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Background To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance. Results Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis , promoting rumen epithelial VFAs absorption and reducing ruminal inflammation. Conclusions This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.

The objective of this study was to investigate the effect of microencapsulated bioactive compounds from lemongrass mixed dragon fruit peel pellet (MiEn-LEDRAGON) supplementation on fermentation characteristics, nutrient degradability, methane production, and the microbial diversity using in vitro gas production technique. The study was carried out using a completely randomized design (CRD) with five levels of MiEn-LEDRAGON supplementation at 0, 1, 2, 3, and 4% of the total dry matter (DM) substrate. Supplementation of MiEn-LEDRAGON in the diet at levels of 3 or 4% DM resulted in increased (p < 0.05) cumulative gas production at 96 hours (h) of incubation time, reaching up to 84.842 ml/ 0.5 g DM. Furthermore, supplementation with 3% MiEn-LEDRAGON resulted in higher in vitro nutrient degradability and ammonia–nitrogen concentration at 24 h of the incubation time when compared to the control group (without supplementation) by 5.401% and 11.268%, respectively (p < 0.05). Additionally, supplementation with MiEn-LEDRAGON in the diet led to an increase in the population of Fibrobacter succinogenes at 24 h and Butyrivibrio fibrisolvens at 12 h, while decreasing the population of Ruminococcus albus , Ruminococcus flavefaciens , and Methanobacteriales (p < 0.05). Moreover, supplementation of MiEn-LEDRAGON in the diet at levels of 2 to 4% DM resulted in a higher total volatile fatty acids (VFA) at 24 h, reaching up to 73.021 mmol/L (p < 0.05). Additionally, there was an increased proportion of propionic acid (C3) and butyric acid (C4) at 12 h (p < 0.05). Simultaneously, there was a decrease in the proportion of acetic acid (C2) and the ratio of acetic acid to propionic acid (C2:C3), along with a reduction of methane (CH 4 ) production by 11.694% when comparing to the 0% and 3% MiEn-LEDRAGON supplementation (p < 0.05). In conclusion, this study suggests that supplementing MiEn-LEDRAGON at 3% of total DM substrate could be used as a feed additive rich in phytonutrients for ruminants.

The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.

This study aimed to evaluate the effects of partial reducing rumen-protected Lys (RPLys) on rumen fermentation and microbial composition in heifers. Three ruminal fistulated Holstein Friesian bulls were used to determine the effective degradability of RPLys using an in situ method at incubation times of 0, 2, 6, 12, 16, 24, 36, and 48 h. Thereafter, 36 Holstein heifers at 90 days of age were assigned to one of two dietary treatments: a theoretically balanced amino acid diet (PC group; 1.21% Lys, 0.4% Met) or a 30% Lys-reduced diet (PCLys group, 0.85% Lys, 0.4% Met). Rumen fluid samples from five heifers in each group were extracted using esophageal tubing on day 90 to determine pH, microprotein, ammonia, volatile fatty acids, and microbial communities. Results showed that the effective ruminal degradability was 25.76%. Furthermore, differences in rumen fermentation parameters and alpha diversity of the microbiota between the two groups were not significant, but beta diversity was significant. Based upon relative abundance analysis, short-chain fatty acid–producing bacteria, including Sharpea, Syntrophococcus, [Ruminococcus]_gauvreauii_group, Acetitomaculum, and [Eubacterium]_nadotum_group belonging to Firmicutes, were significantly decreased in the PCLys group. Spearman’s analysis revealed a positive correlation between the butyrate molar proportion and the relative abundance of butyrate-producing bacteria such as [Eubacterium]_nadotum_group, Coprococcus_1, Ruminococcaceae_UCG_013, Pseudoramibacter, and Lachnospiraceae_UCG_010. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis further validated that RPLys deduction influenced energy metabolism. Together, our findings highlight the role of RPLys or Lys in butyrate-producing bacteria. However, the number of bacteria affected by Lys was very limited and insufficient to alter rumen fermentation.Key Points• Reducing 30% Lys via rumen-protected Lys did not affect rumen fermentation parameters and alpha diversity of microbiota of Holstein heifers. It meant that the ruminal fermentation pattern was not changed.• Reducing 30% Lys via rumen-protected lysine significantly decreased relative abundance of short-chain fatty acid–producing bacteria belonging to Firmicutes.• Functions of microorganisms were changed by reducing 30% Lys via rumen-protected Lys, especially amino acid metabolism. It may affect the amino acid composition of microprotein.

Background Regular use of high-concentrate diets can improve the growth of animals, especially high-yielding cattle and sheep. However, high-concentrate diets can alter rumen fermentation and microbial community structure, leading to rumen acidosis. Therefore, this study aimed to investigate the effects of 5,6-dimethylbenzimidazole (5,6-DMB) and cobalt supplementation in high-concentrate diets on rumen fermentation and microorganisms and ruminal fluid metabolome in sheep. Methods Twelve rumen-fistulated Kazakh rams (age: 8 months; average initial body weight [BW]: 39.23 ± 2.61 kg) were randomly allocated to two groups ( n  = 6 rams/group): control (CON) and DMB. Sheep in the CON group were fed a basal diet (concentrate-to-forage ratio of 70:30), whereas those in the DMB group were fed a basal diet supplemented with 100 mg/d 5,6-DMB (analytical purity ≥ 99%) and 0.5 mg/kg cobalt (cobalt chloride as supplementary Co, zeolite powder as carrier; Co content ≥ 1%). Notably, the study lasted for 32 days (adaptation period: 1–14 days; experimental period: 15–32 days). During the experiment, feed samples and residual feed were collected, weighed, and recorded. Rumen fluid samples were collected at 0 h before morning feeding and at 1, 3, 5, and 7 h after feeding on days 29–32 of the experiment to measure ruminal pH. Results Ruminal pH was significantly higher ( P  < 0.01) in the DMB group than in the CON group at 1, 3, 5, and 7 h after feeding. Microbiota analysis showed that the dominant phyla in the two groups were Firmicutes (46.70%), Bacteroidetes (43.79%), and Proteobacteria (2.66%). Additionally, the dominant genera were Prevotella (14.78%), Quinell a (7.47%), Succiniclasticum (7.40%), Rikenellaceae_RC9_gut_group (4.44%), NK4A214_group (3.89%), and Ruminococcus (3.67%). Alpha diversity analysis showed that Simpson and Shannon indices were significantly higher ( P  < 0.05) in the DMB group than in the CON group. Metabolome analysis identified 20 significantly different metabolites between the two groups, including 12 positive ions and 8 negative ions. Pathway enrichment analysis showed that the metabolites were mainly enriched in 16 differential metabolic pathways, including fatty acid metabolism and tricarboxylic acid cycle. Correlation analysis revealed an association between ruminal microorganisms and metabolites (propionate, L-malic acid, and arginine). Conclusions Supplementing high-concentrate diets with 5,6-DMB (100 mg/d) and cobalt (0.5 mg/kg) increased ruminal pH, ammonia nitrogen concentration, and propionate concentration to a certain extent, reduced lactate concentration and lactate dehydrogenase activity, regulated ruminal microbial community structure ( Quinella and Succinivibrio ), and improved rumen metabolite levels (L-malate, pyruvate, and acetate concentrations). Conclusively, these findings suggest that supplementing high-concentrate diets with 5,6-DMB and cobalt may promote vitamin B12 synthesis and improve energy utilization efficiency.

Robert Hungate, considered the father of rumen microbiology, was the fi rst to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal fl ora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were fi rst described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques(such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were fi rst made in the rumen, which have not been recognized in a broader sense.

Background and Aim: Feeding ruminants must notice the degradability of feed, especially protein. Microbial rumen requires ammonia from rumen degradable protein (RDP) beside that ruminant require bypass protein or rumen undegradable protein (RUP) and microbial crude protein. The aim of the study was to discover the best RDP:RUP ratio in beef cattle diets commonly used by Indonesian farmers using an in vitro methodology. Materials and Methods: Samples of Pennisetum purpureum, Leucaena leucocephala, Indigofera zollingeriana, cassava, maize, palm kernel cake, rice bran, and tofu waste were formulated into dietary treatments (dry matter [DM] basis). All experiments were carried out using a 3×3×2 factorial, randomized block design with three replications. Treatments consisted of three protein levels (12%, 14%, and 16%), two energy levels (65% and 70%), and three RDP:RUP ratio levels (55:45, 60:40, and 65:35). The experimental diets were incubated in vitro using buffered rumen fluid for 48 h at 39°C. After incubation, the supernatants were analyzed to determine pH, ammonia concentration, total volatile fatty acid (VFA), and microbial protein synthesis. The residues were analyzed to determine DM, organic matter, protein, and RUP digestibility. Results: Increased protein, energy, and RDP levels increased digestibility, ammonia concentrations, total VFAs, and microbial protein synthesis (p<0.05), while rations with 16% protein lowered these parameters (p<0.05). Conclusion: Increased dietary protein (from 12% to 14% DM), energy (from 65% to 70% DM), and RDP (from 55% to 65% crude protein [CP]) levels increased nutrient digestibility, ammonia concentration, total VFA levels, and microbial protein synthesis. The diet containing 14% DM dietary protein and 70% DM energy, which contained 55%, 60%, or 65% CP RDP optimally increased nutrient digestibility, ammonia concentration, total VFA levels, and microbial protein synthesis. Thus, feed based on these RDP:RUP ratios can optimize ruminant productivity.

Background Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and management condition, a potential new trait that can be used to increase high-quality milk production. It is unknown to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to MPY. Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels. Results Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis. In addition, the rumen microbiome of high-MPY cows had lower relative abundances of organisms with methanogen and methanogenesis functions, suggesting that these cows may produce less methane. Metabolomics analysis revealed that the relative concentrations of rumen microbial metabolites (mainly amino acids, carboxylic acids, and fatty acids) and the absolute concentrations of volatile fatty acids were higher in the high-MPY cows. By associating the rumen microbiome with the rumen metabolome, we found that specific microbial taxa (mainly Prevotella species) were positively correlated with ruminal microbial metabolites, including the amino acids and carbohydrates involved in glutathione, phenylalanine, starch, sucrose, and galactose metabolism. To detect the interactions between the rumen microbiome and host metabolism, we associated the rumen microbiome with the host serum metabolome and found that Prevotella species may affect the host’s metabolism of amino acids (including glycine, serine, threonine, alanine, aspartate, glutamate, cysteine, and methionine). Further analysis using the linear mixed effect model estimated contributions to the variation in MPY based on different omics and revealed that the rumen microbial composition, functions, and metabolites, and the serum metabolites contributed 17.81, 21.56, 29.76, and 26.78%, respectively, to the host MPY. Conclusions These findings provide a fundamental understanding of how the microbiome-dependent and host-dependent mechanisms contribute to varied individualized performance in the milk production quality of dairy cows under the same management condition. This fundamental information is vital for the development of potential manipulation strategies to improve milk quality and production through precision feeding. BxqLxBKbCzpZFnc4fCyo4T Video Abstract

The aim of the present study was to describe age-related changes in anatomic, functional and microbial variables during the rumen development process, as affected by the feeding system (supplemental feeding v. grazing), in goats. Goats were slaughtered at seven time points that were selected to reflect the non-rumination (0, 7 and 14 d), transition (28 and 42 d) and rumination (56 and 70 d) phases of rumen development. Total volatile fatty acid (TVFA) concentration (P= 0·002), liquid-associated bacterial and archaeal copy numbers (P< 0·01) were greater for supplemental feeding v. grazing, while rumen pH (P< 0·001), acetate molar proportion (P= 0·003) and solid-associated microbial copy numbers (P< 0·05) were less. Rumen papillae length (P= 0·097) and extracellular (P= 0·093) and total (P= 0·073) protease activity potentials in supplemented goats tended to be greater than those in grazing goats. Furthermore, from 0 to 70 d, irrespective of the feeding system, rumen weight, rumen wall thickness, rumen papillae length and area, TVFA concentration, xylanase, carboxymethylcellulase activity potentials, and microbial copy numbers increased (P< 0·01) with age, while the greatest amylase and protease activity potentials occurred at 28 d. Most anatomic and functional variables evolved progressively from 14 to 42 d, while microbial colonisation was fastest from birth to 28 d. These outcomes suggest that the supplemental feeding system is more effective in promoting rumen development than the grazing system; in addition, for both the feeding systems, microbial colonisation in the rumen is achieved at 1 month, functional achievement at 2 months, and anatomic development after 2 months.

In the present study, following the measurement of methane emissions from 160 mature ewes three times, a subset of twenty ewes was selected for further emission and physiological studies. Ewes were selected on the basis of methane yield (MY; g CH4/kg DM intake) being low (Low MY: >1 sd below the mean; n 10) or high (High MY: >1 sd above the mean; n 10) when fed a blended chaff ration at a fixed feeding level (1·2-fold maintenance energy requirements). The difference between the Low- and High-MY groups observed at the time of selection was maintained (P= 0·001) when remeasured 1–7 months later during digesta kinetics studies. Low MY was associated with a shorter mean retention time of particulate (P< 0·01) and liquid (P< 0·001) digesta, less amounts of rumen particulate contents (P< 0·01) and a smaller rumen volume (P< 0·05), but not apparent DM digestibility (P= 0·27) or urinary allantoin excretion (P= 0·89). Computer tomography scanning of the sheep's rumens after an overnight fast revealed a trend towards the Low-MY sheep having more clearly demarcated rumen gas and liquid phases (P= 0·10). These findings indicate that the selection of ruminants for low MY may have important consequences for an animal's nutritional physiology.