34 pages, 477 KB  
Review
Revisiting Environmental Sustainability in Ruminants: A Comprehensive Review
by Yufeng Shang, Tingting Ju, Upinder Kaur, Henrique A. Mulim, Shweta Singh, Jacquelyn Boerman and Hinayah Rojas de Oliveira
Agriculture 2026, 16(2), 149; https://doi.org/10.3390/agriculture16020149 - 7 Jan 2026
Viewed by 286
Abstract
Ruminant livestock production faces increasing pressure to reduce environmental impacts while maintaining productivity and food security. This comprehensive review examines current strategies and emerging technologies for enhancing environmental sustainability in ruminant systems. The review synthesizes recent advances across four interconnected domains: genetic and [...] Read more.
Ruminant livestock production faces increasing pressure to reduce environmental impacts while maintaining productivity and food security. This comprehensive review examines current strategies and emerging technologies for enhancing environmental sustainability in ruminant systems. The review synthesizes recent advances across four interconnected domains: genetic and genomic approaches for breeding environmentally efficient animals, rumen microbiome manipulation, nutritional strategies for emission reduction, and precision management practices. Specifically, genetic and genomic strategies demonstrate significant potential for long-term sustainability improvements through selective breeding for feed efficiency, methane reduction, and enhanced longevity. Understanding host–microbe interactions and developing targeted interventions have also shown promising effects on optimizing fermentation efficiency and reducing methane production. Key nutritional interventions include dietary optimization strategies that improve feed efficiency, feed additives, and precision feeding systems that minimize nutrient waste. Furthermore, management approaches encompass precision livestock farming technologies including sensor-based monitoring systems, automated feeding platforms, and real-time emission measurement tools that enable data-driven decision making. Integration of these approaches through system-based frameworks offers the greatest potential for achieving substantial environmental improvements while maintaining economic viability. In addition, this review identifies key research gaps including the need for standardized measurement protocols, long-term sustainability assessments, and economic evaluation frameworks. Future directions emphasize the importance of interdisciplinary collaboration, policy support, and technology transfer to accelerate adoption of sustainable practices across diverse production systems. Full article
(This article belongs to the Special Issue The Threats Posed by Environmental Factors to Farm Animals)
16 pages, 271 KB  
Article
Ensiling Time and Mixed Microbe Fermented Liquid Modulate In Vitro Digestibility and Rumen Fermentation of Fermented Total Mixed Rations
by Sineenart Polyorach, Wichai Suphalucksana, Ampon Klompanya, Chalermpon Yuangklang, Metha Wanapat, Seangla Cheas, Anusorn Cherdthong, Sungchhang Kang, Pongsatorn Gunun, Nirawan Gunun, Suban Foiklang, Phongthorn Kongmun, Nattaya Montri and Kanokrat Srikijkasemwat
Vet. Sci. 2026, 13(1), 6; https://doi.org/10.3390/vetsci13010006 - 20 Dec 2025
Viewed by 227
Abstract
This study investigated how varying the ensiling period and the level of mixed microbes fermented liquid (MMFL) influences the chemical composition, in vitro degradability, rumen fermentation profile, and microbial ecology of fermented total mixed rations (FTMR). A completely randomized 4 × 4 factorial [...] Read more.
This study investigated how varying the ensiling period and the level of mixed microbes fermented liquid (MMFL) influences the chemical composition, in vitro degradability, rumen fermentation profile, and microbial ecology of fermented total mixed rations (FTMR). A completely randomized 4 × 4 factorial design was used, incorporating four fermentation durations (0, 7, 14, and 21 days) and four MMFL inclusion rates (0, 0.5, 1.0, and 1.5% of DM). Both factors exerted significant effects on FTMR quality (p < 0.05). The combination of a 14-day fermentation period with 0.5% MMFL consistently produced the most desirable outcomes. Under these conditions, crude protein concentration rose from 12.0% to 14.3% of DM, while neutral-detergent fiber declined from 54.2% to 49.1%. Improvements were also observed in in vitro digestibility, with DM and OM increasing by 9–12% relative to the untreated control (p < 0.05). Fermentation end-products were enhanced, as total volatile fatty acids increased by 15% (92.4 vs. 80.1 mmol/L), and the molar proportion of propionate increased from 24.5 to 29.2 mol/100 mol, thereby lowering the acetate-to-propionate ratio (2.4 vs. 3.0; p < 0.05). Estimated methane production declined by 18% (p < 0.01). Microbial counts reflected a shift toward a more efficient fermentative community, with bacterial and fungal populations increasing by 21% and 18%, and protozoa decreasing by 25% (p < 0.05). Overall, moderate MMFL supplementation during a 14-day ensiling phase enhanced nutrient conservation and fermentation efficiency, suggesting practical value for improving FTMR utilization in ruminant systems. Further in vivo and economic evaluations remain necessary. Full article
(This article belongs to the Special Issue Feed Fermentation and Animal Health: Nutrition and Metabolism)
15 pages, 670 KB  
Article
Diet Acceptance and Utilization Responses to Increasing Doses of Thymol in Beef Steers Consuming Forage
by Emma P. Fukuda, Jordan P. Suter, Russell W. Jessup and Merritt L. Drewery
Animals 2025, 15(24), 3637; https://doi.org/10.3390/ani15243637 - 17 Dec 2025
Viewed by 206
Abstract
Thymol is an antimicrobial terpene with potential as a feed additive for cattle; however, in vivo data describing the response of forage-fed beef cattle to the increasing provision of thymol is limited. As thymol may affect palatability and exert antimicrobial effects on rumen [...] Read more.
Thymol is an antimicrobial terpene with potential as a feed additive for cattle; however, in vivo data describing the response of forage-fed beef cattle to the increasing provision of thymol is limited. As thymol may affect palatability and exert antimicrobial effects on rumen microbes, defining its effects in vivo is critical to inform adoption. Accordingly, the objectives of this study were to evaluate cattle acceptance of thymol and characterize the effects of increasing thymol doses on diet utilization and ruminal fermentation, with the overarching goal of identifying a maximum tolerable dose for beef cattle. Two 4 × 4 Latin Square experiments were conducted using beef steers consuming forage and providing thymol dosed on alfalfa. Experiment 1 assessed acceptance of thymol at increasing concentrations (0, 110, 220, and 330 mg/kg intake), and experiment 2 assessed diet utilization and fermentation in response to one of four thymol doses: 0, 120, 240, and 480 mg/kg intake. For experiment 1, thymol dose did not affect treatment or forage intake (p ≥ 0.17). For experiment 2, thymol did not linearly or quadratically affect (p ≥ 0.28) forage organic matter (OM) intake or OM digestibility. There were also no linear or quadratic effects (p ≥ 0.09) on ruminal ammonia-N, volatile fatty acids, or pH. These data indicate that thymol can be provided to beef cattle at up to 330 mg/kg intake and 480 mg/kg intake without negatively impacting acceptance and diet utilization, respectively. Full article
(This article belongs to the Special Issue Feed Additives in Animal Nutrition)
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20 pages, 4350 KB  
Article
Rumen Microbial Diversity and Metabolome Analysis Reveals the Effects of Alkaline Metal Ion Complexes on Muscle Quality of Lambs
by Yang Zi, Yilin Yang, Mingyue Li, Yalin Li, Ziyi An, Mengjiao Liu, Chi Ma, Feng Gao and Changqing Li
Biology 2025, 14(12), 1791; https://doi.org/10.3390/biology14121791 - 16 Dec 2025
Viewed by 335
Abstract
This study investigated the effects of dietary supplementation with an alkaline metal ion complex (AMIC) on growth performance, meat quality, rumen microbiota, and metabolome in Hu lambs. Fifty lambs were randomly assigned to either a control group (basal diet) or an AMIC group [...] Read more.
This study investigated the effects of dietary supplementation with an alkaline metal ion complex (AMIC) on growth performance, meat quality, rumen microbiota, and metabolome in Hu lambs. Fifty lambs were randomly assigned to either a control group (basal diet) or an AMIC group (basal diet + 0.15% AMIC) for 60 days. The results showed that AMIC significantly increased carcass weight, Longissimus dorsi area, crude protein, intramuscular fat, ash content, and meat luminosity (L*). Amino acid profiles and key flavor compounds were elevated, while off-flavor hydrocarbons were reduced. 16S rRNA sequencing revealed that AMIC altered rumen microbiota composition, enriching butyrate-producing genera such as Butyrivibrio and Saccharofermentans. Metabolomic analysis identified 398 differentially expressed metabolites, with upregulated pathways including butanoate metabolism and xylene degradation. Correlation analyses indicated strong associations between specific microbial taxa, metabolites, and meat quality traits. These findings suggest that AMIC enhances meat quality by modulating rumen microbial ecology and metabolic pathways, leading to improved nutrient deposition and flavor development. This study provides novel insights into the microbe–metabolite–muscle axis in ruminants and supports the use of AMIC as a dietary strategy for quality lamb production. Full article
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17 pages, 6244 KB  
Article
Host-Adapted Ruminal Microbiota Investigation and Functional Validation of Duolang Sheep-Derived Ligilactobacillus salivarius KS1018
by Zixuan Wang, Yuchen Jia, Shiyu Duan, Hui Jiang, Cong Peng, Mingwei Mao, Yiping Zhu and Jing Li
Vet. Sci. 2025, 12(12), 1177; https://doi.org/10.3390/vetsci12121177 - 10 Dec 2025
Viewed by 280
Abstract
This study characterized the rumen microbiota of Duolang sheep, a Xinjiang local breed, to identify potential probiotics for Hu sheep. 16S rRNA sequencing revealed that Duolang sheep possessed a distinct rumen microbial structure (beta-diversity, p < 0.05), lower diversity (higher Simpson index, p [...] Read more.
This study characterized the rumen microbiota of Duolang sheep, a Xinjiang local breed, to identify potential probiotics for Hu sheep. 16S rRNA sequencing revealed that Duolang sheep possessed a distinct rumen microbial structure (beta-diversity, p < 0.05), lower diversity (higher Simpson index, p < 0.01), and a higher Firmicutes-to-Bacteroidetes ratio compared to Hu sheep. Subsequently, a Duolang-derived strain, Ligilactobacillus salivarius (L. salivarius) KS1018, was evaluated in a 56-day feeding trial with Hu sheep. Supplementation enhanced systemic immunity (serum IgG and IgM) and antioxidant status (SOD) (p < 0.05). Metabolic profiles were also modified, with serum β-hydroxybutyrate (BHB) level increasing significantly in both medium-dose (p < 0.001) and high-dose (p < 0.05) groups, whereas BUN and lipid markers (TG, CHOL) elevated significantly in the medium-dose (p < 0.05) and high-dose group (p < 0.05), respectively. The strain with medium- and high-dose also reduced fecal crude fat (p < 0.01) and influenced mucosal secretory immunoglobulin A (sIgA) by increasing levels in the duodenum while decreasing them in the rumen (p < 0.05). Ruminal histology was also altered (p < 0.01). Spearman’s correlation analysis showed that Prevotellaceae_UCG-003 was positively correlated with serum BUN (p < 0.001), IgM (p < 0.05), BHB (p < 0.01), and SOD (p < 0.01). Overall, L. salivarius KS1018 improved antioxidant capacity, systemic and mucosal immunity, and ruminal structure in Hu sheep, demonstrating its potential to influence host–microbe interactions in livestock. Full article
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20 pages, 1239 KB  
Article
Effects of Initiation Age of Starter Feeding on Growth Performance, Immunity and Antioxidant Capacity, Gastrointestinal Development, and Microbial Communities in Suckling Lambs
by Shaoyang Pang, Xiangjian Peng, Shu Li, Junli Niu, Wenqi Wang, Yanfeng Liu, Cunxi Nie and Wenju Zhang
Microorganisms 2025, 13(11), 2490; https://doi.org/10.3390/microorganisms13112490 - 30 Oct 2025
Viewed by 498
Abstract
The optimal timing for initiating starter feeding in lambs remains controversial, warranting a systematic evaluation of its effects across multiple indicators. This study investigated the effects of initiating starter feeding at 7, 14, or 21 days of age on growth performance, rumen fermentation, [...] Read more.
The optimal timing for initiating starter feeding in lambs remains controversial, warranting a systematic evaluation of its effects across multiple indicators. This study investigated the effects of initiating starter feeding at 7, 14, or 21 days of age on growth performance, rumen fermentation, serum immunity, gastrointestinal development, and microbiota in Hu lambs. Forty-five newborn lambs were randomly assigned to three groups (n = 15 per group) and fed starter until slaughter at weaning (60 days). The 14-day group exhibited significantly higher body weight (BW) at 49 and 60 days compared with the 7-day group (p < 0.05), and greater average daily gain (ADG) during 28–35 days than the 21-day group. Rumen ammonia nitrogen (NH3-N), acetate, propionate, valerate, and total volatile fatty acids (VFAs) were higher in the 7-day and 14-day groups than in the 21-day group (p < 0.05). The 14-day group showed lower pro-inflammatory cytokines (IL-1β, TNF-α) and higher immunoglobulins (IgA, IgG, IgM) and anti-inflammatory cytokines (IL-2, IL-4) (p < 0.05). This group also displayed improved rumen papilla width, jejunal villus dimensions, and reduced crypt depth. Beneficial microbes such as Christensenellaceae_R-7_group and Butyrivibrio were enriched in the 14-day and 21-day groups. In conclusion, initiating starter feeding at 14 days of age optimizes growth, rumen function, immune response, and colonization of beneficial microbiota in Hu lambs. Full article
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12 pages, 1649 KB  
Article
Untargeted GC-MS Metabolic Profiling of Anaerobic Gut Fungi Reveals Putative Terpenoids and Strain-Specific Metabolites
by Lazarina V. Butkovich, Candice L. Swift, Chaevien S. Clendinen, Heather M. Olson, Samuel O. Purvine, Oliver B. Vining and Michelle A. O’Malley
Metabolites 2025, 15(9), 578; https://doi.org/10.3390/metabo15090578 - 29 Aug 2025
Viewed by 1410
Abstract
Background/Objectives: Anaerobic gut fungi (Neocallimastigomycota) are biotechnologically relevant, lignocellulose-degrading microbes with under-explored biosynthetic potential for secondary metabolites. Untargeted metabolomic profiling with gas chromatography–mass spectrometry (GC-MS) was applied to two gut fungal strains, Anaeromyces robustus and Caecomyces churrovis, to establish a foundational [...] Read more.
Background/Objectives: Anaerobic gut fungi (Neocallimastigomycota) are biotechnologically relevant, lignocellulose-degrading microbes with under-explored biosynthetic potential for secondary metabolites. Untargeted metabolomic profiling with gas chromatography–mass spectrometry (GC-MS) was applied to two gut fungal strains, Anaeromyces robustus and Caecomyces churrovis, to establish a foundational metabolomic dataset to identify metabolites and provide insights into gut fungal metabolic capabilities. Methods: Gut fungi were cultured anaerobically in rumen-fluid-based media with a soluble substrate (cellobiose), and metabolites were extracted using the Metabolite, Protein, and Lipid Extraction (MPLEx) method, enabling metabolomic and proteomic analysis from the same cell samples. Samples were derivatized and analyzed via GC-MS, followed by compound identification by spectral matching to reference databases, molecular networking, and statistical analyses. Results: Distinct metabolites were identified between A. robustus and C. churrovis, including 2,3-dihydroxyisovaleric acid produced by A. robustus and maltotriitol, maltotriose, and melibiose produced by C. churrovis. C. churrovis may polymerize maltotriose to form an extracellular polysaccharide, like pullulan. GC-MS profiling potentially captured sufficiently volatile products of proteomically detected, putative non-ribosomal peptide synthetases and polyketide synthases of A. robustus and C. churrovis. The triterpene squalene and triterpenoid tetrahymanol were putatively identified in A. robustus and C. churrovis. Their conserved, predicted biosynthetic genes—squalene synthase and squalene tetrahymanol cyclase—were identified in A. robustus, C. churrovis, and other anaerobic gut fungal genera. Conclusions: This study provides a foundational, untargeted metabolomic dataset to unmask gut fungal metabolic pathways and biosynthetic potential and to prioritize future efforts for compound isolation and identification. Full article
(This article belongs to the Section Microbiology and Ecological Metabolomics)
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22 pages, 2868 KB  
Article
Impact of Heat Stress on Rumen Fermentation Patterns and Microbiota Diversity and Its Association with Thermotolerance in Indigenous Goats
by Mullakkalparambil Velayudhan Silpa, Veerasamy Sejian, Chinnasamy Devaraj, Artabandhu Sahoo and Raghavendra Bhatta
Fermentation 2025, 11(8), 450; https://doi.org/10.3390/fermentation11080450 - 1 Aug 2025
Viewed by 1206
Abstract
Goats are considered to be the ideal climate-resilient animal species in the tropics. Fewer studies are documented assessing the heat stress response of caprine ruminal microbiota, which can also be a crucial indicator of the resilience and/or adaptability of animals. This study was [...] Read more.
Goats are considered to be the ideal climate-resilient animal species in the tropics. Fewer studies are documented assessing the heat stress response of caprine ruminal microbiota, which can also be a crucial indicator of the resilience and/or adaptability of animals. This study was conducted to comparatively assess the heat stress responses of two indigenous goat breeds, Nandidurga and Bidri, based on changes associated with the rumen fermentation pattern and distribution pattern of rumen microbiota. A total of 24 adult animals were randomly allocated into four groups of six animals each, NC (n = 6; Nandidurga control), NHS (n = 6; Nandidurga heat stress), BC (n = 6; Bidri control) and BHS (n = 6; Bidri heat stress). The animals were reared in climate chambers for a duration of 45 days wherein the NC and BC animals were maintained under thermoneutral temperature while the NHS and BHS animals were subjected to simulated heat stress. Heat stress was observed to significantly reduce the rumen ammonia, extracellular CMCase, intracellular carboxy methyl cellulase (CMCase) and total CMCase both in Nandidurga and Bidri goats. In addition to this, a significant reduction in acetate, propionate and total volatile fatty acids (VFAs) was observed in Nandidurga goats. The V3–V4 16s rRNA sequencing further revealed a significant alteration in the rumen microbiota in heat-stressed Nandidurga and Bidri goats. While both the breeds exhibited nearly similar responses in the rumen microbial abundance levels due to heat stress, breed-specific differences were also observed. Furthermore, the LEFSe analysis revealed a significant alteration in the abundances of microbes at the genus level, which were observed to be relatively greater in Bidri goats than Nandidurga goats. Furthermore, these alterations were predicted to impair the functional pathways, especially pathways associated with metabolism. This study therefore provided an insight into the rumen microbial dynamics in heat-stressed goats. Though both the breeds exhibited excellent resilience to the subjected heat stress, there were relatively less ruminal alterations in Nandidurga goats than in Bidri goats. Full article
(This article belongs to the Special Issue Research Progress of Rumen Fermentation)
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24 pages, 3960 KB  
Article
Effect of Dietary Tyrosine on Behavior and Ruminal Meta-Taxonomic Profile of Altay Sheep with Different Temperaments
by Asmita Thapa, Weidong Huang, Shahab Ur Rehman, Muhammad Hammad Zafar, Jinying Zhang, Luoyang Ding and Mengzhi Wang
Vet. Sci. 2025, 12(8), 684; https://doi.org/10.3390/vetsci12080684 - 22 Jul 2025
Viewed by 872
Abstract
The objective of this study was to evaluate the effect of tyrosine on behavior and ruminal meta-taxonomic profile of Altay sheep. Twelve rams with the lowest behavioral responses to humans and twelve rams with the highest behavioral responses were sorted into calm and [...] Read more.
The objective of this study was to evaluate the effect of tyrosine on behavior and ruminal meta-taxonomic profile of Altay sheep. Twelve rams with the lowest behavioral responses to humans and twelve rams with the highest behavioral responses were sorted into calm and nervous groups, respectively. Following the 2 × 2 factorial design, the rams from each group were equally assigned two treatments of a basal diet and a diet with an extra 4 g of tyrosine for 30 d. The temperament trait, growth performance, rumen fermentation parameters, ruminal epithelium antioxidant capacity, and rumen microbial composition were measured at the end of the feeding experiment. The results showed that tyrosine treatment led to a decreased number of crosses in the arena test in nervous sheep (p < 0.05). The tyrosine treatment led to increased antioxidant markers in the rumen epithelium, such as catalase, total antioxidant capacity, and GSH content in rumen epithelial tissues (p < 0.05) in calm and nervous sheep. The total volatile fatty acids and propionic acid content in the rumen were increased by tyrosine treatment in nervous and calm sheep (p < 0.05). The rumen microbial study revealed that the dominant microbial genera were Cryptobacteroides, Prevotella, Limivicinus, Quinella, UBA1711, RUG740, Sachharofermentans, Limomorpha, Soladiphilus, Flexinia, and others in both the tyrosine treatment and temperament groups. A combined effect of treatment and temperament was seen on the abundance of two microbial genera, UBA1711 and RUG740 (p < 0.05). These findings suggest that tyrosine-treated Altay sheep would experience less stress during production, resulting in reduced oxidative stress in the rumen epithelium and improved propionic acid production in the rumen compared with that of basal-diet-treated Altay sheep. Meanwhile, the effect of the dietary tyrosine treatment on ruminal microbial diversity was lower, suggesting lesser degradation of tyrosine by ruminal microbes in Altay sheep. Full article
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19 pages, 3218 KB  
Article
Multi-Omics Integration Reveals the Impact of Gastrointestinal Microbiota on Feed Efficiency in Tan Sheep
by Guohan Sun, Xiaohong Han, Tonggao Liu, Xinrui Zhang, An Shi, Chong Yang and Jinzhong Tao
Microorganisms 2025, 13(7), 1608; https://doi.org/10.3390/microorganisms13071608 - 8 Jul 2025
Viewed by 1097
Abstract
The rumen and intestinal microbiota play a pivotal role in the digestion and absorption processes of ruminants. Elucidating the mechanisms by which gastrointestinal microbiota influence the feed conversion ratio (FCR) in ruminants is significantly important for enhancing feed utilization efficiency in these animals. [...] Read more.
The rumen and intestinal microbiota play a pivotal role in the digestion and absorption processes of ruminants. Elucidating the mechanisms by which gastrointestinal microbiota influence the feed conversion ratio (FCR) in ruminants is significantly important for enhancing feed utilization efficiency in these animals. In this study, RT-qPCR, 16S rRNA sequencing, and metabolomic techniques were systematically employed to compare the microbial community structures in the rumen, cecum, and rectum, as well as the differences in rumen metabolites between high- and low-FCR Tan sheep. The results showed that, compared to the HFCR group of Tan sheep, the LFCR group exhibited a significant reduction in unclassified_f__Selenomonadaceae, Blvii28_wastewater-sludge_group, and Papillibacter in the rumen; a significant increase in Lachnospiraceae_AC2044_group and Sanguibacteroides; a significant reduction in unclassified_f__Peptostreptococcaceae, Clostridium_sensu_stricto_1, and Parasutterella in the cecum; a significant increase in norank_f__Bacteroidales_UCG-001; and a significant reduction in norank_f__Muribaculaceae, Blautia, and Turicibacter in the rectum. There is a significant positive correlation between Parasutterella in the cecum and three microorganisms, including unclassified_f__Selenomonadaceae, in the rumen. Additionally, Blvii28_wastewater-sludge_group was positively correlated with Lactobacillus. Furthermore, unclassified_f__Selenomonadaceae in the rumen was positively correlated with Turicibacter, unclassified_f__Peptostreptococcaceae, and Breznakia in the rectum. Blvii28_wastewater-sludge_group also showed positive correlations with Blautia, norank_f__Muribaculaceae, and Clostridium_sensu_stricto_1, while Papillibacter was positively correlated with Faecalitalea. The metabolomic results indicated that, compared to the HFCR group, 261 differential metabolites, including Phenylacetylglutamine and Populin, in the rumen of Tan sheep in the LFCR group were significantly downregulated, whereas 36 differential metabolites, including Glycyl-L-tyrosine, were significantly upregulated. Furthermore, the rumen microbe unclassified_f__Selenomonadaceae exhibited positive correlations with significantly differential metabolites such as L-tryptophan, Etiocholanolone glucuronide, N-acetyl-O-demethylpuromycin, and 6-deoxyerythronolide B. Blvii28_wastewater-sludge_group and Papillibacter also exhibited positive correlations with Icilin. High and low FCRs in the rumen of Tan sheep were investigated, especially in relation to unclassified_f__Selenomonadaceae, Blvii28_wastewater-sludge_group, and Papillibacter. Correlations can be seen with microorganisms such as Parasutatella and Lactobacillus in the cecum; Turicibacter, norank_f__Bacteroideales_UCG-001, and Blautia in the rectum; and metabolites such as L-tryptophan, Etiocholanolone glucuronide, and N-acetyl-O-demethylpuromycin. This reveals the role of microorganisms in the digestion and absorption of Tan sheep feed, thus providing a preliminary basis for further research on the microbial regulation of ruminant animal feed utilization and a theoretical basis for improving Tan sheep feed utilization efficiency. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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18 pages, 3150 KB  
Article
Synergistic Adaptations of Yak Rumen Microbiota, Metabolites and Host to Altitudinal
by Jianming Ren, Xiong Ma, Pengfei Zhao, Lan Zhang, Shiyu Tao, Xiangyan Wang and Bingang Shi
Microorganisms 2025, 13(7), 1543; https://doi.org/10.3390/microorganisms13071543 - 30 Jun 2025
Cited by 2 | Viewed by 999
Abstract
Rumen microbiota and metabolites play important roles in energy metabolism and immune regulation in the host. However, the underlying mechanisms of their interaction with the host to regulate yak plateau adaptation remain unknown. In this study, the effects of altitude on the rumen [...] Read more.
Rumen microbiota and metabolites play important roles in energy metabolism and immune regulation in the host. However, the underlying mechanisms of their interaction with the host to regulate yak plateau adaptation remain unknown. In this study, the effects of altitude on the rumen microbiome, metabolome, and fermentation parameters of yaks were analyzed. The fiber content of pasture grasses increased with altitude, while crude protein content was significantly higher at an altitude of 2800 m (T2800) compared to an altitude of 4500 m (T4500) (p < 0.05). The acetic acid, propionic acid, and volatile fatty acids of yaks in the T4500 group were significantly higher than in the T2800 group (p < 0.05). Simpson’s index of rumen microorganisms in the T4500 group of yaks was significantly higher than in T2800 and T3500 yaks. The relative abundance of Rikenellaceae_RC9_gut_group and Succiniclasticum was significantly higher in T4500 than in T2800, while Prevotella and Streptococcus were more abundant in T2800 than in T4500. Rumen metabolomics analyses revealed that yak rumen metabolites at different altitudes were influenced by forage and altitude, mainly affecting energy metabolism and fatty acid biosynthesis (such as purine and glycerophospholipid metabolism). In summary, altitude may influence rumen microbes and metabolites through pasture nutrient composition. Full article
(This article belongs to the Special Issue Gut Bacterial Community: Competition and Mutualism)
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21 pages, 1321 KB  
Review
Exploration of Multi-Source Lignocellulose-Degrading Microbial Resources and Bioaugmentation Strategies: Implications for Rumen Efficiency
by Xiaokang Lv, Zhanhong Qiao, Chao Chen, Jinling Hua and Chuanshe Zhou
Animals 2025, 15(13), 1920; https://doi.org/10.3390/ani15131920 - 29 Jun 2025
Cited by 4 | Viewed by 1056
Abstract
Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive [...] Read more.
Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems. Full article
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25 pages, 5190 KB  
Article
In Vitro Evaluation of Enzymatically Transformed Alfalfa Saponins on Methane Reduction, Rumen Microbes and Metabolomics in Goats
by Ran Zhang, Xinran Bao, Xingqi Shi, Shixuan Jin, Ying Meng, Zhiwei Li, Zhumei Du and Xuebing Yan
Animals 2025, 15(11), 1516; https://doi.org/10.3390/ani15111516 - 22 May 2025
Cited by 1 | Viewed by 978
Abstract
Alfalfa (Medicago sativa L.) saponins (AS), primarily pentacyclic triterpenoids, may reduce methane emissions from goats (Capra hircus L.). This study evaluated the methane-suppressing potential of Aspergillus niger β-glucosidase-modified AS using in vitro rumen fermentation (0.10 mg/mL inoculum, 24 h incubation, gas [...] Read more.
Alfalfa (Medicago sativa L.) saponins (AS), primarily pentacyclic triterpenoids, may reduce methane emissions from goats (Capra hircus L.). This study evaluated the methane-suppressing potential of Aspergillus niger β-glucosidase-modified AS using in vitro rumen fermentation (0.10 mg/mL inoculum, 24 h incubation, gas chromatography detection). Among the 21 alfalfa cultivars, Pegasis (fall dormancy 9) exhibited the highest antioxidant efficacy (half maximum effective concentration 2.13 mg/mL) and the lowest ferric-reducing activity (0.32 μM Fe2+/g) (p < 0.05). Fresh/silage AS reduced methane proportions to 4.50–5.21% of total gas, while enzymatic biotransformation further decreased it to 3.34–3.48% (p < 0.05). Methanogen abundance declined by 20.10–44.93%, and general anaerobic fungi declined by 34.22–44.66% compared to untreated AS (p < 0.05). Metabolomics linked methane suppression to six pathways, including zeatin biosynthesis (via nucleotide metabolites accumulation) and prolactin signaling pathway (via bioactive molecules downregulation), suggesting impaired methanogen energy metabolism and hydrogen flux redirection as mechanisms. Enzymatic AS also enhanced volatile fatty acid production, indicating improved fiber digestion. These in vitro findings demonstrate that enzyme-treated AS modulates rumen fermentation through dual methane mitigation and nutrient utilization enhancement, offering a sustainable feed additive strategy for livestock. Full article
(This article belongs to the Section Small Ruminants)
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Article
Effects of Chenopodium album L. Substitution Levels and Harvest Time on In Vitro Rumen Fermentation and Methane Production in Early-Fattening Hanwoo Steers
by Narantuya Batburged, Gui-Seck Bae, Gurbazar Damdinsuren, Sang-Yoon Kim, Hye-An Lee, Soo-Yeon Jung, In-Ki Kang, Da-Hyun Choi and Chang-Hyun Kim
Animals 2025, 15(10), 1372; https://doi.org/10.3390/ani15101372 - 9 May 2025
Viewed by 1462
Abstract
This study investigated the feasibility of incorporating Chenopodium album L. (CAL) into ruminant feed ingredients through evaluating the effects of harvest time and substitution levels on in vitro rumen fermentation. In the first phase, a sole-substrate experiment was conducted using CAL harvested from [...] Read more.
This study investigated the feasibility of incorporating Chenopodium album L. (CAL) into ruminant feed ingredients through evaluating the effects of harvest time and substitution levels on in vitro rumen fermentation. In the first phase, a sole-substrate experiment was conducted using CAL harvested from June to August, analyzing its chemical composition and total saponins content. The impact of harvest time on fermentation parameters was assessed with CAL as the sole substrate. The second phase involved a mixed-substrate experiment using an early-fattening Hanwoo diet (30% rice straw and 70% concentrate), where increasing proportions of CAL (control: 0%, T1: 5%, T2: 10%, T3: 15%, and T4: 20%) replaced rice straw. Seasonal variations in CAL composition influenced the fermentation characteristics. CAL harvested in July exhibited higher fermentability, with total volatile fatty acids (TVFAs) reaching 103.87 mM at 72 h. In contrast, CAL harvested in August showed lower fermentability and digestibility. However, August-harvested CAL was selected for the subsequent experiment, as it provided a more practical balance of sufficient biomass yield and a higher saponins concentration, aligned with the study’s methane mitigation objectives, while also exhibiting a fiber composition comparable to that of rice straw. We hypothesized that the saponins in CAL contribute to methane reductions. Supplementation with 15% of CAL significantly reduced methane production per gram of inoculated and digested dry matter (p < 0.05), likely due to differences in crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), and saponins content. However, despite having the lowest fiber content, T4 (20% CAL) exhibited the lowest in vitro dry matter digestibility (IVDMD), suggesting that factors such as saponins, CAL’s chemical composition, or microbial shifts may have hindered digestibility. Ammonia–nitrogen production increased from 0 to 3 h, but it continuously decreased between 3 and 9 h due to microbial growth and nitrogen assimilation, as microbes incorporate ammonia into their biomass (p < 0.05). Fermentation characteristics further revealed that the acetate-to-propionate (A/P) ratio decreased with increasing CAL levels, with T4 showing the lowest ratio (1.55 at 72 h), confirming a shift toward propionate-based fermentation. Notably, T2 (10% CAL) showed an optimized fermentation efficiency, producing the highest TVFA concentration at 24 h (98.28 mM). These findings highlight the potential for using CAL as a functional feed ingredient, with moderate substitution levels (10–15%) enhancing fermentation efficiency while reducing methane production. Full article
(This article belongs to the Section Animal Nutrition)
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