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Keywords = ruminal microbiota

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21 pages, 7854 KB  
Article
Effect of Dietary Calcium Nitrate Addition on Methane Emission, Nitrogen Excretion, and Ruminal Fermentation Parameters and Microbiota in Liuyang Black Goats
by Mingming Li, Ting Liu, Chen Zheng, Xuan Nan, Jun Wang, Baicong Chen and Hanfang Zeng
Animals 2026, 16(8), 1150; https://doi.org/10.3390/ani16081150 - 10 Apr 2026
Viewed by 186
Abstract
This research explored how dietary supplementation of calcium nitrate influences methane emissions, nitrogen excretion, ruminal fermentation parameters, and microbiota in Liuyang black goats. A total of twelve male goats from this breed were divided into two groups: one serving as a control group [...] Read more.
This research explored how dietary supplementation of calcium nitrate influences methane emissions, nitrogen excretion, ruminal fermentation parameters, and microbiota in Liuyang black goats. A total of twelve male goats from this breed were divided into two groups: one serving as a control group (CON), while the other received a treatment of 3% calcium nitrate (CAL). The research was conducted over a period of 40 days and comprised two separate trial phases. A 10-day adaptation period and a 5-day sampling period (days 11–15) for each stage. Results showed that incorporating calcium nitrate significantly reduced the emissions of methane (CH4) (p < 0.05) and carbon dioxide (CO2) (p < 0.05). Moreover, the use of calcium nitrate modified the trends in ruminal fermentation, resulting in an increase in pH (p < 0.05). Moreover, the ratio of acetate to propionate (A:P) was notably reduced in the CAL group (p < 0.05), indicating a shift toward enhanced production of propionate. At the microbial level, an increased presence of Bacteroidota and Prevotella was observed in the CAL group (p < 0.05). In contrast, the CON group exhibited elevated levels of Firmicutes and Methanobrevibacter (p < 0.05). This finding suggests that calcium nitrate plays a significant role in reducing methane emissions and also affects the fermentation processes in the rumen along with the microbiota of Liuyang black goats. Further research is needed to examine the long-term implications of calcium nitrate supplementation on the health and productivity of these goats. Full article
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20 pages, 746 KB  
Article
Evaluation of the Hindgut Microbiota and Volatile Fatty Acid Profile of Steers Fed Finishing Feedlot Ration Supplemented with or Without Calcium Gluconate
by Osman Y. Koyun, Evann E. Rowland, Jeferson M. Lourenco, Kenneth E. Griswold, Joseph J. Baloyi, Francis L. Fluharty, T. Dean Pringle, Alexander M. Stelzleni, R. Lawton Stewart and Todd R. Callaway
Microorganisms 2026, 14(4), 802; https://doi.org/10.3390/microorganisms14040802 - 1 Apr 2026
Viewed by 275
Abstract
Growing Angus steers (n = 20) were blocked by weight and randomly assigned to one of two treatment groups: Control group (CON, n = 10) fed a feedlot ration ad libitum, or a ruminally protected hydrogenated fat-embedded calcium gluconate (HFCG) treatment group (HFCG, [...] Read more.
Growing Angus steers (n = 20) were blocked by weight and randomly assigned to one of two treatment groups: Control group (CON, n = 10) fed a feedlot ration ad libitum, or a ruminally protected hydrogenated fat-embedded calcium gluconate (HFCG) treatment group (HFCG, n = 10), which was fed the control ration top-dressed at 16 g/head/day for 55 days. During the slaughter process, digesta samples were collected from the cecum, colon, and rectum. Acetate concentrations were greater in the cecal and rectal digesta of steers (p ≤ 0.05) in the HFCG treatment group. Propionate concentrations were greater in the cecal, colonic, and rectal (p ≤ 0.05) digesta of steers in the HFCG treatment group. Butyrate concentrations were greater (p = 0.098) in the colon digesta of steers in the HFCG treatment group; however, they were not different in the cecal and rectal digesta. To determine the microbial composition within each section of the hindgut, DNA was extracted, and 16S rRNA gene sequencing was performed. Data were analyzed using a General Linear Model with dietary treatment as the main effect. Species richness in the cecum, colon, and rectum was not different between treatments. Erysipelotrichaceae, Peptostreptococcaceae, and Atopobiaceae abundances were increased (p ≤ 0.05) in the cecal bacterial community of steers in the HFCG group, while a significant decrease (p ≤ 0.05) in Rikenellaceae and Muribaculaceae abundances was recorded within the same bacterial community. In the colon bacterial community of steers in the HFCG group, Ruminococcaceae and Muribaculaceae abundances were elevated (p ≤ 0.05), while there was a reduction (p ≤ 0.05) in Lachnospiraceae, Erysipelotrichaceae, Atopobiaceae, and Peptostreptococcaceae abundances. Paeniclostridium, Romboutsia, and Turicibacter abundances were increased (p ≤ 0.05) in the cecal bacterial community of steers in the HFCG group, while there was a decrease (p ≤ 0.05) in Rikenellaceae_RC9 _gut_group abundance within the same bacterial community. In the colon microbiota of steers in the HFCG group, Turicibacter abundance was decreased (p ≤ 0.05). Supplementing growing steers with HFCG impacted some members of the bacterial populations, which have important roles in gut homeostasis and health, along with the formation of beneficial end-products in the gastrointestinal tract. Full article
(This article belongs to the Special Issue Advances in Host-Gut Microbiota)
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26 pages, 8506 KB  
Article
Multi-Omics Analysis Reveals That Alkaline Mineral Complex Reshapes Rumen Mucosal Microbiota and Metabolites and Enhances Rumen Epithelial Barrier Function in Fattening Cattle
by Xingyu Liu, Li Gu, Jia Li, Xiaowan Liu, Quan Mo, Liping Gou, Yixin Wang, Jiancheng Qi and Zhicai Zuo
Animals 2026, 16(6), 992; https://doi.org/10.3390/ani16060992 - 22 Mar 2026
Viewed by 343
Abstract
High-concentrate diets are widely used to enhance growth performance in fattening beef cattle; however, they often compromise rumen epithelial integrity, increasing the risk of rumenitis and systemic inflammation. Supplementation with alkaline mineral complex (AMC) has been shown to alleviate these adverse effects, although [...] Read more.
High-concentrate diets are widely used to enhance growth performance in fattening beef cattle; however, they often compromise rumen epithelial integrity, increasing the risk of rumenitis and systemic inflammation. Supplementation with alkaline mineral complex (AMC) has been shown to alleviate these adverse effects, although the underlying mechanisms remain largely unexplored. In this study, AMC supplementation was associated with improved rumen epithelial integrity and remodeling of the rumen microbiota, characterized by a reduction in Bacteroidota and Prevotella, and an enrichment of Sarcina sp. DSM11001 and Fibrobacter spp., with the latter identified as a key microbial biomarker in the AMC group. Integrated metabolomic and transcriptomic analyses revealed activation of the tryptophan metabolism pathway and accumulation of several anti-inflammatory metabolites, including sulfinpyrazone, Thr-Leu, and 4-guanidinobutyric acid. These metabolomic changes were correlated with the upregulation of tight junction pathways and increased expression of related proteins, which in turn were associated with enhanced epithelial barrier integrity and reduced systemic inflammation in the AMC group. Collectively, these findings suggest that AMC supplementation may protect rumen epithelial integrity by modulating the microbial community and altering ruminal metabolite profiles. This study provides insights into nutritional strategies to prevent epithelial damage under high-concentrate feeding conditions and support the potential use of AMC to maintain rumen health in fattening cattle. Full article
(This article belongs to the Collection Feeding Cattle for Health Improvement)
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21 pages, 2373 KB  
Article
Coated Betaine Improves Lamb Meat Quality and Flavor by Modulating Rumen Microbial Flora
by Shude Shi, Xiongxiong Li, Shangwu Ma, Yuzhu Sha, Yuling Qu and Shengguo Zhao
Animals 2026, 16(6), 970; https://doi.org/10.3390/ani16060970 - 20 Mar 2026
Viewed by 280
Abstract
The sensory quality and flavor of lamb meat, critical to market competitiveness, are influenced by rumen microbial fermentation and dietary management strategies. Coated betaine (CBet), a rumen-protected methyl donor, exerts systemic nutritional regulation in ruminants. This study explored the effects of CBet supplementation [...] Read more.
The sensory quality and flavor of lamb meat, critical to market competitiveness, are influenced by rumen microbial fermentation and dietary management strategies. Coated betaine (CBet), a rumen-protected methyl donor, exerts systemic nutritional regulation in ruminants. This study explored the effects of CBet supplementation on lamb meat quality using 18 Dorset ♂ × Hu sheep ♀ F1 crossbred lambs, randomly assigned to either a control group (basal diet) or a 0.20% CBet-supplemented diet for 60 days (n = 9 per group). The results demonstrated that CBet significantly increased ruminal concentrations of total volatile fatty acids (TVFAs), acetic acid, propionic acid, and butyric acid (p < 0.05). Additionally, CBet supplementation enhanced muscle redness (a*), crude fat, crude ash, heptadecanoic acid (C17:0), and tricosanoic acid (C23:0) (p < 0.05) while decreasing shear force and the concentration of cis-13,16-docosadienoic acid (C22:2) (p < 0.05). Furthermore, CBet elevated characteristic flavor compounds (e.g., nonanal) and their relative odor activity values (ROAVs), and decreased undesirable odors (e.g., dodecanal) (p < 0.05). As illustrated in the graphical abstract, these improvements were mediated through regulatory effects of CBet on rumen microbiota composition, muscle fatty acids, amino acids, and volatile flavor compounds. Specifically, CBet significantly increased the relative abundances of Firmicutes, Proteobacteria, Prevotella, and Bifidobacterium in the rumen (p < 0.05) and altered the Firmicutes/Bacteroidota ratio. In conclusion, dietary supplementation with 0.20% CBet effectively enhances lamb meat quality and flavor, effects closely associated with changes in the abundance of key ruminal microbial taxa. Full article
(This article belongs to the Section Animal Nutrition)
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17 pages, 1727 KB  
Article
In Vitro Degradation of Chlorpyrifos by the Ruminal Microbes: Insights from the Rumen Metagenome
by Pradeep Kumar Malik, Archit Mohapatra, Shraddha Trivedi, Atul Purushottam Kolte, Artabandhu Sahoo and Raghavendra Bhatta
Microorganisms 2026, 14(3), 581; https://doi.org/10.3390/microorganisms14030581 - 4 Mar 2026
Viewed by 407
Abstract
In vitro studies were conducted in a series to investigate if the ruminal microbes are capable of degrading chlorpyrifos. This in vitro study presents the results from three experiments: Exp. I was conducted without feed, while Exp II and III were conducted with [...] Read more.
In vitro studies were conducted in a series to investigate if the ruminal microbes are capable of degrading chlorpyrifos. This in vitro study presents the results from three experiments: Exp. I was conducted without feed, while Exp II and III were conducted with feed, either with or without methanol for dissolving chlorpyrifos, respectively. A basal diet comprising finger millet straw and concentrate was prepared. Incubation medium with feed but without chlorpyrifos served as the control. A total of six replicates each of control and chlorpyrifos spiked were used for the incubation. The pesticide concentration in the incubation medium before and after 24 h of incubation was analyzed using GC-MS/MS. The genomic DNA was isolated from the incubation fluid of the individual samples, and the shotgun metagenomic sequencing was performed. The clean reads were taxonomically classified using the Kraken2 database, and microbial classification at different taxonomic ranks was separated using Pavian v1.0. The microbial genes in the metagenome data were predicted and assigned functional roles using the MetaErg v1.2.3 pipeline. The assigned KEGG Orthology (KO), EC numbers (Enzyme Commission number), Gene Ontology (GO), and corresponding NCBI taxonomy information relevant to chlorpyrifos metabolism/degradation were retrieved. Results from the study revealed that the chlorpyrifos concentration was decreased from 5.78 to 1.64 ppm over 24 h of in vitro incubation with feed. Similar alpha and beta diversity indices between control and chlorpyrifos treatments revealed that the richness and the evenness of the microbial population were not affected by the presence of chlorpyrifos in the rumen fluid. There was no difference in the microbiota affiliated to the major phyla such as Bacteroidota, Fibrobacterota, Bacillota, and Pseudomonadota. The EC 3.1.8.1, EC 3.1.3.1, EC 1.14.13.-, and EC 1.1.1.- reported for chlorpyrifos degradation were not detected in the metagenome, and only EC 3.1.1.1 was identified, which demonstrated that degradation of chlorpyrifos was carried out by the affiliated enzyme carboxylesterase. The presence of GO:0004035, GO:0004364, GO:0019637, GO:0016791, and GO:0042178 in the metagenome strengthens that the chlorpyrifos degradation in the present study was primarily assigned to the rumen microbiota. This in vitro study provided insights into the rumen microbiota involved in the chlorpyrifos degradation and the initial clue that the rumen microbes are capable of degrading chlorpyrifos. Further, the animal studies in different species with the variable levels of chlorpyrifos are also warranted to confirm the efficacy of rumen microbes in mixed syntrophy and determine the threshold capabilities of the ruminal microbes. Full article
(This article belongs to the Special Issue Microbial Communities and Biodegradation)
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25 pages, 7608 KB  
Article
Intestinal Microbiota Mediates the Beneficial Effects of γ-Polyglutamic Acid on Calcium Homeostasis and Bone Properties in Lambs
by Xingfu Zhang, Lili Guo, Yabo Zhao, Wurilege Wei, Jing Zhang, Lingli Dai, Bin Yang, Zaixia Liu, Xu Wang, Chen Bai, Ruiping Du, Manman Tong, Shuyi Li, Jianmeng Wang, Yanyong Sun and Liwen Song
Int. J. Mol. Sci. 2026, 27(5), 2373; https://doi.org/10.3390/ijms27052373 - 4 Mar 2026
Viewed by 379
Abstract
Optimizing calcium metabolism is crucial for skeletal development and overall productivity in growing ruminants. Twenty-four Sunite lambs were randomly assigned to four groups and fed 0, 0.6, 1.2, or 2.4 g/(d·head) of γ-PGA for 60 days. Growth performance, serum parameters, duodenal morphology and [...] Read more.
Optimizing calcium metabolism is crucial for skeletal development and overall productivity in growing ruminants. Twenty-four Sunite lambs were randomly assigned to four groups and fed 0, 0.6, 1.2, or 2.4 g/(d·head) of γ-PGA for 60 days. Growth performance, serum parameters, duodenal morphology and calcium transporter expression, bone microarchitecture, and duodenal microbiota were analyzed. Supplementation with 1.2 g/(d·head) of γ-PGA (the M group) yielded optimal results, significantly improving final body weight and size. It enhanced duodenal health, evidenced by increased villus height, crypt depth, and microvilli density. Crucially, this dose significantly upregulated the expression of key duodenal calcium transporters (TRPV5/6, CaBPD9k, PMCA, VDR, claudin-12) and altered systemic calcium-regulating hormones (elevated calcitriol, PTH, FGF23). Bone micro-CT analysis revealed changes in trabecular architecture indicative of active remodeling. 16S rRNA sequencing and weighted OTU co-expression network analysis (WOCNA) revealed that γ-PGA reshaped the duodenal microbiota and identified core microbial modules strongly associated with host phenotypes. Genera such as [Eubacterium]_ruminantium_group, Fusicatenibacter, and Prevotella emerged as central hubs. In conclusion, dietary γ-PGA at 1.2 g/(d·head) enhances calcium absorption and bone metabolism in lambs through a coordinated modulation of intestinal integrity and calcium transport, systemic endocrine responses, and the duodenal microbial community, with specific microbiota identified as potential key mediators associated with these effects. Full article
(This article belongs to the Special Issue Regulatory Network of Bone Metabolism)
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19 pages, 2331 KB  
Article
Effects of Rhodotorula Yeast Culture on Nutrient Apparent Digestibility and Rumen Health in Sheep
by Jie Ma, Jianlong Dang, Huiru Ma, Guang Yang, Ke Wang, Xinyu Lu, Xiangtan Su, Xinhao Zhang, Feilong Liu and Aiqin Gao
Biology 2026, 15(5), 390; https://doi.org/10.3390/biology15050390 - 27 Feb 2026
Viewed by 373
Abstract
The potential of Rhodotorula yeast culture (RYC) in animal production remains underexplored. This study investigated the effects of RYC supplementation on nutrient apparent digestibility, rumen tissue morphology, fermentation parameters, and fungal microbiota in sheep. Twenty-four three-month-old male Dorper × Han crossbred sheep (weight [...] Read more.
The potential of Rhodotorula yeast culture (RYC) in animal production remains underexplored. This study investigated the effects of RYC supplementation on nutrient apparent digestibility, rumen tissue morphology, fermentation parameters, and fungal microbiota in sheep. Twenty-four three-month-old male Dorper × Han crossbred sheep (weight 36 ± 4 kg) were selected and randomly divided into four groups, with six sheep in each group: the control group (CON) was fed a basal diet, and the three treatment groups were supplemented with 10, 20, or 40 g/d of RYC (RYC10, RYC20, RYC40), respectively. The results showed that RYC supplementation significantly increased (p < 0.05) the apparent digestibility of dry matter, crude protein, neutral detergent fiber, and acid detergent fiber, and the apparent digestibility of CP and ADF was significantly higher in the RYC20 than in the other groups (p < 0.05). Rumen papillae length and muscular layer thickness were significantly greater (p < 0.05) in RYC-treated groups compared to the CON group, and the RYC20 group exhibited significantly greater rumen papilla length and muscularis propria thickness than the other experimental groups (p < 0.05). Furthermore, ruminal pH and bacterial crude protein content were significantly elevated (p < 0.05), while ammonia nitrogen concentration was significantly reduced (p < 0.05). The RYC40 group exhibited significantly higher rumen pH and BCP concentrations, and significantly lower NH3-N concentration, compared to the other experimental groups (p < 0.05). The concentrations of acetate, propionate, butyrate, and total volatile fatty acids were also significantly higher (p < 0.05) in RYC groups. For RYC20, rumen acetic acid, propionic acid, butyric acid, isobutyric acid, total volatile fatty acid content and the acetate-to-propionate ratio were significantly higher than those of the other experimental groups (p < 0.05). Analysis of fungal community revealed that RYC increased the relative abundance of fibrolytic fungi (e.g., Neocallimastix, Caecomyce, Piromyces). Supplementation of RYC at 20 g/d optimizes apparent nutrient digestibility and rumen tissue development in ruminants, while maintaining favorable rumen fermentation characteristics and selectively enhancing the growth of core fibrolytic fungi; this dosage achieves the optimal balance of biological performance and economic feasibility, and is thus recommended as the optimal practical supplementation dosage for ruminant production. Full article
(This article belongs to the Section Zoology)
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29 pages, 730 KB  
Review
Dietary Fiber Regulation of Gut Microbiota and Bile Acid Metabolism in Animals: Implications for Animal Nutrition
by Jinhua Lai, Jürgen Zentek and Łukasz Marcin Grześkowiak
Vet. Sci. 2026, 13(2), 209; https://doi.org/10.3390/vetsci13020209 - 23 Feb 2026
Viewed by 815
Abstract
Dietary fiber (DF) is a fundamental component of animal nutrition and has been widely studied for its nutritional and physiological functions in animals. While existing studies mainly focus on the independent effects of DF on gut microbiota or bile acids (BAs), the mechanisms [...] Read more.
Dietary fiber (DF) is a fundamental component of animal nutrition and has been widely studied for its nutritional and physiological functions in animals. While existing studies mainly focus on the independent effects of DF on gut microbiota or bile acids (BAs), the mechanisms underlying their interactions remain poorly understood. DF interacts closely with gut microbiota, promoting the production of beneficial metabolites such as short-chain fatty acids, which subsequently influence BA metabolism through microbial deconjugation and dehydroxylation processes, generating free and secondary BA essential for host health. Together, the gut microbiota and BA play key roles in mediating the effects of DF on intestinal and systemic physiology via the gut–liver axis. Although DF contributes to energy supply, nutrient digestion, and regulation of gut microbiota and BA metabolism, its physiological effects vary depending on fiber source, type, chemical composition, inclusion level, and animal species. Ruminant and non-ruminant animals differ in their capacity to utilize DF, with extensive fermentation occurring in the rumen of ruminants, whereas fermentation in non-ruminants mainly occurs in the hindgut and is more limited. Consequently, inappropriate DF supplementation may impair gastrointestinal function and overall physiological status. This review summarizes the diverse effects of different DF types in animals and critically examines the complex and bidirectional interactions among DF, gut microbiota, and BA metabolism, highlighting knowledge gaps that require further investigation to optimize DF application in animal nutrition. Full article
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14 pages, 935 KB  
Article
Metagenomic Insights into the Modulatory Effects of Thiamine Supplementation for Treating Subclinical Ketosis Dairy Cows
by Fuguang Xue, Fan Zhang, Qinghao Zhuang, Ling Jiang, Mengjie Sun, Jinliang Shang and Benhai Xiong
Animals 2026, 16(4), 680; https://doi.org/10.3390/ani16040680 - 21 Feb 2026
Viewed by 366
Abstract
(1) Background: The objective of this study was to investigate the modulatory effects of thiamine on BHBA metabolism, milk yield, and the rumen microbial ecosystem. (2) Methods: A total of 24 SCK dairy cows with similar body conditions were selected and randomly allocated [...] Read more.
(1) Background: The objective of this study was to investigate the modulatory effects of thiamine on BHBA metabolism, milk yield, and the rumen microbial ecosystem. (2) Methods: A total of 24 SCK dairy cows with similar body conditions were selected and randomly allocated to SCK (SCK) or SCK with thiamine supplement (SCKT) treatment. Twelve healthy dairy cows served as the control (CON) treatment. Milk yield, milk quality, ruminal fermentability parameters, rumen and fecal microbial communities were further measured. (3) Results: Thiamine significantly decreased BHBA content, milk CFUs, and somatic cells, while significantly increasing milk yield, milk fat, acetate, and the A/P ratio (p < 0.05). Thiamine-treated cows exhibited significantly increased ruminal and fecal Proteobacteria but significantly decreased ruminal Firmicutes (p < 0.05) as well as fecal Spirochaetes and Cyanobacteria (p < 0.05), compared with SCK cows. Functional analysis showed that differential rumen bacteria exhibited high energy metabolism, nucleotide metabolism, and glycan biosynthesis and metabolism, while the metabolism of terpenoids and polyketides were the primary functional pathways of differential fecal microbiota. (4) Conclusions: Thiamine supplementation in SCK cows effectively alleviated subclinical ketosis by reducing BHBA content, enhancing ruminal fermentability, and proliferating rumen microbial communities, leading to improved milk yield in the early-lactation period. Full article
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22 pages, 3684 KB  
Article
Combination of Feed Additives in the Diet of Jersey Cows and Their Impacts on Production, Milk Quality and Rumen Environment
by Patrícia Taís Wolschick, Maksuel Gatto de Vitt, Andriéli Vanessa Kroth, Maisa Damo, Melânia de Jesus da Silva, Luiz Eduardo Lobo e Silva, Roger Wagner, Miklos Maximiliano Bajay, Camila Ten Kathen Jung, Gilberto Vilmar Kozloski and Aleksandro Schafer da Silva
Fermentation 2026, 12(2), 118; https://doi.org/10.3390/fermentation12020118 - 19 Feb 2026
Viewed by 870
Abstract
The combination of additives in ruminant diets is a growing strategy focused on cow health and productivity; therefore, the additives need to have synergistic effects when combined. Because of this, the objective of this study was to evaluate the effects of combining functional [...] Read more.
The combination of additives in ruminant diets is a growing strategy focused on cow health and productivity; therefore, the additives need to have synergistic effects when combined. Because of this, the objective of this study was to evaluate the effects of combining functional additives (biocholine, live yeasts, Yucca schidigera extract, and exogenous enzymes) on the productive performance, milk quality, rumen environment, oxidative status, and metabolic parameters of lactating Jersey cows maintained in an intensive system as well as verifying whether the effects on metabolism and the rumen environment (volatile fatty acids and microbiota) directly or indirectly influence productive efficiency. Eighteen Jersey cows in their second lactation were used, distributed in a completely randomized design into two groups: control, receiving a basal diet, and treatment, receiving the same diet plus the additive mixture. The experiment lasted 56 days. Dry matter intake, milk production and composition, feed efficiency, apparent digestibility, volatile fatty acid profile, rumen microbiota, hematological and biochemical parameters, and oxidative stress markers were evaluated. The combination of additives was able to increase milk production and production corrected for fat, protein, and energy, without altering dry matter intake, resulting in greater feed efficiency. There was an increase in milk protein content from day 28 onwards. In the rumen, a reduction in the protozoan population and an increase in the proportion of propionic acid were observed, without altering the ruminal pH or the total production of volatile fatty acids. The apparent digestibility of crude protein was higher in the treated group. The consumption of additives also promoted specific changes in the ruminal microbiota, with a greater abundance of microorganisms associated with carbohydrate degradation and less activity of pathways related to denitrification. From a systemic point of view, the treatment reduced markers of oxidative stress (reactive oxygen species—ROS and thiobarbituric acid reactive substances—TBARS), decreased creatine kinase and cholinesterase activity, and increased serum fructosamine concentration, indicating antioxidant, anti-inflammatory effects and improved energy status, respectively. It is concluded that the combination of plant biocholine, yeasts, Yucca schidigera extract, and exogenous enzymes improves productive efficiency, promotes ruminal fermentation, and contributes to greater metabolic and oxidative stability in lactating Jersey cows. Full article
(This article belongs to the Special Issue Research Progress of Rumen Fermentation, 2nd Edition)
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15 pages, 2591 KB  
Article
Gut Microbiome Signatures of Aging Associated with Intramuscular Fat Deposition in Tan Sheep
by Xin Yuan, Xuelong Su, Daohua Zhuang, Huitong Zhou, Zecheng Tang, Chenshuo Li, Jiqing Wang, Bingang Shi, Yuzhu Luo, Shaobin Li and Fangfang Zhao
Animals 2026, 16(4), 661; https://doi.org/10.3390/ani16040661 - 19 Feb 2026
Viewed by 419
Abstract
Intramuscular fat (IMF) content determines marbling levels and influences the sensory and edible qualities of livestock meat. Its deposition is influenced by the animal’s age and gut microbial community. This study assessed age-related differences in IMF deposition and shifts in gut microbiota between [...] Read more.
Intramuscular fat (IMF) content determines marbling levels and influences the sensory and edible qualities of livestock meat. Its deposition is influenced by the animal’s age and gut microbial community. This study assessed age-related differences in IMF deposition and shifts in gut microbiota between yearlings (1-year-old) and mature (4-year-old) grazing Tan sheep. Then correlations among these factors were examined to investigate the potential role of gut bacteria in IMF deposition. The results demonstrated that mature sheep exhibited higher IMF content in shoulder and rump muscles (p < 0.05), elevated serum lipid levels (p < 0.001), and increased lipolytic enzyme abundances in the liver and pancreas (p < 0.05), compared with yearlings. In contrast, the concentrations of acetate and propionate in ruminal and colonic contents were lower in mature sheep (p < 0.05), despite a higher abundance of lipolytic and synthetic enzymes in colonic content (p < 0.05). Gut microbial diversity differed between age groups, particularly in the rumen and colon, with clear shifts in specific bacterial taxa. Correlation analyses revealed that the abundance of Copromorpha and RUG420 in the colon were positively correlated with IMF content in shoulder and rump muscles, and serum lipid levels (including free fatty acids, FFA; low-density lipoprotein, LDL; high-density lipoprotein, HDL; and very-low-density lipoprotein, VLDL), but negatively correlated with propionate content (|r| > 0.45, FDR < 0.05). Conversely, the abundance of Cryptobacteroides in the colon was negatively correlated with IMF content in shoulder muscle (r < −0.6, FDR < 0.05), and with the levels of triglyceride (TG), LDL, HDL, and VLDL, while showing positive correlations with acetate and propionate contents (r > 0.45, FDR < 0.05). These findings highlight the potential role of specific colon bacteria (Copromorpha, RUG420, and UBA5905) in IMF deposition, identifying them as candidate bacteria for further investigation regarding their effects on meat quality. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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16 pages, 1043 KB  
Review
Advances in Intestinal Glucose Absorption Regulation for Ruminant Energy Efficiency Improvement
by Yan Ye, Xiongfei Zhang, Junhu Yao and Xinjian Lei
Animals 2026, 16(4), 659; https://doi.org/10.3390/ani16040659 - 19 Feb 2026
Viewed by 577
Abstract
Ruminants can use volatile fatty acids from rumen fermentation for energy, but substantial starch may bypass the rumen and enter into the small intestine under a high-grain diet. In theory, intestinal starch digestion is energetically more efficient than ruminal fermentation. However, ruminants have [...] Read more.
Ruminants can use volatile fatty acids from rumen fermentation for energy, but substantial starch may bypass the rumen and enter into the small intestine under a high-grain diet. In theory, intestinal starch digestion is energetically more efficient than ruminal fermentation. However, ruminants have inherent limits in starch hydrolysis and glucose transport. Small intestinal starch digestion relies on pancreatic α-amylase. Several studies have indicated that functional amino acids (Leu or Phe) may enhance amylase secretion or activity to improve starch digestion. In contrast, strategies to increase glucose absorption efficiency in the small intestine have received less attention. Thus, this review focuses on the effects of diet, ontogeny, environment, and intestinal microbiota on intestinal glucose absorption and their potential mechanisms. The T1R2/T1R3 glucose-sensing pathways, transporting pathways, and related hormones within the small intestine were systematically reviewed. The advantages and limitations of major approaches regarding glucose absorption including portal vein intubation, nutrient perfusion, everted intestinal sacs in vitro, Ussing chamber, brush-border membrane vesicle, D-xylose test, organoid, and nanosensing are also discussed. Importantly, we propose potential strategies to improve small intestinal glucose absorption (e.g., artificial sweeteners and glucagon-like peptide 2-related modulation). Overall, this review summarizes promising regulatory targets to enhance small intestinal glucose absorption and improve energy efficiency in ruminants. Full article
(This article belongs to the Section Animal Physiology)
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20 pages, 3322 KB  
Article
Oral Administration of Lactobacillus amylovorus Alleviates Diarrhea by Restoring Gut Microbiota and SCFAs in Neonatal Goats
by Mudathir Y. Abdulrahman, Nasir A. Ibrahim, Mohamed Osman Abdalrahem Essa, Saber Y. Adam, Raza Mohai Ud Din, Rifat Ullah Jan, Nosiba S. Basher, Mokhtar Rejili, Shaaban S. Elnesr, Ahmed A. Saleh, Hosameldeen Mohamed Husien and Mengzhi Wang
Animals 2026, 16(4), 633; https://doi.org/10.3390/ani16040633 - 16 Feb 2026
Viewed by 544
Abstract
Diarrhea in kids is a significant health and economic concern for small-scale ruminant farms. This study aims to investigate the properties of Lactobacillus amylovorus as a treatment for kids with diarrhea and its effect on the composition of the gut microbiota. A total [...] Read more.
Diarrhea in kids is a significant health and economic concern for small-scale ruminant farms. This study aims to investigate the properties of Lactobacillus amylovorus as a treatment for kids with diarrhea and its effect on the composition of the gut microbiota. A total of 20 neonatal goats (approximately 2 months old) were divided into three groups: healthy control (HC, n = 4), diarrhea (D, n = 8), and diarrhea treated with probiotic (DT, n = 8). We tracked gut microbial profiles, fecal consistency, short-chain fatty acids (SCFAs), and clinical symptoms. Probiotic-treated kids recovered fully from diarrhea within two weeks, while their untreated counterparts showed signs of clinical deterioration and gradual emaciation. Kids with diarrhea had lower microbial richness, according to alpha diversity analysis, and this was only partially restored after probiotic treatment. The kids with diarrhea had the lowest Shannon, ACE, Simpson, Dominance, Pielou-e, and Chao1 indices compared to the HC group, while the administration of Lactobacillus amylovorus significantly (p < 0.05) restored their normal enrichment in the DT group compared to the D group. The healthy group had a higher abundance of Verrucomicrobiota, while Firmicutes and Bacteroidota predominated in all groups. Bacteroides and Akkermansia predominated in the healthy and treated groups. At the genus level, analysis showed elevated levels of Escherichia-Shigella and UCG-005 in kids with diarrhea. In addition, the concentration of each SCFA in the D group was significantly (p < 0.05) lower than in the HC group. This study provides novel evidence that Lactobacillus amylovorus administration not only alleviates diarrhea but also uniquely restores the production of key SCFAs—including butyrate, acetate, and propionate—in neonatal goats, a finding not previously reported in this species. The concurrent recovery of microbial diversity and SCFA profiles highlights the dual mechanistic potential of Lactobacillus amylovorus as a gut microbiota modulator and metabolic therapeutic in young ruminants. These results lend credence to its potential as a probiotic treatment for small ruminant enteric diseases. Full article
(This article belongs to the Special Issue Nutritional Regulation of Gut Microbiota in Animals)
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59 pages, 9480 KB  
Review
The Keto–Inflammatory Network: From Systems Biology to Biological Code
by Burim N. Ametaj
Dairy 2026, 7(1), 19; https://doi.org/10.3390/dairy7010019 - 16 Feb 2026
Viewed by 1187
Abstract
The transition from energy sufficiency to deficiency triggers complex metabolic and immune adaptations that have traditionally been viewed through a reductionist pathological lens. During early lactation, coordinated mobilization of adipose tissue, muscle protein, and bone minerals supports milk synthesis, with ketogenesis specifically arising [...] Read more.
The transition from energy sufficiency to deficiency triggers complex metabolic and immune adaptations that have traditionally been viewed through a reductionist pathological lens. During early lactation, coordinated mobilization of adipose tissue, muscle protein, and bone minerals supports milk synthesis, with ketogenesis specifically arising from hepatic oxidation of non–esterified fatty acids. This review introduces the Keto–Inflammatory Network (KIN), a novel framework positioning ketonemia as an evolutionarily conserved adaptive response rather than inherent metabolic dysfunction. The KIN integrates β–hydroxybutyrate (BHB) signaling with immune modulation, epigenetic regulation, circadian rhythms, and microbiota interactions. Through mechanisms including NLRP3 inflammasome inhibition, HDAC–mediated epigenetic modifications, and HCAR2 receptor activation, ketone bodies orchestrate anti–inflammatory responses while maintaining metabolic flexibility. Building upon important precedent work recognizing beneficial roles of ketones in ruminant metabolism, this review synthesizes recent advances in immunometabolism and systems biology into an integrated framework. The KIN encompasses calcium–ketone integration through the Calci–Keto–Inflammatory Code (CKIC), temporal regulation via the Ketoinflammatory Clock, and trans–kingdom signaling through microbiota interactions. In dairy cattle, this perspective reframes periparturient ketonemia as existing on a continuum from adaptive to pathological, with biological meaning determined by integrated metabolic–inflammatory patterns rather than absolute ketone concentrations. The CKIC paradigm, while requiring prospective validation, suggests novel therapeutic approaches leveraging ketone signaling for inflammatory diseases, autoimmune conditions, and metabolic disorders while challenging traditional threshold–based ketosis management strategies. This systems–level understanding opens new avenues for precision interventions that work with, rather than against, evolved adaptive mechanisms refined through millions of years of mammalian evolution. By distinguishing ketonemia (measurable ketone elevation) from pathological ketosis (dysregulated ketone accumulation), and by integrating evidence from both ruminant and monogastric models, this review provides a comprehensive framework for next–generation metabolic medicine. Full article
(This article belongs to the Section Dairy Animal Health)
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16 pages, 320 KB  
Article
Biotechnological Valorization of Almond Hulls via Solid-State Fermentation with Saccharomyces cerevisiae and Fibrolytic Enzyme Supplementation: Enhancing Ruminal Fermentation and Reducing Greenhouse Gas Emissions
by Khalil Abid
Fermentation 2026, 12(2), 106; https://doi.org/10.3390/fermentation12020106 - 12 Feb 2026
Viewed by 800
Abstract
Valorization of agricultural by-products is a key component of circular strategies aimed at enhancing the sustainability of livestock systems. Almond hulls (AHs), a major residue of the almond-processing industry, are characterized by their high non-fiber carbohydrate (NFC) content, but low crude protein (CP) [...] Read more.
Valorization of agricultural by-products is a key component of circular strategies aimed at enhancing the sustainability of livestock systems. Almond hulls (AHs), a major residue of the almond-processing industry, are characterized by their high non-fiber carbohydrate (NFC) content, but low crude protein (CP) content and ruminal fermentation. This study evaluated the effects of treating AHs with exogenous fibrolytic enzymes (EFEs) and Saccharomyces cerevisiae (SC) via solid-state fermentation. Treatments were applied individually or in combination (SC + EFEs). The effects on chemical composition and ruminal fermentation were assessed. EFEs reduced the fiber content and increased the NFC content. This accelerated ruminal fermentation and reduced the lag time. However, it did not change the overall fermentation extent. SC increased the CP content and ether extract but reduced the NFC content. This modification promoted the growth of ruminal bacteria. As a result, the ruminal fermentation extent, ruminal degradability and volatile fatty acid (VFA) content improved. However, methane (CH4) and carbon dioxide (CO2) emissions relative to the substrate, degraded substrate and total gas emission were not affected. SC + EFEs had synergistic effects. This further increased the CP content and ether extract and reduced the NFC and fiber contents. The treatment modulated ruminal microbiota by decreasing protozoa and increasing bacteria. It also reduced the fermentation lag time and enhanced the fermentation extent, degradability and VFA production favoring propionate formation. Additionally, it reduced CH4 and CO2 emissions per unit of degraded substrate and the total gas emission. Overall, the SC + EFEs represent an effective approach to enhance the nutritional value of AHs while partially mitigating greenhouse gas emissions relative to substrate utilization and fermentation pathways. Full article
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