The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency

Sex-specific microbiota associations with backfat thickness, eye muscle area, and rumen fermentation in Qinchuan cattle

BACKGROUND

Ruminant livestock are essential for global food production, and understanding sex-specific rumen fermentation and microbial differences is key to improving production efficiency and meat quality. This study explored sex-specific variations in backfat thickness, eye muscle area, rumen fermentation, and microbiota in Qinchuan cattle.

RESULTS

The results revealed that heifers exhibited higher backfat thickness, butyrate concentrations, and acetate/propionate ratio, whereas bulls had larger eye muscle areas and higher propionate concentrations. Volatile fatty acids (VFAs) transport-related genes (CA4, DRA, and NHE1) were more highly expressed in bulls. Heifers showed greater microbial diversity with distinct sex-specific community structures. Bulls had a higher abundance of Prevotella, while butyrate-producing bacteria like Butyrivibrio and Pseudobutyrivibrio were more abundant in heifers. Functional predictions revealed that bulls were enriched in glycan biosynthesis and amino acid metabolism pathways, whereas heifers showed enhanced lipid metabolism pathways. Correlation analyses showed that backfat thickness was positively correlated with acetate and butyrate production, and acetate/propionate ratio, but negatively correlated with Veillonellaceae_UCG-001. Eye muscle area was negatively correlated with isobutyrate production and the abundance of Elusimicrobium and Anaeroplasma, but positively correlated with Lachnospiraceae_NK3A20_group. Redundancy analysis (RDA) identified propionate and butyrate as key drivers of microbial community differences. The Random Forest model identified key predictors for backfat thickness, including rumen fermentation parameters, microbial taxa, and metabolic pathways, explaining 28% of the variation. However, eye muscle area was not well predicted by the current parameters.

CONCLUSION

These findings enhance our understanding of sex-specific microbial and metabolic profiles, offering potential strategies for optimizing livestock management and breeding programs.

Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows

Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH₃-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.

The Vital Roles of Agricultural Crop Residues and Agro-Industrial By-Products to Support Sustainable Livestock Productivity in Subtropical Regions

Sustainable livestock production is a critical component of global food security and environmental stewardship. Agricultural crop residues, such as cereal straws, stovers, and hulls, as well as agro-industrial by-products, including oilseed meals, distillery wastes, and fruit/vegetable processing residues, are generated in large quantities worldwide, and these residues can be used in the diet of the animals to reduce the feed production cost and sustainability. In this review, we found that the use of treated crop residues in the diet of animals increased the production performance without causing any side effects on their health. Additionally, we also noticed that using these crop residues also mitigates the methane production in ruminants and feed costs, particularly for harvesting the feed crops. Traditionally, these materials have often been underutilized or even disposed of improperly, leading to wastage of valuable nutrients and potential environmental pollution. By incorporating these materials into animal feed formulations, livestock producers can benefit from several key advantages. The review further discusses the challenges and considerations involved in the effective utilization of these alternative feed resources, such as variability in nutrient composition, anti-nutritional factors, and the need for appropriate preprocessing and formulation strategies. Emerging technologies and innovative approaches to optimize the integration of crop residues and by-products into sustainable livestock production systems and also reduce global warming, particularly methane, CO2 and other particles that affect the environment after burning these crop residues, are also highlighted. By synthesizing the current knowledge and exploring the multifaceted benefits, this review underscores the vital roles that agricultural crop residues and agro-industrial by-products can play in fostering the sustainability and resilience of livestock production, ultimately contributing to global food security and environmental stewardship.

A Comparison Between High- and Low-Performing Lambs and Their Impact on the Meat Quality and Development Level Using a Multi-Omics Analysis of Rumen Microbe-Muscle-Liver Interactions

Through an integrated multi-omics analysis of rumen microbial communities, muscle transcriptomes, metabolic profiles, and liver metabolic profiles, this study systematically compared high- and low-performing lambs to elucidate their divergent effects on meat quality attributes and growth development. A total of 100 male lambs with similar birth weight (3.07 ± 0.06 kg) were selected within 72 h. All test lambs were synchronized weaning at 45 days of age and uniformly fed the same diet (total mixed ration) in the same pen until 180 days of age, with ad libitum access to food and water throughout this period. Subsequently, the eight lambs with the highest (HADG) and lowest (LADG) average daily gains were slaughtered for performance evaluation and multi-omics analysis. This study found that HADG lambs increased body weight, muscle fiber diameter, eye muscle area, improved amino acid (histidine, arginine, valine, isoleucine, essential amino acid/total amino acid, and essential amino acid/nonessential amino acid), and fatty acid (linoleic acid, behenic acid, and arachidonic acid) composition enhanced rumen enzymes (pepsase, lipase, xylanase, amylase, and carboxymethyl cellulose) and promoted efficient fermentation (p < 0.05). Analysis of microbial populations indicated a notable increase in Prevotella levels within the rumen of HADG lambs. Furthermore, the rumen markers Schwartzia and Streptococcus exhibited significant correlations with differential meat quality traits. Analysis of the muscle transcriptome indicated a significant correlation between the turquoise module and host phenotypes, particularly body weight. Additionally, muscle metabolism is primarily concentrated within the black module; however, it exhibits a significant correlation with the host body phenotype in the yellow module (p < 0.05). Moreover, liver metabolites, rumen microbes, host phenotype, and muscle transcripts were significantly correlated (p < 0.05). In conclusion, the interactions among rumen microbes, muscle, and liver in lambs promote rumen fermentation, which in turn regulate muscle transcriptional activity and modify metabolic profiles in both the liver and muscle. Moreover, PCK1, SPP1, FGF7, NR4A1, DUSP5, GADD45B, etc., can be candidate genes for muscle growth and development. This finding provides a theoretical basis for further exploiting the production potential of Hu lambs.

Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle

BACKGROUND

Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies.

RESULTS

This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles.

CONCLUSIONS

The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.

Herbal formula alleviates heat stress by improving physiological and biochemical attributes and modulating the rumen microbiome in dairy cows

Heat stress significantly impacts dairy cow productivity, health, and welfare. This study evaluated a self-developed herbal formula as a dietary intervention to mitigate heat stress. A total of 198 lactating cows were divided into two groups: a Control group receiving standard total mixed rations and a Herbs group supplemented with herbal formula for 60 days. Various parameters were assessed, including milk yield and composition, antioxidant capacity, immune responses, stress-related gene expression, and rumen microbial composition. Compared to the Control group, cows in the Herbs group showed improved feed intake, milk yield and quality, rumination frequency, and enhanced antioxidant activity and immune response. Rumen microbiome analysis revealed a reduced relative abundance of Proteobacteria and Ochrobactrum in the Herbs group, along with an enrichment of beneficial genera such as Lachnospira. Functional predictions indicated that the Herbs group exhibited enhanced glycolysis/gluconeogenesis, pyruvate metabolism, and starch and sucrose metabolism, reflecting improved fermentation efficiency and energy utilization. In conclusion, the herbal formula improved physiological and biochemical attributes, boosted antioxidant and immune responses, and modulated the rumen microbiome, contributing to the alleviation of heat stress in dairy cows. These findings highlight its potential as a natural dietary strategy to support dairy cow health and productivity under heat stress conditions.

Oregano essential oil and monensin in supplementing cattle on deferred pasture

The aim of this study was to evaluate the effects of adding oregano essential oil (OEO) and monensin as supplements for Nellore cattle raised on deferred pasture of Urochloa brizantha 'Marandu'. A protein-energy supplement was provided at a rate of 5 g/kg of body weight with the following treatments: Control - no additives, Monensin-60 mg/kg of supplement, OEO3-3 g/animal/day of OEO, and OEO6-6 g/animal/day of OEO. Twenty-four Nellore cattle were used, with an average age of 16 ± 3 months and average weight of 209 kg ± 5.4 kg distributed over 12 paddocks. A completely randomised design was employed with three replications (paddocks). The supplements were added for 84 days split into three 28-day grazing cycles. Animal performance and forage availability were evaluated. There was no interaction between the use of additives and the grazing cycle or the effect of these factors on the variables related to forage (p > 0.05). Additionally, there was no effect from the interaction or the use of additives on body weight, average daily gain, total weight gain and stocking rate (p > 0.05). A reduction in animal performance was seen during the third grazing cycle along with an increase in the stocking rate (p < 0.05). There were no additional gains in terms of performance or productivity per area from the use of OEO or monensin in the protein-energy supplementation of cattle raised on deferred grazing.

Chromium yeast promotes milk protein synthesis by regulating ruminal microbiota and amino acid metabolites in heat-stressed dairy cows

The intensifying global warming may increase the impact of heat stress on the dairy industry. Our previous study showed that chromium yeast (CY) alleviated the negative effects of heat stress and improved the lactation performance by increasing milk protein content and yield in mid-lactation dairy cows. This study further investigated whether the increased milk protein after CY supplementation results from the promotion of microbial crude protein (MCP) synthesis by regulating rumen microorganisms and amino acid metabolites. Twelve heat-stressed dairy cows were divided into two treatment groups: one with CY supplementation (0.36 mg Cr/kg DM) and the other without CY supplementation. Samples were collected after eight weeks of formal experiment in a hot summer with the mean temperature-humidity index of 79.0 ± 3.13. Dietary CY supplementation did not affect rumen pH, total volatile fatty acid, acetate, propionate, isobutyrate, butyrate, isovalerate, and valerate, but increased ruminal MCP concentration (P < 0.05). Simultaneously, the alpha or beta diversity of rumen microbial bacteria were not influenced by CY supplementation. At genus level, supplementation with CY increased the relative abundances of Olsenella, Lachnospiraceae _UCG-002, and Shuttleworthia (P < 0.05) and decreased those of Enterobacter, Escherichia-Shigella, Oribacterium, and Bacteroidetes_BD2-2 (P < 0.05). There were 17 up-regulated and 57 down-regulated differential metabolites in the CON and CY groups. The partial least-squares discriminant analysis (PLS-DA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) scores clearly distinguished the two groups. Chromium yeast supplementation reduced the concentrations of D-(+)-proline, DL-glutamic acid, DL-lysine, Gly-l-pro, L-(-)-serine, L-(+)-alanine, and L-(+)-aspartic acid (P < 0.05) in the ruminal fluid, which were involved in arginine biosynthesis (P = 0.029), glutathione metabolism (P = 0.047), lysine degradation (P = 0.069), and D-amino acid metabolism (P = 0.084). Spearman correlation analysis showed that milk protein content was positively correlated with MCP and negatively correlated with amino acid concentrations in the ruminal fluid (P < 0.05). Collectively, CY supplementation promoted the utilization of amino acids by rumen microorganisms to synthesize MCP, thereby increasing milk protein content and yield in heat-stressed dairy cows.

A Meta-Analysis of Dietary Inhibitors for Reducing Methane Emissions via Modulating Rumen Microbiota in Ruminants

BACKGROUND

Rumen methane emissions (RMEs) significantly contribute to global greenhouse gas emissions, underscoring the essentials to identify effective inhibitors for RME mitigation. Despite various inhibitors shown potential in reducing RME by modulating rumen microbes, their impacts include considerable variations and inconsistency.

OBJECTIVES

We aimed to quantitatively assess the impacts of various methane inhibitors on RME, rumen microbial abundance, and fermentation in ruminants. Additionally, the relationships between microbial abundance and RME were examined through meta-regressions.

METHODS

Meta-analysis and meta-regression were conducted to assess the impacts of methane inhibitions, including 3-nitrooxypropanol, ionophores, nitrate, triglycerides, phytochemicals, and co-inhibitors, on RME and rumen microbiota in beef, dairy cattle, and sheep.

RESULTS

Analyses of 922 datasets from 274 experiments revealed that inhibitors, except ionophores (P = 0.43), significantly reduced RME, with co-inhibitors displaying the highest efficacy (standardized mean difference -2.1, P < 0.01). Inhibitors' effects were more pronounced in sheep relative to beef and dairy cattle. Inhibitors decreased the abundance of ciliates and methanogens, with positive correlations observed between Dasytrichidae (P = 0.05), Entodinomorphs (P ≤ 0.001), Methanobacteriale (P = 0.001), and fungi (P < 0.01) with RME. Among inhibitors, triglycerides exhibited simultaneous reduction in methanogen, ciliate, and fungal abundances. 3-Nitrooxypropanol and triglycerides increased H2 in the rumen whereas reducing the acetate-propionate ratio, especially in beef. The H2 emission was negatively correlated (P < 0.01) and acetate-to-propionate ratio was positively correlated (P < 0.001) with RME.

CONCLUSIONS

Microbes, including Dasytrichidae, Entodinomorphs, Methanobacteriale, and fungi, significantly attribute to RME, and co-inhibitors have the highest efficacy in limiting RME and reducing microbial abundances. This study underscores the roles of both host and microbiota in modulating the inhibitor efficacy in RME, informing the refinement of rumen additives to mitigate RME from meat and milk production.

Studies on fatty acids and microbiota characterization of the gastrointestinal tract of Tianzhu white yaks

Introduction

The gut microbiota significantly influences the host's production performance and health status, with different gastrointestinal tissues exhibiting functional diversity reflected in their microbial diversity.

Methods

In this study, five adult male Tianzhu white yaks (4.5 years old) were selected and fed under the same nutritional conditions. After the feeding experiment, the yaks were slaughtered, and chyme samples were collected from the rumen, abomasum, jejunum, and colon for 16S rRNA full-length sequencing and volatile fatty acid analysis.

Results

The results showed that the microbial composition and diversity of the rumen and abomasum were similar, with close genetic distances and functional projections. In contrast, the jejunum and colon had distinct microbial compositions and diversity compared to the rumen and abomasum. At the phylum level, the dominant phyla in the rumen, abomasum, and colon were Firmicutes and Bacteroidetes, while in the jejunum, the dominant phyla were Firmicutes and Proteobacteria. The abundance of Firmicutes differed significantly between the jejunum (87.24%) and the rumen (54.67%), abomasum (67.70%), and colon (65.77%). Similarly, Bacteroidetes showed significant differences between the jejunum (2.21%) and the rumen (36.54%), abomasum (23.81%), and colon (28.12%). At the genus level, Rikenellaceae_RC9_gut_group and Christensenellaceae_R-7_group were dominant in both the rumen and abomasum. In the jejunum, Romboutsia and Paeniclostridium were dominant, while Rikenellaceae_RC9_gut_group and UCG-005 were the dominant genera in the colon. At the species level, rumen_bacterium_g_Rikenellaceae_RC9_gut_group and rumen_bacterium_g_Christensenellaceae_R-7_group were dominant in both the rumen and abomasum, while Clostridium_sp._g_Romboutsia and bacterium_g_Paeniclostridium were unique to the jejunum. Ruminococcaceae_bacterium_g_UCG-005 and bacterium_g_Rikenellaceae_RC9_gut_group were unique to the colon. KEGG functional prediction of the microbiota indicated that the dominant functions in the rumen, abomasum, colon, and jejunum were amino acid metabolism, glycan biosynthesis and metabolism, carbohydrate metabolism, and membrane transport, respectively, reflecting the digestive functions of these organs. Volatile fatty acid analysis showed that the concentrations of acetic acid, propionic acid, and butyric acid in the rumen were significantly higher than those in the abomasum, jejunum, and colon (p < 0.05). Among these, the propionic acid concentration in the jejunum was significantly lower than in the abomasum and colon. Additionally, correlation analysis results indicated that acetic acid and butyric acid were significantly positively correlated with the ruminal bacterial community (p < 0.05). The total volatile fatty acid concentration was highest in the rumen, decreased to less than one-fifth of the rumen's total volatile fatty acid concentration in the abomasum and jejunum, and then reached a second peak in the colon.

Conclusion

This study explored the microbial composition and differential bacterial genera in the rumen and intestines of Tianzhu white yak, comparing the differences in volatile fatty acid levels and microbial composition and function across different regions. This is important for understanding their gastrointestinal microbiota's spatial heterogeneity.

The quality of Tibetan sheep meat from pastures was synergistically regulated by the rumen microbiota and related genes at different phenological stages

Meat quality is a key indicator of meat performance in ruminants, and its mechanism and regulation are also key to ruminant research. Studies have shown that animal meat quality is related to the gut microbiota. In this study, RT-qPCR and 16S omics were employed to assess meat quality and intestinal microbiota. The objective was to investigate the influence of seasonal variations on the meat quality of Tibetan sheep ewes by examining the rumen microflora, meat quality attributes, and associated gene expression profiles over three distinct months: May, August, and December.The results indicate that muscle tenderness was significantly greater (p < 0.001) in the grass period than in the regrowth and dry grass periods and was highest in the longest dorsal muscle. The cooking rate of the foreleg muscle was significantly greater (p < 0.05) than that during the regrowth and dry grass periods, and the pH24h significantly differed (p < 0.05) across the different seasonal periods. The crude protein content of the longest back muscle and the foreleg muscle was significantly greater (p < 0.001) than that of the wither and grass stages during the regrowth period and slightly decreased during the grass stage. The crude fat and crude ash contents of the three groups differed significantly, and the fat content during the grass stage was significantly (p < 0.05) greater than that during the regrowth stage and the wither stage. Expression analysis of genes related to meat quality revealed that the expression of the ADSL gene was significantly greater (p < 0.05) in the anterior and posterior leg muscles during the grass period than during the regrowth and wilting periods, whereas the expression of the FABP3 gene was lower than that during these two periods. Correlation analysis revealed that Rikenellaceae_RC9_gut_group was significantly positively correlated (p < 0.05) with shear forceand cooked meat percentage and significantly negatively correlated (p < 0.05). Ruminococcus and Butyrivibrio were significantly positively correlated (p < 0.05) with CAST and highly significantly positively correlated (p < 0.05). In conclusion, meat quality during different seasons is regulated by the rumen microbiota and their associated genes.

Physicochemical profiles of mixed ruminal microbes in response to surface tension and specific surface area

Introduction

In ruminants, a symbiotic rumen microbiota is responsible for supporting the digestion of dietary fiber and contributes to health traits closely associated with meat and milk quality. A holistic view of the physicochemical profiles of mixed rumen microbiota (MRM) is not well-illustrated.

Methods

The experiment was performed with a 3 × 4 factorial arrangement of the specific surface area (SSA: 3.37, 3.73, and 4.44 m2/g) of NDF extracted from rice straw and the surface tension (ST: 54, 46, 43, and 36 dyn/cm) of a fermented medium in a fermentation time series of 6, 12, 24, 48 h with three experimental units. Here, we used three rumen-fistulated adult Liuyang black goats as the rumen liquid donors for this experiment.

Results

It was found that increasing SSA decreased the average acetate/propionate ratio (A/P, p < 0.05) and increased the molarity of propionate (p < 0.05). Increasing ST decreased total volatile fatty acid (tVFA) concentration (p < 0.01). Greater SSA increased (p < 0.01) MRM hydrophobicity, whereas increasing ST increased MRM cell membrane permeability (p < 0.01). The neutral detergent fiber digestibility (NDFD, r = 0.937) and tVFA (r = 0.809) were positively correlated with the membrane permeability of MRM.

Discussion

The surface tension of the artificial medium and substrate-specific surface area had a significant influence on MRM's fermentation profiles, hydrophobicity, and permeability. The results suggest that physical environmental properties are key in regulating rumen fermentation function and homeostasis in the gastrointestinal tract ecosystem.

Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction

With extreme nutritional substrate deficiency, the adaptive responses of the gastrointestinal microbiota and host metabolism are largely unknown. Here, we successfully established a microbial substrate deficiency model in the rumen without solid diet introduction in neonatal lambs. In the absence of solid diet, we observed a reduction in the Simpson Index of rumen bacteria, along with a marked decline in the abundance of keystone microorganisms such as Prevotella, Selenomonas, Megasphaera, and Succiniclasticum, indicating a simplified microbial interaction network. Additionally, more urea and NH3-N production facilitated microbial efficient nitrogen utilization to prioritize ammonia as a nitrogen source for survival, reallocating energy to overcome nutritional limitations and sustain their viability. In addition, enriched archaea (Methanosarcina, Methanomicrobium, Methanobrevibacter, and Methanobacterium) promoted hydrogen removal and the growth of nitrogen-producing microorganisms (Pecoramyces, Piromyces, Caecomyces, and Orpinomyces). It also reinforced the glutamate-glutamine pathway, as evidenced by the higher expression of glnA, GLUL, gdhA, and ureAB, suggesting enhanced internal cycling of nitrogen for microbial survival. This selfish microbial survival strategy deprived the host of adequate volatile fatty acids for energy metabolism, resulting in the downregulation of rumen epithelial cell cycle proteins (CCNB1, CCNE), abnormal mitochondrial morphology, and reduced mitochondrial deoxyribonucleic acid copy number and adenosine triphosphate production. Overall, these findings revealed the adaptive survival strategies of rumen microbiota with solid diet deficiency in early life, which caused alterations in epithelial cell mitochondrial function.

Microencapsulated Escape Lysine with Tannin as an Adjuvant in Sheep Diets

The use of escape protein, which is absorbed in the small intestine, can improve the production of ruminant animals because it meets their protein requirements better. This study hypothesized that wax lipid matrices are effective encapsulants for escape lysine in ruminants and tested tannin extract as an adjuvant. Forty intact male Santa Ines × Dorper sheep (~4 months old, BW 23 ± 1.2 kg) were allocated, in a randomized block design, to four treatments: control group (no lysine addition), supplementation with free lysine, escape lysine, and escape lysine + tannin extract. The ether extract intake was higher in the sheep fed escape lysine + tannin compared to the control and free lysine group. The sheep fed escape lysine presented higher DM and aNDF eating efficiency (p ≤ 0.05) compared to the free lysine and control groups. Escape lysine with and without tannin presented greater TDN compared to free lysine and control. The NFCs were lower in the free lysine diet, and the crude protein digestibility was higher in the sheep fed lysine + tannin and the control group compared to the escape and free lysine groups. The lysine treatments did not affect (p > 0.05) the performance, ingestive behavior, and blood parameters. The rectal temperature was higher in the sheep fed lysine escape compared to those fed free lysine. The sheep fed escape lysine + tannin exhibited reduced (p ≤ 0.05) large particles and improved peNDF 12 h after feeding. The escape lysine diet, regardless of the addition of tannin, improved the total digestible nutrients and eating efficiency, without affecting the performance, feed conversion, and blood variables of the sheep.

Saccharomyces Cerevisiae Diet Supplementation Affects Nutrient Digestibility and Milk and Mozzarella Cheese Yield in Dairy Buffalo Cows During the Transition

The aim of the trial was to evaluate the influence of diet supplementation with Saccharomyces cerevisiae on nutrient digestibility and milk and mozzarella cheese yield in buffalo cows during the transition period. Twenty buffalo cows in the last month of pregnancy were equally divided into two groups (control, C, and treated, T) homogeneous for parity and milk yield at the previous lactation. The diet of group T was supplemented with 100 g/head/day of a product containing Saccharomyces cerevisiae (Sc 47- CNCM I-4407) for 4 weeks before and after calving. Dry matter intake and the body condition score were not affected by the dietary treatment. In contrast, organic matter, protein, NDF, and ADF digestibility significantly (p < 0.01) increased. Group T showed a higher milk yield (kg 10.5 vs. 9.2, p < 0.05) but lower milk fat (g/kg 76.0 vs. 80.1, p < 0.05). The buffalo standard milk (FPCM = 740 kcal) yield was higher in the treated group (kg 16.8 vs. 15.0, p < 0.05), whereas the mozzarella cheese yield was not affected by the treatment (p > 0.05). These findings indicate that supplementation of the diet of buffaloes with Saccharomyces cerevisiae during the transition period results in notable enhancements in nutrient digestibility and milk yield. These outcomes are worthy of further investigation.

The cow GUTBIOME CY study: investigating the composition of the cattle gut microbiome in health and infectious disease transmission in cyprus

BACKGROUND

Recent evidence suggests that the lower gut microbiome of ruminants presents roles in their health and environment, including the development of the mucosal immune system, milk production efficiency and quality and subsequent methane emissions. However, there are proportionately fewer studies on this complex microbial community in cattle and region-focus studies are non- existent.

METHODS

Herein, we present the research protocol of the GUTBIOME CY project pertaining to determine the composition of the lower gut microbiome in dairy cows situated in 37 farms across five districts of the island of Cyprus. Detailed questionnaires on animal husbandry and farming practices will be gathered from each farm. Faecal, milk (individual and bulk) and water samples will also be collected from cows and their offspring. Samples will be analysed using a combination of molecular biology and bioinformatics pipelines to define microbiome profiles and antimicrobial resistance (AMR). Information collected from the questionnaires will be used to test for associations between animal husbandry or farming practices and microbiome components and AMR.

DISCUSSION

Collected samples will establish the first dairy cattle biobank in the country for contributing substantially towards scientific advancements in microbiome research and providing insights to all stakeholders, tailored to the unique agricultural context of Cyprus.

Circadian Rhythm Enhances mTORC1/AMPK Pathway-Mediated Milk Fat Synthesis in Dairy Cows via the Microbial Metabolite Acetic Acid

Livestock may respond differently to circadian rhythms, leading to differences in the composition of the animal products. Nevertheless, the circadian effects on rumen microorganisms and animal products are poorly understood. In the study, it was found that dairy cows exhibited increased milk fat levels, decreased acetic acid concentrations in the rumen fluid, and elevated acetic acid levels in the blood during the night compared to those of the day. Correlational analyses suggested a high association between Succiniclasticum, Lactobacillus, Prevotellacene NK3B31_group, Muribaculaceae_unclassified, etc., which were significantly enriched in rumen fluid at night, and milk fat levels. The differential metabolite Vitamin B6, significantly elevated at night, promoted the translocation of acetic acid into the circulation by increasing the level of rumen epithelial MCT1 protein expression. In addition, we found that both acetic acid treatment time and dose modulated the expression of lipid metabolism transcription factors (PPARγ, PPARα, and SREBP1c) and downstream genes (FASN, SCD1, ACCα, and CPT1A). Additionally, the mTORC1 and AMPK pathways were responsible for the effects of acetic acid on transcription factors and genes involved in lipid metabolism. Differences in rumen microbial taxa were observed between the day and night. Microbial metabolite (acetic acid) was found to be absorbed into the bloodstream and entered the mammary gland at night at a significantly elevated level. This regulation impacted the expression of lipid metabolism-related transcription factors (PPARγ, PPARα, and SREBP1c), as well as downstream genes through the mTORC1 and AMPK signaling pathways, ultimately affecting milk fat synthesis. These findings provide a new perspective for the microbial regulation of milk synthesis.

Interaction Between Liver Metabolism and Gut Short-Chain Fatty Acids via Liver-Gut Axis Affects Body Weight in Lambs

The gut-liver axis and its interactions are essential for host physiology. Thus, we examined the jejunal microbiota, fermentation parameters, digestive enzymes, morphology, and liver metabolic profiles in different growth development lambs to investigate the liver-gut axis's role in their development. One hundred male Hu lambs of similar birth weight and age were raised under the same conditions until they reached 180 days of age. Subsequently, the eight lambs with the highest (HADG) and lowest (LADG) average daily weight gains were slaughtered for index assessment. The study indicates that the body weight, carcass weight, propanoic acid, butyric acid, propanoic acid ratio, butyric acid ratio, and digestive enzymes (beta-glucosidase, microcrystalline cellulase, xylanase, and carboxymethyl cellulase) were significantly higher in HDAG lambs than in LADG lambs (p < 0.05). Additionally, there were no significant differences in the jejunal microbiota's structure and function among lambs at different growth development stages (p > 0.05). Overall, our analysis revealed that HADG lambs compared to LADG lambs exhibited an up-regulation of metabolites (such as spermine, cholic acid, succinic acid, betaine, etc.) that were positively correlated with the butyric acid ratio, propanoic acid ratio, propanoic acid, xylanase, microcrystalline cellulase, beta-glucosidase, amylase, carboxymethyl cellulase, carcass weight, and body weight, while these metabolites were negatively correlated with the kidney, acetic acid, acetic acid/ propanoic acid, and acetic acid ratio. Furthermore, there was a significant correlation between liver metabolism and jejunal microbiota. This study revealed significant differences in hepatic metabolites and jejunal fermentation among lambs at different growth stages, which may inform targeted regulation strategies to enhance lamb productivity.

Saccharomyces cerevisiae and Kluyveromyces marxianus yeast co-cultures modulate the ruminal microbiome and metabolite availability to enhance rumen barrier function and growth performance in weaned lambs

In lambs, weaning imposes stress that can contribute to impaired rumen epithelial barrier functionality and immunological dysregulation. In this study, the effects of a yeast co-culture consisting of Saccharomyces cerevisiae and Kluyveromyces marxianus (NM) on rumen health in lambs was evaluated, with a focus on parameters including growth performance, ruminal fermentation, and epithelial barrier integrity, ruminal metabolic function, and the composition of the ruminal bacteria. In total, 24 lambs were grouped into four groups of six lambs including a control (C) group fed a basal diet, and N, M, and NM groups in which lambs were fed the basal diet respectively supplemented with S. cerevisiae yeast cultures (30 g/d per head), K. marxianus yeast cultures (30 g/d per head), and co-cultures of both yeasts (30 g/d per head), the experiment lasted for 42 d. Subsequent analyses revealed that relative to the C group, the average daily gain (ADG) of lambs in the NM group was significantly greater and exhibited significant increases in a range of mRNA relative expression including monocarboxylate transporter 1 (MCT1), (Na+)/hydrogen (H+) exchanger 1 (NHE1), (Na+)/hydrogen (H+) exchanger 3 (NHE3), proton-coupled amino acid transporter 1 (PAT1), vacuolar H+-ATPase (vH+ ATPase), claudin-1, occludin in the rumen epithelium (P < 0.05). Compared with the C group, the pH of the rumen contents in the NM group was significantly decreased , and the concentrations of acetate, propionate, and butyrate were significantly increased (P < 0.05). Analysis of the rumen bacteria showed that the NM group exhibited increases in the relative abundance of Prevotella, Treponema, Moryella, Fibrobacter, CF231 and Ruminococcus (P < 0.05). Metabolomics analyses revealed an increase in the relative content of phthalic acid and cinnamaldehyde in the NM group as compared to the C group (P < 0.05), together with the greater relative content of L-tyrosine, L-dopa, rosmarinic acid, and tyrosol generated by the tyrosine metabolic pathway (P < 0.05). Spearman's correlation analyses revealed relative abundance levels of Fibrobacter and Ruminococcus were positively correlated with the mRNA relative expression levels of PAT1, NHE3, and zonula occluden-1 (ZO-1), as well as with tyrosol, phthalic acid, and cinnamaldehyde levels (P < 0.05). Ultimately, these results suggest that dietary supplementation with NM has a wide range of beneficial effects on weaned lambs and is superior to single bacterial fermentation. These effects include improvements in daily gain and rumen epithelial barrier integrity, as well as improvements in the composition of the rumen microbiome, and alterations in tyrosine metabolic pathways.

Energy Metabolite, Immunity, Antioxidant Capacity, and Rumen Microbiota Differences Between Ewes in Late Gestation Carrying Single, Twin, and Triplet Fetuses

The objective of this study was to investigate the differences in the energy metabolites, immunity, antioxidant capacity, and rumen microbiota of ewes with different numbers of fetuses. Thirty healthy ewes were selected and divided into single- (SL, n = 10), twin- (TL, n = 10), and triplet-fetal (PL, n = 10) ewes according to the number of fetuses. Sampling was carried out on days 21 (Q21) and 7 (Q7) before lambing. The results show no differences (p > 0.05) in the DMI and BW of ewes with different numbers of fetuses, and the body condition score (BCS) of PL ewes was lower (p < 0.05) than that of SL ewes. The concentrations of β-hydroxybutyric acid (BHBA), non-esterified fatty acids (NEFA), interleukin-2 (IL-2), interleukin-6 (IL-6), and tumor necrosis factor α (TNF-α) in the PL ewes were higher (p < 0.05), while the glucose (Glu), triglyceride (TG), total cholesterol (TC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) values were lower (p < 0.05) than those of the SL ewes. ANOSIM analysis showed that the rumen bacterial structure of the SL, TL, and PL ewes was different on days Q21 and Q7. The relative abundance of Firmicutes and Bacteroidota in the rumen was affected (p < 0.05) by the number of fetuses: the relative abundance of Firmicutes (Ruminococcus, Butyrivibrio, Christensenellaceae_R-7_group, Lachnospiraceae_AC2044_group, Lachnospiraceae_XPB1014_group, and Anaeroplasma) was higher (p < 0.05), while that of Bacteroidota (Prevotella, Prevotellaceae_UCG-003, and Prevotellaceae_UCG-001) was lower (p < 0.05) in the SL ewes than in the PL ewes. In summary, the rumen microbial structure and energy metabolites of ewes in late gestation with different numbers of fetuses were different. Triplet-fetal ewes were characterized by lower BCS and antioxidant capacity and were prone to the triggering of inflammatory responses.

The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis

Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives. Further, recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.

Comparative Analysis of Microbiota in Jiani Yaks with Different Rib Structures

The Jiani yak is a nationally renowned species that is known for its meat which is rich in various minerals, amino acids, and proteins. The rumen microbiota plays a critical role in gastrointestinal health and feed degradation, contributing proteins, lipids, and volatile fatty acids (VFAs) essential for milk and meat production. However, there is limited knowledge about the microbiota of free-ranging Jiani yaks, especially those with 15 ribs. Rumen fluid samples were collected from yaks with 14 (PL) ribs and 15 (DL) ribs from a slaughterhouse in Jiani County, China. The total DNA of rumen fluid microorganisms was extracted for microbiota sequencing. Our results revealed 643,713 and 656,346 raw sequences in DL and PL animals, respectively, with 611,934 and 622,814 filtered sequences in these two yak groups. We identified 13,498 Amplicon Sequence Variants (ASVs), with 2623 shared between DL and PL animals. The ratio of Bacteroidota to Firmicutes differed between PL (3.04) and DL (2.35) animals. Additionally, 6 phyla and 21 genera showed significant differences between yaks with 14 and 15 ribs, leading to altered microbiota functions, with 51 and 35 notably different MetaCyc and KEGG pathways, respectively. Hence, the microbiota of yaks with 15 ribs differs from those with 14 ribs. Therefore, these microbiota-related comparative investigations will provide insights into yak husbandry practices and genetic selection strategies for their improved productivity in harsh environments.

Utility of dairy microbiome as a tool for authentication and traceability

Milk microbiome contributes substantially to the formation of specific organoleptic and physicochemical characteristics of dairy products. The assessment of the composition and abundance of milk microbiota is a challenging task strongly influenced by many environmental factors. Specific dairy products may be designated by the Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) labeling, which however, occasionally fail to differentiate them according to specific quality characteristics, which are defined by different microbiota-driven reactions. Combining the above limitations, the scope of the present study, was to summarize the existing information toward three main issues. First, to assess the influence level of the diet type and grazing to rumen-GI tract, mammary gland, and udder microbiome formation in ruminants. Second, to discuss the factors affecting milk microbiota, as well as the effect of the endo-mammary route on milk microbial taxa. Lastly, to evaluate "milk microbiome" as a tool for product differentiation, according to origin, which will contribute to a more robust PDO and PGI labeling. Although the limitations are still a matter of fact (especially considering the sample collection, process, evaluation, and avoidance of its contamination), significant progress has been made, regarding the identification of the factors affecting dairy products' microbiota and its core composition. In conclusion, although so far not totally efficient in dairy products molecular identification, with the progress in soil, water, plant, and animal host's microbiota assembly's characterization, microbiomics could provide a powerful tool for authentication and traceability of dairy products.

Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement

The ruminant microbiome plays a key role in the health, feed utilization and environmental impact of ruminant production systems. Microbiome research provides insights to reduce the environmental footprint and improve meat and milk production from ruminants. However, the microbiome composition depends on the ruminant species, habitat and diet, highlighting the importance of having a good representation of ruminant microbiomes in their local environment to translate research findings into beneficial approaches. This information is currently lacking. In this study, we examined the metadata of farmed ruminant microbiome studies to determine global representativeness and summarized information by ruminant species, geographic location, body site, and host information. We accessed data from the International Nucleotide Sequence Database Collaboration via the National Center for Biotechnology Information database. We retrieved 47,628 sample metadata, with cattle accounting for more than two-thirds of the samples. In contrast, goats, which have a similar global population to cattle, were underrepresented with less than 4% of the total samples. Most samples originated in Western Europe, North America, Australasia and China but countries with large ruminant populations in South America, Africa, Asia, and Eastern Europe were underrepresented. Microbiomes from the gastrointestinal tract were the most frequently studied, comprising about 87% of all samples. Additionally, the number of samples from other body sites such as the respiratory tract, milk, skin, reproductive tract, and fetal tissue, has markedly increased over the past decade. More than 40% of the samples lacked basic information and many were retrieved from generic taxonomic classifications where the ruminant species was manually recovered. The lack of basic information such as age, breed or sex can limit the reusability of the data for further analysis and follow-up studies. This requires correct taxonomic assignment of the ruminant host and basic metadata information using accepted ontologies adapted to host-associated microbiomes. Repositories should require this information as a condition of acceptance. The results of this survey highlight the need to encourage studies of the ruminant microbiome from underrepresented ruminant species and countries worldwide. This shortfall in information poses a challenge for the development of microbiome-based strategies to meet sustainability requirements, particularly in areas with expanding livestock production systems.

Integrating genome- and transcriptome-wide association studies to uncover the host-microbiome interactions in bovine rumen methanogenesis

The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota-mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome- and transcriptome-wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome-wide association study (GWAS). In contrast, the transcriptome-wide association study (TWAS) of rumen microbiota detected 28,260 significant gene-microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host-microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants.

Impact of virginiamycin on the ruminal microbiota of feedlot cattle

Growth-promoting antibiotics have been used in cattle, but concern about antimicrobial overuse has prompted a re-evaluation of this practice. To evaluate changes in the ruminal microbiota of feedlot cattle by virginiamycin, a total of 76 crossbreed beef cattle from 2 batches of cattle at different sampling periods (B1 and B2) were divided into 2 groups: one receiving virginiamycin in their diet (ATB) and the other receiving the same diet without any growth promoter (CON). The use of virginiamycin was associated with significant changes in the diversity and composition of the ruminal microbiota of cattle in B1, but not in cattle in B2. Several bacterial taxa were significantly more abundant in samples from CON, e.g., an unclassified genus of the TM7 phylum, whereas others were associated with the use of virginiamycin, e.g., Holdemania and Selenomonas spp. In conclusion, virginiamycin can affect bacterial diversity and composition in the rumen of feedlot cattle, but its effect is inconsistent in different seasons of the year.

Investigating the chemical composition, digestion and fermentation of Alternanthera sessilis red plant and its effect on the performance of fattening lambs

The present experiment was conducted to evaluate the nutritional value of red Alternanthera sessilis for fattening lambs when they were replaced with alfalfa forage. Forty growing lambs with an average weight of 21.12 kg and an age of 5 months were randomly assigned to four experimental treatments. Growth performance, nutrient digestibility, rumen fermentation parameters, protozoa population, blood parameters, and composition of carcass components were evaluated. The results of this experiment showed that the use of Alternanthera sessilis in the diet significantly reduced feed intake, increased the average daily weight gain, and improved the feed conversion ratio compared to the control treatment (P < 0.05). The digestibility of dry matter and protein was significantly increased (P < 0.05), while the digestibility of neutral detergent fiber, acid detergent fiber, and organic matter showed a numerical increase. Diets containing different levels of the Alternanthera sessilis plant did not affect pH, but the increase in the amount of this plant in the diet led to an increase ammonia nitrogen concentration and rumen protozoa population (P < 0.05). The addition of Alternanthera sessilis to the diet significantly reduced the concentration of blood glucose and cholesterol and increased the concentration of blood urea nitrogen (P < 0.05). Except for the weight of the thigh and neck, the effect of experimental treatments on other carcass components was not significant. Overall, the results of this experiment showed that using the Alternanthera sessilis plant in the rations of fattened lambs as a substitute for alfalfa forage not only had no negative effect on the studied parameters but also improved them in some cases. Therefore, Alternanthera sessilis can be used in rations of fattened lambs as a substitute for part of alfalfa forage.

Impact of oil type and savory plant on nutrient digestibility and rumen fermentation, milk yield, and milk fatty acid profile in dairy cows

Fat supplements are well known for their multiple beneficial effects on ruminant health, reproduction and productivity, and as a source for certain bioactive compounds in ruminant products. On the other hand, numerous phytochemicals have demonstrated the potential to improve rumen fermentation through modifying the volatile fatty acid (VFA) pattern to favour those with greater energy efficiency, boosting microbial protein synthesis, and decreasing methane emission and ruminal ammonia concentration. Savory is an aromatic plant rich in various phytochemicals (mainly carvacrol and flavonoids) that can alter ruminal metabolism of dietary fatty acids, potentially increasing the production of some bioactive compounds such as conjugated linoleic acids (CLAs). This study aimed to investigate combined effects of oil type (fish oil (FO) versus soybean oil (SO)) and the inclusion of savory (Satureja khuzistanica) plant (SP) in the diet on total tract digestibility of nutrients, rumen fermentation, milk yield and milk fatty acid profile in dairy cattle. Eight multiparous lactating Holstein cows were used in a replicated 4 × 4 Latin square design experiment with four diets and four 21-d periods. During each experimental period consisted of 14 days of adaptation and a 7-day sampling period, cows were randomly assigned to one of the four dietary treatments: the diet supplemented with 2% (DM basis) fish oil (FOD) or soybean oil (SOD), the FOD or SOD plus 370 g DM/d/head SP (FODs, SODs, respectively). The experimental diets were arranged in a 2 × 2 factorial design, with the fat sources as the first and SP as the second factor. The FO-supplemented diets had lower dry matter intake (DMI) and higher total tract digestibility than SO-supplemented diets (P < 0.05), and including SP in the diet improved total tract digestibility of dry matter (DM), organic matter (OM), ether extract (EE), and non-fibrous carbohydrates (NFC) (P < 0.05) without negatively affecting DMI. Rumen pH was lower with SO than with FO diets (P < 0.01) and increased with SP inclusion in the diet (P < 0.05). Total protozoa count and ruminal ammonia concentration decreased, and the branched-chain VFA (BCVFA) proportion increased with SP inclusion in the diet (P < 0.05). Milk production, as well as the concentration and yield of milk components (except lactose concentration) were higher with SO than with FO diets (P < 0.05), but these variables remained unaffected by SP. The milk concentrations of both non-esterified fatty acids (NEFA) and beta-hydroxybutyrate (BHB) were lower with SO compared to FO diets, and these variables were reduced by SP (P < 0.01). The proportions of both mono- and polyunsaturated FA (MUFA and PUFA, respectively) in milk were higher with FO than with SO diets (P < 0.01), and their proportions increased by SP at the expense of saturated FA (SFA) (P < 0.01). Including SP in the diet increased the proportions of all the milk n-3 FA (C18:3c, C20:5, and C22:6) by 21%, 40%, and 97%, respectively, and those of conjugated linoleic acids (C18:2 (c9,t11-CLA) and C18:2 (t10,c12-CLA)) by 23% and 62%, respectively. There was no interaction between oil type and SP for the assessed variables. Fish oil, despite reducing milk production and milk components, was more effective than soybean oil in enriching milk with healthy FA. These findings also show promise for SP as a feed additive with the potential to improve total tract digestibility, rumen fermentation and milk FA composition.

Microbial-Metabolomic Exploration of Tea Polyphenols in the Regulation of Serum Indicators, Liver Metabolism, Rumen Microorganisms, and Metabolism in Hu Sheep

This study investigated the impact of tea polyphenols on serum indices, rumen microorganisms, rumen metabolism, and liver metabolism in Hu sheep. Sixty healthy lambs, aged three months and with similar average weights, were chosen and randomly assigned to control (CON), TP400, TP800, and TP1200 groups, each consisting of fifteen lambs. The control group received a basal diet, while the experimental groups were provided with basal diet supplemented with 400 mg/kg, 800 mg/kg, and 1200 mg/kg of tea polyphenols, respectively. Compared with the CON group, the addition of tea polyphenols to the diet significantly increased serum IgA, GSH-Px, and TSOD. In addition, tea polyphenols were able to increase rumen pH but had no significant effect on the rumen NH3-N, VFA molar content, and the microbial top 10 phylum and genus levels. Moreover, Firmicutes predominated in the network map of the top 80 abundant microorganisms at the genus level, identifying 13 biomarkers at the genus level. In addition, strong correlations were observed between liver and rumen metabolites, particularly between rumen succinic acid and liver alanyl-serine and methylmalonic acid. Furthermore, tea polyphenol additions changed the enrichment of liver and rumen metabolites in the top five KEGG metabolic pathways, but 400-1200 mg/kg additions had no negative impact on the liver and rumen. In summary, TP significantly influences rumen and liver metabolites in Hu sheep, enhancing lamb immunity and antioxidant capacity, with 400 mg/kg being the most effective dosage.

Effects of yak rumen anaerobic fungus Orpinomyces sp. YF3 fermented on in vitro wheat straw fermentation and microbial communities in dairy goat rumen fluid, with and without fungal flora

Rumen fungi play an essential role in the breakdown of dietary fibrous components, facilitating the provision of nutrients and energy to the host animals. This study investigated the fermentation characteristics and effects on rumen microbiota of yak rumen anaerobic fungus Orpinomyces sp. YF3 in goat rumen fluid, both with and without fungal flora, utilizing anaerobic fermentation bottles. Crushed and air-dried wheat straw served as the fermentation substrate, and cycloheximide was used to eradicate microorganisms from the rumen fluid of dairy goats. The experiment compromised four treatment groups (2×2 factorial design): control (C); yak fungus group (CF, Orpinomyces sp. YF3); goat fungi eliminated group (CA, antibiotic: 0.25 mg/mL cycloheximide); goat fungi eliminated+yak fungus group (CAF). Each treatment had six replicates. Fermentation characteristics and microbial composition of the fermentation media were analyzed using one-way analysis of variance and high-throughput sequencing technology. The findings revealed that in the Orpinomyces sp. YF3 addition group (CF and CAF groups), there were significant increases in ammonia nitrogen concentration by 70%, total volatile fatty acids (VFA) by 53%, as well as acetate, isobutyrate, and valerate concentrations, and the ratio of acetate to propionate (p < 0.05), while the propionate proportion declined by 13%, alongside a reduction of butyrate concentration (p < 0.05). Similarly, in the CF and CAF groups, there were a notable increase in the relative abundance of Bacteroidota, Synergistota, Desulfobacterota, Actinobacteria, and Fusobacteriota, alongside a decrease in the relative abundance of Fibrobacterota and Proteobacteria (p < 0.05). Bacteria exhibiting increased relative abundance were positively correlated with the activity of carboxymethyl cellulase and avicelase, total VFA concentration, and acetate proportion, while showing a negatively correlation with propionate proportion. In conclusion, supplementing rumen fermentation media with yak rumen anaerobic fungus Orpinomyces sp. YF3 led to an increase in bacteria associated with fibre degradation and acetic acid production, a decrease in propionate-producing bacteria, enhanced the activity of plant cell wall degrading enzymes, and promoted cellulose degradation, ultimately elevating total VAF concentration and acetate proportion. This presents a novel approach to enhance roughage utilization in ruminants.

Comparative Analysis of Gut Bacterial Diversity in Wild and Domestic Yaks on the Qinghai-Tibetan Plateau

The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production.

Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep

The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.

Restriction of growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria

The accelerated rise in antimicrobial resistance (AMR) poses a significant global health risk, necessitating the exploration of alternative strategies to combat pathogenic infections. Biofilm-related infections that are unresponsive to standard antibiotics often require the use of higher-order antimicrobials with toxic side effects and the potential to disrupt the microbiome. Probiotic therapy, with its diverse benefits and inherent safety, is emerging as a promising approach to prevent and treat various infections, and as an alternative to antibiotic therapy. In this study, we isolated novel probiotic bacteria from the gut of domestic goats (Capra hircus) and evaluated their antimicrobial and anti-biofilm activities against the 'ESKAPE' group of pathogens. We performed comprehensive microbiological, biochemical, and molecular characterizations, including analysis of the 16S-rRNA gene V1-V3 region and the 16S-23S ISR region, on 20 caprine gut-derived lactic acid bacteria (LAB). Among these, six selected Lactobacillus isolates demonstrated substantial biofilm formation under anaerobic conditions and exhibited robust cell surface hydrophobicity and autoaggregation, and epithelial cell adhesion properties highlighting their superior enteric colonization capability. Notably, these Lactobacillus isolates exhibited broad-spectrum growth inhibitory and anti-biofilm properties against 'ESKAPE' pathogens. Additionally, the Lactobacillus isolates were susceptible to antibiotics listed by the European Food Safety Authority (EFSA) within the prescribed Minimum Inhibitory Concentration limits, suggesting their safety as feed additives. The remarkable probiotic characteristics exhibited by the caprine gut-derived Lactobacillus isolates in this study strongly endorse their potential as compelling alternatives to antibiotics and direct-fed microbial (DFM) feed supplements in the livestock industry, addressing the escalating need for antibiotic-free animal products.

Characterization of BrGH3A, a bovine rumen-derived glycoside hydrolase family 3 β-glucosidase with a permuted domain arrangement

The bovine rumen contains a large consortium of residential microbes that release a variety of digestive enzymes for feed degradation. However, the utilization of these microbial enzymes is still limited because these rumen microorganisms are mostly anaerobes and are thus unculturable. Therefore, we applied a sequence-based metagenomic approach to identify a novel 2,445-bp glycoside hydrolase family 3 β-glucosidase gene known as BrGH3A from the metagenome of bovine ruminal fluid. BrGH3A β-glucosidase is a 92-kDa polypeptide composed of 814 amino acid residues. Unlike most glycoside hydrolases in the same family, BrGH3A exhibited a permuted domain arrangement consisting of an (α/β)6 sandwich domain, a fibronectin type III domain and a (β/α)8 barrel domain. BrGH3A exhibited greater catalytic efficiency toward laminaribiose than cellobiose. We proposed that BrGH3A is an exo-acting β-glucosidase from Spirochaetales bacteria that is possibly involved in the intracellular degradation of β-1,3-/1,4-mixed linkage glucans that are present in grass cell walls. BrGH3A exhibits rich diversity in rumen hydrolytic enzymes and may represent a member of a new clan with a permuted domain topology within the large family.

Association of litter size with the ruminal microbiome structure and metabolomic profile in goats

The Yunshang black goat is a renowned mutton specialist breed mainly originating from China that has excellent breeding ability with varying litter sizes. Litter size is an important factor in the economics of goat farming. However, ruminal microbiome structure might be directly or indirectly regulated by pregnancy-associated factors, including litter sizes. Therefore, the current experiment aimed to evaluate the association of different litter sizes (low versus high) with ruminal microbiome structure by 16S rRNA gene sequencing and metabolomic profiling of Yunshang black does. A total of twenty does of the Yunshang Black breed, approximately aged between 3 and 4 years, were grouped (n = 10 goats/group) into low (D-l) and high (D-h) litter groups according to their litter size (the lower group has ≤ 2 kids/litter and the high group has ≧ 3 kids/litter, respectively). All goats were sacrificed, and collected ruminal fluid samples were subjected to 16S rRNA sequencing and LC-MS/MC Analysis for ruminal microbiome and metabolomic profiling respectively. According to PCoA analysis, the ruminal microbiota was not significantly changed by the litter sizes among the groups. The Firmicutes and Bacteroidetes were the most dominant phyla, with an abundance of 55.34% and 39.62%, respectively. However, Ruminococcaceae_UCG-009, Sediminispirochaeta, and Paraprevotella were significantly increased in the D-h group, whereas Ruminococcaceae_UCG-010 and Howardella were found to be significantly decreased in the D-l group. The metabolic profiling analysis revealed that litter size impacts metabolites as 29 and 50 metabolites in positive and negative ionic modes respectively had significant differences in their regulation. From them, 16 and 24 metabolites of the D-h group were significantly down-regulated in the positive ionic mode, while 26 metabolites were up-regulated in the negative ionic mode for the same group. The most vibrant identified metabolites, including methyl linoleate, acetylursolic acid, O-desmethyl venlafaxine glucuronide, melanostatin, and arginyl-hydroxyproline, are involved in multiple biochemical processes relevant to rumen roles. The identified differential metabolites were significantly enriched in 12 different pathways including protein digestion and absorption, glycerophospholipid metabolism, regulation of lipolysis in adipocytes, and the mTOR signaling pathway. Spearman's correlation coefficient analysis indicated that metabolites and microbial communities were tightly correlated and had significant differences between the D-l and D-h groups. Based on the results, the present study provides novel insights into the regulation mechanisms of the rumen microbiota and metabolomic profiles leading to different fertility in goats, which can give breeders some enlightenments to further improve the fertility of Yunshang Black goats.

Changes on the rumen microbial community composition in dairy cows subjected to an acidogenic diet

In modern breeding systems, cows are subjected to many stress factors. Animals fed with a high-grain diet may have a decreased rumen pH, which would lead to subacute ruminal acidosis syndrome. The aim of this study was to investigate the evolution of microbial community composition in cows undergoing a dietary stress challenge. Twelve cows were subjected to a challenge period consisted in a rapid change of ration, from a normal (45.4:54.6 forage: concentrate) to a high-grain content diet (24.8:75.2 forage: concentrate) to induce sub-acute ruminal acidosis. Individual rumen fluid content samples were collected before (T0), and during the challenge (T3, T14, T28). DNA from rumen contents was extracted, purified, and sequenced to evaluate Bacterial populations and sequencing was performed on Illumina MiSeq. The effect of animal conditions on rumen microbial community was quantified through a linear mixed model. The acidogenic diet created 2 main clusters: ruminal hypomotility (RH) and milk fat depression (MFD). The microbial composition did not differ in T0 between the 2 groups, while during the challenge Ruminococcus spp., Treponema spp., Methanobrevibacter spp., and Methanosphaera spp. concentrations increased in RH cows; Succinivibrio spp. and Butyrivibrio spp. concentrations increased in MFD cows. Prevotella spp. and Ruminococcus spp., were negatively correlated, while Christenellaceae family were positively correlated with both Methanobrevibacter spp. and Methanosphaera spp. Moreover, the same diet affected differently cows' microbiota composition, underlying the impact of the host effect. Other studies are necessary to deepen the relationship between microbiota composition and host.

Relationship between Rumen Microbial Differences and Phenotype Traits among Hu Sheep and Crossbred Offspring Sheep

This experiment was conducted to investigate the effect of three-way hybrid sheep and Hu sheep on serum indicators, rumen fermentation, rumen enzyme activity, and microorganisms in sheep. Healthy and similar birth weights from three groups (Hu, n = 11; Charolais × Australian White × Hu, CAH, n = 11; Charolais × Dorper × Hu, CDH, n = 11) were selected to be fed by the ewes until 45 days of age. Subsequently, they were weaned intensively and underwent short-term fattening for 3 months along with selected male lambs fed intensively. During this period, they were fed and watered ad libitum. Blood and rumen fluid were collected and analyzed for serum indicators and rumen fluid microorganisms, enzyme activity, and VFA, respectively, at the end of the fattening period. Compared with Hu lamb, the offspring of the three-way hybrid lamb showed significant improvements in body weight, serum lactate dehydrogenase, and creatinine content. However, there was no significant effect on serum immunity and antioxidant indices. In addition, the rumen fluid volatile fatty acid (VFA) molar concentration and microcrystalline cellulose and lipase content were significantly lower in the three-way hybrid lamb compared to Hu lamb, but β-glucosidase, amylase, pepsin, and VFA molar ratio were not significantly affected. Subsequently, 16S rRNA sequencing diversity analysis revealed that three-way hybrid lamb significantly increased rumen microbial ACE and Chao1 indices compared to Hu lamb. Meanwhile, the abundance of Verrucomicrobiota and Synergistota significantly increased at the phylum level. Correlation analysis showed that Prevotella had the highest proportion, while Rikenellaceae_RC9_gut_group correlated most closely with others genus. The microbial communities isovaleric acid molar concentration and proportion were strongly correlated. In addition, there were significant differences in correlations between microbial communities and isobutyric acid, butyric acid and valeric acid content, and their molar proportion, but they were not significantly correlated with digestive enzymes. From the functional enrichment analysis, it was found that hybrid progeny were mainly enriched in the pyruvate metabolism, microbial metabolism in diverse environments, carbon metabolism, and quorum sensing pathways. In contrast, the Hu sheep were primarily enriched in the cysteine and methionine, amino sugar and nucleotide sugar, and biosynthesis of secondary metabolite pathways. These results suggest that hybridization can play a role in regulating organismal metabolism and improve animal production performance by influencing the structure and characteristics of microbial communities.

A Review of the Rumen Microbiota and the Different Molecular Techniques Used to Identify Microorganisms Found in the Rumen Fluid of Ruminants

Variations in environments, including climate, diet, and agricultural practices, significantly impact the composition and microbial activity. A profound understanding of these adaptations allows for the improvement of nutrition and ruminant production. Therefore, this review aims to compile data from the literature on the rumen microbiota and molecular techniques for identifying the different types of microorganisms from the rumen fluid of ruminants. Analyzing the literature on rumen microbiology in different ruminants is complex due to microbial interactions, influenced by the environment and nutrition of these animals. In addition, it is worth noting that the genera of protozoa and fungi most evident in the studies used in this review on the microbiology of rumen fluid were Entodinium spp. and Aspergillus spp., respectively, and Fibrobacter spp. for bacteria. About the techniques used, it can be seen that DNA extraction, amplification, and sequencing were the most cited in the studies evaluated. Therefore, this review describes what is present in the literature and provides an overview of the main microbial agents in the rumen and the molecular techniques used.

Host and rumen microbiome contributions to feed efficiency traits in Holstein cows

It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then the h2 reflects only the contribution of the direct genetic effects quantified as direct heritability (hd2), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho2). The objectives of this study were to estimate h2, hd2,m2, and ho2 for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd2 estimates were always 10% to 15% lower than h2 estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m2 estimates were moderate for all traits, and up to 26% for milk energy. The ho2 was greater than the sum of hd2 and m2, suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.

Molecular detection of ruminal micro-flora and micro-fauna in Saudi Arabian camels: Effects of season and region

This study investigated and explored the availability of micro-flora and micro-fauna in the ruminal contents of Arabian camel (Camelus dromedarius) from three different regions in Saudi Arabia along with two seasons. Samples were prepared and tested by conventional polymerase chain reaction (PCR). This study confirmed that the bacterial flora were dominating over other microbes. Different results of the availability of each microbe in each region and season were statistically analyzed and discussed. There was no significant effect of season on the micro-flora or micro-fauna however, the location revealed a positive effect with Ruminococcus flavefaciens (p < 0 0.03) in the eastern region. This study was the first to investigate the abundance of micro-flora and micro-fauna in the ruminal contents of camels of Saudi Arabia. This study underscores the significance of camel ruminal micro-flora and micro-fauna abundance, highlighting their correlation with both seasonality and geographic location. This exploration enhances our comprehension of camel rumination and digestion processes. The initial identification of these microbial communities serves as a foundational step, laying the groundwork for future in-depth investigations into camel digestibility and nutritional requirements.

Epiberberine: a potential rumen microbial urease inhibitor to reduce ammonia release screened by targeting UreG

Rumen microbial urease inhibitors have been proposed for regulating nitrogen emission and improving nitrogen utilization efficiency in ruminant livestock industry. However, studies on plant-derived natural inhibitors of rumen microbial urease are limited. Urease accessory protein UreG, plays a crucial role in facilitating urease maturation, is a new target for design of urease inhibitor. The objective of this study was to select the potential effective inhibitor of rumen microbial urease from major protoberberine alkaloids in Rhizoma Coptidis by targeting UreG. Our results showed that berberine chloride and epiberberine exerted superior inhibition potential than other alkaloids based on GTPase activity study of UreG. Berberine chloride inhibition of UreG was mixed type, while inhibition kinetics type of epiberberine was uncompetitive. Furthermore, epiberberine was found to be more effective than berberine chloride in inhibiting the combination of nickel towards UreG and inducing changes in the second structure of UreG. Molecular modeling provided the rational structural basis for the higher inhibition potential of epiberberine, amino acid residues in G1 motif and G3 motif of UreG formed interactions with D ring of berberine chloride, while interacted with A ring and D ring of epiberberine. We further demonstrated the efficacy of epiberberine in the ruminal microbial fermentation with low ammonia release and urea degradation. In conclusion, our study clearly indicates that epiberberine is a promising candidate as a safe and effective inhibitor of rumen microbial urease and provides an optimal strategy and suitable feed additive for regulating nitrogen excretion in ruminants in the future. KEY POINTS: • Epiberberine is the most effective inhibitor of rumen urease from Rhizoma Coptidis. • Urease accessory protein UreG is an effective target for design of urease inhibitor. • Epiberberine may be used as natural feed additive to reducing NH3 release in ruminants.

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

BACKGROUND

Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species.

RESULTS

We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea.

CONCLUSIONS

The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

Relationships among bacterial cell size, diversity, and taxonomy in rumen

Introduction

The rumen microbial community plays a crucial role in the digestion and metabolic processes of ruminants. Although sequencing-based studies have helped reveal the diversity and functions of bacteria in the rumen, their physiological and biochemical characteristics, as well as their dynamic regulation along the digestion process in the rumen, remain poorly understood. Addressing these gaps requires pure culture studies to demystify the intricate mechanisms at play. Bacteria exhibit morphological differentiation associated with different species. Based on the difference in size or shape of microorganisms, size fractionation by filters with various pore sizes can be used to separate them.

Methods

In this study, we used polyvinylidene difluoride filters with pore sizes of 300, 120, 80, 40, 20, 8, 6, 2.1, and 0.6 μm. Bacterial suspensions were successively passed through these filters for the analysis of microbial population distribution using 16S rRNA gene sequences.

Results

We found that bacteria from the different pore sizes were clustered into four branches (> 120 μm, 40-120 μm, 6-20 μm, 20-40 μm, and < 0.6 μm), indicating that size fractionation had effects on enriching specific groups but could not effectively separate dominant groups by cell size alone. The species of unclassified Flavobacterium, unclassified Chryseobacterium, unclassified Delftia, Methylotenera mobilis, unclassified Caulobacteraceae, unclassified Oligella, unclassified Sphingomonas, unclassified Stenotrophomonas, unclassified Shuttleworthia, unclassified Sutterella, unclassified Alphaproteobacteria, and unclassified SR1 can be efficiently enriched or separated by size fractionation.

Discussion

In this study, we investigated the diversity of sorted bacteria populations in the rumen for preliminary investigations of the relationship between the size and classification of rumen bacteria that have the potential to improve our ability to isolate and culture bacteria from the rumen in the future.

Supplementation with Astragalus Root Powder Promotes Rumen Microbiota Density and Metabolome Interactions in Lambs

The gut microbiota is highly symbiotic with the host, and the microbiota and its metabolites are essential for regulating host health and physiological functions. Astragalus, as a feed additive, can improve animal immunity. However, the effects of Astragalus root powder on the rumen microbiota and their metabolites in lambs are not apparent. In this study, thirty healthy Hu sheep lambs with similar body weights (17.42 ± 2.02 kg) were randomly selected for the feeding experiment. Lambs were fed diets supplemented with 0.3% Astragalus root powder, and the rumen microbiota density and metabolome were measured to determine the effects of Astragalus on the health of lambs in the rumen. The results showed that the relative abundance of Butyrivibrio fibrisolvens (Bf), Ruminococcus flavefaciens (Rf), Succiniclasticum (Su), and Prevotella (Pr) in the rumen was increased in the Astragalus group (p < 0.01), and metabolic profiling showed that the metabolites, such as L-lyrosine and L-leucine, were upregulated in the Astragalus group (p < 0.01). KEGG functional annotation revealed that upregulated metabolites were mainly enriched in the pathways of amino acid metabolism, lipid metabolism, fatty acid biosynthesis, and bile secretion in the Astragalus group, and downregulated metabolites were enriched in the pathways of methane metabolism and other pathways. Correlation analysis revealed that butyric acid was positively correlated with Roseburia and Blautia (p < 0.05) and negatively correlated with Desulfovibrio (p < 0.05). Thus, by analyzing the interactions of Astragalus root powder with the density of rumen microorganisms and their metabolites in lambs, it was shown that Astragalus root powder could improve the structure of rumen microbiota and their metabolites and then participate in the regulation of amino acid metabolism, lipid metabolism, immune metabolism, and other pathways to improve the efficiency of energy absorption of the lambs.

Understanding the Diversity and Roles of the Ruminal Microbiome

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

Predicting feed efficiency of Angus steers using the gastrointestinal microbiome

Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome.

Isolation and characterization of strictly anaerobic cellulolytic rumen bacterial species from Sahiwal cattle

Objective

To isolate and characterize cellulolytic rumen bacteria from the rumen of Sahiwal cattle using rumen bacterial inoculum to increase the nutritional value of rice bran used as broiler feed.

Materials and Methods

The ruminal liquid was kept at an optimal pH of 6.9 and a redox potential of less than -300 mV while being incubated anaerobically at 39°C in a medium containing rumen fluid glucose cellobiose agar. By using the Hungate technique, the organisms were detected based on their morphological, physiological, biochemical, and molecular testing.

Results

The findings revealed that the isolated Ruminococcus albus, and Ruminococcus flavifaciens were obligate anaerobic, generally Gram-positive, nonmotile cocci or rod, single or pair, occasionally short chain, producing yellow pigment when grown on cellulose, and having a clear zone around the colonies. Both isolate fermented sugars such as cellobiose, glucose, and lactose, as well as decomposed xylan. The results also showed that the isolates recognized as Ruminococcus spp., a cellulolytic rumen bacterium, were catalase-negative, indole-negative, and gelatin liquefaction-positive.

Conclusion

Isolation and characterization of Ruminococcus spp. may be helpful for Bangladesh in reducing the cost of producing poultry feed and circumventing restrictions on rice bran use. We can also develop more efficient and long-lasting plans to enhance poultry performance and feed efficiency, as well as increase the nutritional value of rice bran used as broiler feed, by understanding how various Ruminococcus spp. function in this process.

Optimizing dietary rumen-degradable starch to rumen-degradable protein ratio improves lactation performance and nitrogen utilization efficiency in mid-lactating Holstein dairy cows

The dietary rumen-degradable starch (RDS) to rumen-degradable protein (RDP) ratio, denoted as the RDS-to-RDP ratio (SPR), has been proven to enhance in vitro rumen fermentation. However, the effects of dietary SPR in vivo remain largely unexplored. This study was conducted to investigate the effect of dietary SPR on lactation performance, nutrient digestibility, rumen fermentation patterns, blood indicators, and nitrogen (N) partitioning in mid-lactating Holstein cows. Seventy-two Holstein dairy cows were randomly assigned to three groups (24 head/group), balanced for (mean ± standard deviation) days in milk (116 ± 21.5), parity (2.1 ± 0.8), milk production (42 ± 2.1 kg/d), and body weight (705 ± 52.5 kg). The cows were fed diets with low (2.1, control), medium (2.3), or high (2.5) SPR, formulated to be isoenergetic, isonitrogenous, and iso-starch. The study consisted of a one-week adaptation phase followed by an eight-week experimental period. The results indicated that the high SPR group had a lower dry matter intake compared to the other groups (p < 0.05). A quadratic increase in milk yield and feed efficiency was observed with increasing dietary SPR (p < 0.05), peaking in the medium SPR group. The medium SPR group exhibited a lower milk somatic cell count and a higher blood total antioxidant capacity compared to other groups (p < 0.05). With increasing dietary SPR, there was a quadratic improvement (p < 0.05) in the total tract apparent digestibility of crude protein, ether extract, starch, neutral detergent fiber, and acid detergent fiber. Although no treatment effect was observed in rumen pH, the rumen total volatile fatty acids concentration and microbial crude protein synthesis increased quadratically (p < 0.05) as dietary SPR increased. The molar proportion of propionate linearly increased (p = 0.01), while branched-chain volatile fatty acids linearly decreased (p = 0.01) with increasing dietary SPR. The low SPR group (control) exhibited higher concentration of milk urea N, rumen ammonia N, and blood urea N than other groups (p < 0.05). Despite a linear decrease (p < 0.05) in the proportion of urinary N to N intake, increasing dietary SPR led to a quadratic increase (p = 0.01) in N utilization efficiency and a quadratic decrease (p < 0.05) in the proportion of fecal N to N intake. In conclusion, optimizing dietary SPR has the potential to enhance lactation performance and N utilization efficiency. Based on our findings, a medium dietary SPR (with SPR = 2.3) is recommended for mid-lactating Holstein dairy cows. Nevertheless, further research on rumen microbial composition and metabolites is warranted to elucidate the underlying mechanisms of the observed effects.

Anaerobic flora, Selenomonas ruminis sp. nov., and the bacteriocinogenic Ligilactobacillus salivarius strain MP3 from crossbred-lactating goats

This study aimed to examine the distribution of anaerobic bacteria in the rumen fluid of Thai crossbred goats and to screen potential probiotic strains capable of producing antimicrobial compounds and inhibiting bacteria that cause milk fat depression. Thirty-four strains of bacteria from the rumen fluid were divided into 13 groups within 12 genera based on 16S rRNA gene sequences. The RF1-5 and RF5-12 were identified as Streptococcus luteliensis and Bacillus licheniformis, respectively, and demonstrated non-ropy exopolysaccharide. Furthermore, mPRGC5T was closely related to Selenomonas caprae JCM 33725 T (97.8% similarity) based on 16S rRNA gene sequences. It exhibited low average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values with related type strains ranging from 84.9 to 86.0%, 21.3 to 21.8%, and 73.8 to 76.1%, respectively. The genotypic and phenotypic characteristics of mPRGC5T strongly support this strain as a new species of the genus Selenomonas for which the name Selenomonas ruminis mPRGC5T was proposed. The type strain is mPRGC5T (= JCM 33724 T = KCTC 25177 T). Ligilactobacillus salivarius MP3 showed antibacterial activity against Cutibacterium acnes subsp. acnes DSM 1897 T and Kocuria rhizophila MIII. The enterolysin A cluster gene was identified in its genome. The auto-aggregation of L. salivarius MP3 was 93.6 ± 0.2%. Additionally, co-aggregation of L. salivarius MP3 with C. acnes DSM 1897 T and K. rhizophila MIII had 92.2 ± 3.4% and 87.3 ± 4.5%, respectively. The adhesion capacity of strain MP3 was 76.11 ± 2.2%. Probiogenomic analysis revealed that L. salivarius MP3 was nonhazardous to animal supplementation and included acid- and bile-tolerant ability. However, strain MP3 contained three antibiotic resistance genes. Thus, the supplementation of L. salivarius MP3 could increase the milk fat content by suppressing C. acnes DSM 1897 T with antibiotic resistance gene horizontal transfer awareness.

Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.