Rumen Microbiota Research Articles

Effect of Dietary Concentrate-to-Forage Ratios During the Cold Season on Slaughter Performance, Meat Quality, Rumen Fermentation and Gut Microbiota of Tibetan Sheep

This study aimed to investigate the effects of different dietary concentrate-to-forage ratios on slaughter performance, meat quality, rumen fermentation, rumen microbiota and fecal microbiota in Tibetan sheep. A total of sixty male Tibetan sheep were equally allocated into three dietary groups based on concentrate-to-forage ratios, i.e., 30:70 (C30), 50:50 (C50), and 70:30 (C70). Compared with the C30 group, sheep fed the C70 diet resulted in a higher (p < 0.05) slaughter live weight (SLW), hot carcass weight (HCW), dressing percentage (DP), eye muscle area, average daily gain (ADG), and ruminal total volatile fatty acids concentration and propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate:propionate ratio. Sheep in the C50 group exhibited a higher (p < 0.05) SLW, HCW, ADG, and ruminal propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate: propionate ratio compared with the C30 group. In rumen fluid, the relative abundance of Butyrivibrio was lower (p = 0.031) in the C30 group, and that of Ruminococcus was higher (p = 0.003) in the C70 group compared with the C50 group. In feces, genus Monoglobus and UCG_002 were the most abundant in the C30 group (p < 0.05), and the relative abundance of Prevotella was significantly higher in the C70 group than in other groups (p = 0.013). Correlation analysis revealed possible links between slaughter performance and meat quality and altered microbiota composition in the rumen and feces of Tibetan sheep. Overall, feeding a C70 diet resulted in superior carcass characteristics and meat quality in Tibetan sheep, thus laying a theoretical basis for the application of short-term remote feeding during the cold season.

Fermented soybean meal modified the rumen microbiota and increased the serum prolactin level in lactating Holstein cows

This study aimed to investigate the effects of fermented soybean meal (FSM) on milk production, blood parameters, and rumen fermentation and microbial community in dairy cows. In this study, 48 healthy Holstein cows (parity, 3.0 ± 0.6; days in milk, 86.0 ± 6.7) were used. Cows were randomly assigned into four groups (CON, T-200, T-400, and T-600) with 12 cows per group. Cows in CON were not supplemented with FSM. Cows in T-200, T-400, and T-600 were supplemented with 200, 400, and 600 g/head/day FSM, respectively. This study lasted 5 weeks (1-week adaptation and 4-week treatment). The results showed that FSM did not affect milk yield and milk components (p > 0.05). In the serum, FSM greatly increased prolactin (p < 0.01), and a dosage effect was observed. Aspartate aminotransferase and total protein were the highest in the T-400 (p < 0.05), and triglycerides was the lowest in T-200 (p < 0.05), and there was no difference for the 3 measurements between the other 3 groups (p > 0.05). In the rumen, FSM did not affect pH, microbial crude protein, acetate, propionate, butyrate, valerate, total volatile fatty acids and the ratio of acetate:propionate (p > 0.05), only changed NH3-N, isobutyrate and isovalerate (p < 0.05). The results of the rumen bacterial 16S rRNA genes sequencing showed that FSM decreased the richness (p < 0.05) and evenness (p < 0.05) of the bacterial communities. PCoA analysis showed that FSH altered the rumen bacterial community (ANOSIM, R = 0.108, p = 0.002). In the relative abundance of phyla, FSM increased Firmicutes (p = 0.015) and Actinobacteriota (p < 0.01) and Patescibacteria (p = 0.012), decreased Bacteroidota (p = 0.024). In the relative abundance of genera, FSM increased Christensenellaceae R-7 group (p = 0.011), Lactococcus (p < 0.01), Candidatus Saccharimonas (p < 0.01), Olsenella (p < 0.01), decreased Muribaculaceae_norank (p < 0.01). Conclusively, supplemented FSM altered the rumen fermentation parameters and bacterial community, and increased serum prolactin level in lactating Holstein cows. These findings may provide an approach to keep the peak of lactation in dairy cows.

An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows.

Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows. The results indicated that the proportions of highly heritable subsets (h2 ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn2+ transport) (P < 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp., Prevotella_sp._E15-22, Prevotella_sp._E13-27, which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) (P < 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 (P < 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp., which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942). Our comprehensive study revealed the distinct heritability patterns of rumen microbial composition, function, and metabolism. Additionally, we shed light on the influence of host SNP variants on the rumen microbes with carbohydrate metabolism and their subsequent effects on lactation performance. Collectively, these findings offer compelling evidence for the host-microbe interactions, wherein cows actively modulate their rumen microbiota through SNP variants to regulate their own lactation performance. Video Abstract.

Exploring the rumen microbial function in Angus bulls with divergent residual feed intake

This study leverages Shotgun metagenomics to assess the rumen microbial community and functionality in Angus bulls with differing residual feed intake-expected progeny difference (RFI-EPD) values, aiming to elucidate the microbial contributions to feed efficiency. Negative RFI-EPD bulls (NegRFI: n=10; RFI-EPD= -0.3883 kg/d) and positive RFI-EPD bulls (PosRFI: n=10; RFI-EPD=0.2935 kg/d) were selected from a group of 59 Angus bulls (average body weight (BW) = 428 ± 18.8 kg; 350 ± 13.4 d of age) fed a high-forage total mixed ration after a 60-d testing period. At the end of the 60-d period, rumen fluid samples were collected for bacterial DNA extraction and subsequent shotgun metagenomic sequencing. Results of the metagenome analysis revealed greater gene richness in NegRFI bulls, compared to PosRFI. Analysis of similarity revealed a small but noticeable difference (P =0.052; R-value = 0.097) in the rumen microbial community of NegRFI and PosRFI bulls. Linear Discriminant Analysis effect size (Lefse) was utilized to identify the differentially abundant taxa. The Lefse results showed that class Fibrobacteria (LDA = 5.1) and genus Fibrobacter (LDA = 4.8) were greater in NegRFI bulls, compared to PosRFI bulls. Relative abundance of the carbohydrate-active enzymes was also compared using Lefse. The results showed greater relative abundance of glycoside hydrolases and carbohydrate-binding modules such as GH5, CBM86, CBM35, GH43, and CBM6 (LDA &amp;gt; 3.0) in NegRFI bulls whereas GH13 and GT2 were greater in PosRFI bulls. The distinct metabolic and microbial profiles observed in NegRFI, compared to PosRFI bulls, characterized by greater gene richness and specific taxa such as Fibrobacter, and variations in carbohydrate-active enzymes, underscore the potential genetic and functional differences in their rumen microbiome. These findings contribute to a deeper understanding of the interplay between rumen microbiota and feed efficiency in Angus bulls, opening avenues for targeted interventions and advancements in livestock management practices.

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.

Dietary supplementation with citrus peel extract in transition period improves rumen microbial composition and ameliorates energy metabolism and lactation performance of dairy cows

BackgroundDuring the transition period, excessive negative energy balance (NEB) lead to metabolic disorders and reduced milk yield. Rumen microbes are responsible for resolving plant material and producing volatile fatty acids (VFA), which are the primary energy source for cows. In this study, we aimed to investigate the effect of citrus peel extract (CPE) supplementation on rumen microbiota composition, energy metabolism and milk performance of peripartum dairy cows.MethodsDairy cows were fed either a basal diet (CON group) or the same basal diet supplemented with CPE via intragastric administration (4 g/d, CPE group) for 6 weeks (3 weeks before and 3 weeks after calving; n = 15 per group). Samples of serum, milk, rumen fluid, adipose tissue, and liver were collected to assess the effects of CPE on rumen microbiota composition, rumen fermentation parameters, milk performance, and energy metabolic status of dairy cows.ResultsCPE supplementation led to an increase in milk yield, milk protein and lactose contents, and serum glucose levels, while reduced serum concentrations of non-esterified fatty acid, β-hydroxybutyric acid, insulin, aspartate aminotransferase, alanine aminotransferase, and haptoglobin during the first month of lactation. CPE supplementation also increased the content of ruminal VFA. Compared to the CON group, the abundance of Prevotellaceae, Methanobacteriaceae, Bacteroidales_RF16_group, and Selenomonadaceae was found increased, while the abundance of Oscillospiraceae, F082, Ruminococcaceae, Christensenellaceae, Muribaculaceae UCG-011, Saccharimonadaceae, Hungateiclostridiaceae, and Spirochaetaceae in the CPE group was found decreased. In adipose tissue, CPE supplementation decreased lipolysis, and inflammatory response, while increased insulin sensitivity. In the liver, CPE supplementation decreased lipid accumulation, increased insulin sensitivity, and upregulated expression of genes involved in gluconeogenesis.ConclusionsOur findings suggest that CPE supplementation during the peripartum period altered rumen microbiota composition and increased ruminal VFA contents, which further improved NEB and lactation performance, alleviated lipolysis and inflammatory response in adipose tissue, reduced lipid accumulation and promoted gluconeogenesis in liver. Thus, CPE might contribute to improve energy metabolism and consequently lactation performance of dairy cows during the transition period.

Changes in the growth performance, serum biochemistry, rumen fermentation, rumen microbiota community, and intestinal development in weaned goats during rumen-protected methionine treatment

Rumen-protected methionine (RPM) such as coated methionine (CM) and 2-hydroxy-4-(methylthio)-butanoic acid isopropyl ester (HMBi) was usually used in dairy cows, but how RPM affects meat goats remains unclear. In this study, thirty weaned male Jianzhou Da’er goats were randomly assigned to one of three treatments: fed basal diet or basal diet supplemented with 0.12% CM or 0.22% HMBi, with the aim of examining their impact on growth performance, serum biochemistry, rumen fermentation, rumen microbiota, and intestinal development in meat goats. The findings indicate that HMBi supplementation led to an increase in body weight, feed intake, and feed-to-gain ratio, whereas CM only resulted in an increase in feed intake (all p &amp;lt; 0.05). Both CM and HMBi resulted in an increase in serum total cholesterol (TC), blood urea nitrogen (BUN), alkaline phosphatase (ALP), and aspartate aminotransferase (AST), albeit with a decrease in serum triglycerides (TG) and β-hydroxybutyric acid (BHB, all p &amp;lt; 0.05). Both CM and HMBi supplementation decreased the rumen butyric acid concentration (both p &amp;lt; 0.05). The 16S rRNA sequencing showed that HMBi supplementation significantly increased the total abundance of Bacteroidetes and Firmicutes. Both CM and HMBi supplements increased the abundance of Rikenella and Proteiniphilum but decreased the abundance of Eisenbergiella, Enterocloster, Massilioclostridium, Eubacterium, Angelakisella, Blastopirellula, Christensenella, and Pseudoruminococcus. CM supplementation specifically increased the abundance of Desulfobulbus, Sodaliphilus, and Coprococcus while decreasing the prevalence of Anaerocella, Mogibacterium, and Collinsella. The supplementation of HMBi significantly enhanced the abundance of Paraprevotella, Bacilliculturomica, Lachnoclostridium, Dysosmobacter, Barnesiella, and Paludibacter, while decreasing the abundance of Butyrivibrio and Pirellula. Moreover, the administration of both CM and HMBi supplementation resulted in an increase in the ammonia-producing and sulfate-reducing bacteria, whereas a decrease was observed in the ammonia-oxidating, health-associated, and disease-associated bacteria. Correlational analysis revealed that TG and BHB had a positive correlation with disease-associated and ammonia-oxidating bacteria, whereas they had a negative correlation with ammonia-producing bacteria. The serum BUN, ALP, and AST were positively correlated with ammonia-producing bacteria but were negatively correlated with ammonia-oxidating bacteria. Furthermore, both CM and HMBi supplementation improve the development of the small intestine, with HMBi having a better effect. In summary, this study indicates that both CM and HMBi supplementation improve lipid metabolism, nitrogen utilization, and intestinal development. The growth promotion effect of HMBi supplementation may be attributed to the increased abundance of volatile fatty acid-producing and nitrogen-utilizing bacteria and improved intestinal development.

Prickly Ash Seeds Improve the Ruminal Epithelial Development and Growth Performance of Hu Sheep by Modulating the Rumen Microbiota and Metabolome

It is known that the addition of feed rich in bioactive components to animal diets will affect rumen fermentation parameters and flora structure. However, research on the regulatory effects of prickly ash seeds (PASs) during rumen development or on the rumen microbiome and its metabolites in sheep is limited. The current study was designed to explore the effects of PASs on sheep rumen development and growth performance using metagenomics and metabolomics. Eighteen 3-month-old Hu lambs were randomly allotted to three different dietary treatment groups: 0% (basal diet, CK), 3% (CK with 3% PAS, low-dose PAS, LPS), and 6% (CK with 6% PAS, high-dose PAS, HPS) PASs. The lambs were slaughtered to evaluate production performance. Our results showed that dietary PAS addition improved the average daily gain and reduced the F/G ratio of the experimental animals. Additionally, the height and width of the rumen papilla in the treatment groups were significantly higher than those in the CK group. The fermentation parameters showed that the levels of acetate and butyrate were significantly higher in the LPS group than in the CK and HPS groups. The propionate levels in the HPS group were significantly higher than those in the CK and LPS groups. Metagenomics analysis revealed that PAS dietary supplementation improved the abundance of Clostridiales and Bacteroidales and reduced the abundance of Prevotella, Butyrivibrio, and Methanococcus. Metabolomic analyses revealed that increased metabolite levels, such as those of serotonin, L-isoleucine, and L-valine, were closely related to growth-related metabolic pathways. The correlations analyzed showed that papilla height and muscular thickness were positively and negatively correlated with serotonin and L-valine, respectively. Average daily gain (ADG) was positively and negatively correlated with L-valine and several Prevotella, respectively. In addition, muscular thickness was positively correlated with Sodaliphilus pleomorphus, four Prevotella strains, Sarcina_sp_DSM_11001, and Methanobrevibacter_thaueri. Overall, PAS addition improved sheep growth performance by regulating beneficial microorganism and metabolite abundances, facilitating bacterial and viral invasion resistance.

Host genetic regulation of specific functional groups in the rumen microbiome of dairy cows: Implications for lactation trait

IntroductionRuminants play a pivotal role in our society by transforming non-consumable substances from industrial by-products and plant fibers into valuable resources such as meat and milk. This remarkable conversion ability is primarily attributed to the rumen microbiota, which is influenced by various factors, including diet, climate, and geographical location. In recent years, increasing research has shown that host factors (breed, genetic variation, etc.) also play vital roles in shaping rumen microbial composition and function in cattle. ObjectiveThis study aims to provide a theoretical basis and an opportunity for further investigating the regulation of lactation traits in dairy cows through host genetics and the interaction with the rumen microbiota. MethodTo investigate the interactions between host genotype, rumen microbiota, and animal phenotype, we curated and analyzed the dairy herd improvement (DHI) data, single nucleotide polymorphisms (SNPs) genotypes, and 16S rumen microbiota data from 1,169 Holstein dairy cows. Heritability and microbiability estimation, along with genome-wide association studies (GWAS) were performed to identify candidate microorganisms and host genetic loci. ResultWe identified thirty-one heritable taxa, whose functions were predominantly enriched in carbohydrate metabolism and energy metabolism. The genome-wide association study revealed that nine heritable bacteria were significantly associated with forty-three SNPs. Functional genes located within or near these SNPs were primarily associated with rumen epithelial development. Additionally, these nine heritable bacteria were primarily annotated as complex polysaccharide degraders and butyrate producers, such as Fibrobacter sp900143055 and Pseudoruminococcus massiliensis, which showed significant associations with milk yield and milk fat percentage. Compared to previous studies, we newly discovered the existence of a high heritability of Olsenella umbonate, Butyrivibrio hungatei, among others.

Microbiological Characteristics of the Gastrointestinal Tracts of Jersey and Holstein Cows.

The gastrointestinal bacterial microbiota is essential for maintaining the health of dairy cows and ensuring their production potential, and it may also help explain the breed-related phenotypic differences. Therefore, investigating the differences in gastrointestinal bacterial microbiota between breeds is critical for deciphering the mechanisms behind these differences and exploring the potential for improving milk production by regulating the gastrointestinal bacterial microbiota. This study holistically examined the differences between rumen and hindgut bacterial microbiota in a large cohort of two breeds of dairy cows, comprising 184 Jersey cows and 165 Holstein cows. Significant distinctions were identified between the rumen and hindgut bacterial microbiota of dairy cows, with these differences being consistent across breeds. A total of 20 breed-differentiated microorganisms, comprising 14 rumen microorganisms and 6 hindgut microorganisms, were screened, which may be the primary drivers of the observed differences in lactation performance between Jersey and Holstein cows. The present study revealed the spatial heterogeneity of the gastrointestinal bacterial microbiota of Jersey and Holstein cows and identified microbial biomarkers of different breeds. These findings enhance our understanding of the differences in the gastrointestinal bacterial microbiota between Jersey and Holstein cows and may provide useful information for optimizing the composition of the intestinal bacterial microbiota of the two breeds of dairy cows.

Dietary β-hydroxybutyrate sodium alters rumen microbiome and nutrient metabolism in the rumen epithelium of young goats

The role of β-hydroxybutyric acid (BHBA) includes providing energy, regulating signaling pathways, and ameliorating the gut microbiota in the host, while its nutrient mechanism to improve rumen epithelium development in young ruminants is still unclear. In this study, a total of 12 female Haimen goats with 30 days of age were chosen and divided into two groups. One group was fed with basic diet (CON), and the other group was fed a basal diet supplemented with 6 g d-1 dietary β-hydroxybutyrate sodium (BHBA-Na). The experimental period was 30 days, and all goats were slaughtered at 60 days of age. The joint analysis of multi-omics, including rumen microbiota, rumen epithelial transcriptome and rumen epithelial metabolomics in young goat model, was performed to systematically investigate the effect of dietary BHBA-Na on rumen development in young goats. As the results, we found that dietary BHBA-Na improved the growth performance of young goat including body weight, average daily gain (ADG) and dry matter intake (DMI) (P<0.05). Dietary BHBA-Na also increased the weight of rumen, and promoted the growth of rumen epithelium development (P < 0.05). The abundance of several beneficial bacteria was increased (Fibrobacter, Succinivibrio, Clostridiales, etc.,). The rumen epithelium transcriptome and metabolomics indicated that BHBA-Na supplementation showed a remarkable effect on the nutrient metabolism of the rumen epithelium. Specifically, the pathways of “fatty acid metabolism”, “cholesterol homeostasis”, “reactive oxygen species (ROS) pathway” and “peroxisome” were activated in response to BHBA-Na addition (P < 0.05). Moreover, the genes (HMGCS2, ECSH1, ACAA2, ECH1, ACADS etc.) and metabolites (succinic acid, alpha-ketoisovaleric acid, etc.) involved in these pathways were also regulated positively (P < 0.05). The rumen epithelium obtained the energy for its development from the process of volatile fatty acids (VFAs) decomposition. Finally, we observed the close correlations among the phenotypes, ruminal microbiota, host genes and epithelial metabolites. Overall, our results revealed that the BHBA-Na promoted the growth and rumen development of young goats possibly by enhancing DMI and regulating the rumen microbiota and the metabolisms of VFA and amino acid in the rumen epithelium.

The effects of compound probiotics on production performance, rumen fermentation and microbiota of Hu sheep.

Fungal probiotics have the potential as feed additives, but less has been explored in ruminant feed up to date. This study aimed to determine the effect of compound probiotics (CPs) with Aspergillus oryzae 1, Aspergillus oryzae 2 and Candida utilis on Hu sheep's growth performance, rumen fermentation and microbiota. A total of 120 male Hu sheep, aged 2 months and with the body weight of 16.95 ± 0.65 kg were divided into 4 groups. Each group consisted of 5 replicates, with 6 sheep per replicate. Group A was the control group fed with the basal diet. Group B, C and D was supplemented with the basal diet by adding 400, 800 and 1,200 grams per ton (g/t) CPs, respectively. The feeding trial lasted for 60 days after a 10-day adaptation period. The results showed that the average daily gain (ADG) of sheep in the CPs groups were significantly higher, the feed/gain were significantly lower than those in group A in the later stage and the overall period. The addition of CPs increased the economic benefit. The levels of CD4+ and the CD4+/CD8+ ratio in the CPs groups were higher than those in Group A. The levels of GSH, IgG, IL-2, IL-6, and IFN-γ in group C were significantly elevated compared with group A. Group B showed a significant increase in rumen NH3-N and cellulase activity. There was no difference in VFAs content between group A and group B, however, with the increasing addition of CPs, the butyric acid and isobutyric acid content tended to decrease. The rumen microbiota analysis indicated that the CPs addition increased the Firmicutes and Proteobacteria abundances, decreased the Bacteroidetes abundance. The correlation analysis showed that Prevotella was negatively correlated with ADG, and the addition of 400 CPs in group B reduced Prevotella's relative abundance, indicating CPs increased sheep growth by decreasing Prevotella abundance. The CPs addition reduced caspase-3, NF-κB and TNF-α expression in liver, jejunum and rumen tissues. In conclusion, the addition of CPs increased the sheep production performance, reduced inflammation, improved rumen and intestinal health. Considering the above points and economic benefits, the optimal addition of CPs as an additive for Hu sheep is 800 g/t.

Revealing host genome–microbiome networks underlying feed efficiency in dairy cows

Ruminants have the ability to digest human-inedible plant materials, due to the symbiotic relationship with the rumen microbiota. Rumen microbes supply short chain fatty acids, amino acids, and vitamins to dairy cows that are used for maintenance, growth, and lactation functions. The main goal of this study was to investigate gene-microbiome networks underlying feed efficiency traits by integrating genotypic, microbial, and phenotypic data from lactating dairy cows. Data consisted of dry matter intake (DMI), net energy secreted in milk, and residual feed intake (RFI) records, SNP genotype, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows. We first assessed marginal associations between genotypes and phenotypic and microbial traits through genomic scans, and then, in regions with multiple significant hits, we assessed gene-microbiome-phenotype networks using causal structural learning algorithms. We found significant regions co-localizing the rumen microbiome and feed efficiency traits. Interestingly, we found three types of network relationships: (1) the cow genome directly affects both rumen microbial abundances and feed efficiency traits; (2) the cow genome (Chr3: 116.5 Mb) indirectly affects RFI, mediated by the abundance of Syntrophococcus, Prevotella, and an unknown genus of Class Bacilli; and (3) the cow genome (Chr7: 52.8 Mb and Chr11: 6.1–6.2 Mb) affects the abundance of Rikenellaceae RC9 gut group mediated by DMI. Our findings shed light on how the host genome acts directly and indirectly on the rumen microbiome and feed efficiency traits and the potential benefits of the inclusion of specific microbes in selection indexes or as correlated traits in breeding programs. Overall, the multistep approach described here, combining whole-genome scans and causal network reconstruction, allows us to reveal the relationship between genome and microbiome underlying dairy cow feed efficiency.

Microbial dysbiosis in the gut–mammary axis as a mechanism for mastitis in dairy cows

Mastitis is a significant and costly disease in dairy cows, reducing milk production and affecting herd health. Recent research highlights the role of gastrointestinal microbial dysbiosis in the development of mastitis. This review focuses on how microbial imbalances in the rumen and intestines can compromise the integrity of the gastrointestinal barriers, allowing harmful bacteria and endotoxins, such as lipopolysaccharide, to enter the bloodstream and reach the mammary gland, triggering inflammation. This process links gastrointestinal health to mammary gland inflammation through the gut–mammary axis. Furthermore, disruptions in glucose metabolism and immune responses are implicated in the progression of mastitis. This review underscores the potential for non‐antibiotic interventions aimed at restoring microbial balance to reduce mastitis incidence, providing new insights into improving dairy cow health and farm productivity. Our findings emphasise the critical need to explore preventive measures targeting the rumen and intestinal microbiota for effective mastitis control.

Fermented Palm Kernel Cake Improves the Rumen Microbiota and Metabolome of Beef Cattle.

In this study, we utilised palm kernel cake as a substrate and fermented it with a composite of bacteria (Pediococcus pentosaceus CGMCC No. 27203 and Lactobacillus plantarum CGMCC No. 27202) and enzymes. We conducted a trial with twenty-four cattle, randomly divided into two groups of twelve cattle each. The control group (CON) was fed the standard farm diet, whereas the treatment group (PKC) received a diet with 3% of soyabean replaced by fermented palm kernel cake. The trial lasted for six weeks. The results showed no significant differences in growth performance between the PKC and CON groups. The abundance of Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes was significantly higher in the PKC group than in the CON group. At the genus level, the abundances of Anaeroplasma, norank_f__Bacteroidales_UCG-001, norank_f__Absconditabacteriales_SR1, norank_f__p-251-o5, Prevotellaceae_NK3B31_group, Prevotellaceae_UCG-001, Prevotellaceae_UCG-004, and Treponema significantly increased in the PKC group. Lipid digestion and absorption pathways were significantly enriched in the PKC group. The results indicate that adding fermented palm kernel cake to the diet can increase the abundance of Bacteroidetes and Fibrobacteres in the rumen of beef cattle, enhancing the ability of the PKC group to degrade protein, carbohydrates, and fibrous materials in the feed, thereby improving the feed utilisation efficiency in beef cattle. Adding fermented palm kernel cake to the diet improved carbohydrate metabolism, metabolism of cofactors and vitamins, and nucleotide metabolism. Correlation analysis between the rumen microbiota and metabolic pathways showed that Prevotellaceae_UCG-001 and Prevotellaceae_UCG-003 were positively correlated with amino acid metabolism, Rikenellaceae_RC9_gut_group and Succiniclasticum were positively correlated with metabolism of cofactors and vitamins, and Prevotella and Ruminococcus were positively correlated with nucleotide metabolism. These findings elucidate the differences in rumen microbiota when fermented palm kernel cake is added to the diet, providing a theoretical basis for the application of fermented palm kernel cake in the diet of beef cattle.

Gender and age-related variations in rumen fermentation and microbiota of Qinchuan cattle.

Our study aimed to investigate the gender and age-related variations in rumen fermentation, serum metabolites, and microbiota in Qinchuan cattle. A total of 38 Qinchuan beef cattle were selected and maintained on a uniform diet for three months. Rumen fluid and blood samples were collected to determine rumen fermentation, serum metabolites, and microbial 16S rRNA sequencing. The results revealed that the concentration of rumen butyrate in female Qinchuan cattle was significantly higher than in males (P<0.05). Isobutyrate, butyrate, and isovalerate exhibited significant age-related differences. Females exhibited lower serum GLU and higher TG, NEFA levels compared to males (P<0.05). Serum ALB and UREA levels increased with age (P<0.05). Furthermore, the alpha diversity of rumen bacteria improved with age (P<0.05), with no gender differences observed. Males had higher relative abundances of Bacteroidota, Verrucomicrobiota, and Cyanobacteria, while females had higher Firmicutes and Desulfobacterota (P<0.05). The cellulose-degrading genus Ruminococcus and propionate-producing genus Succiniclasticum were more abundant in females, whereas the anti-inflammatory genus Lachnospiraceae_NK4A136_group and the hemicellulose-degrading genus Prevotella were more abundant in males (P<0.05). Age-related differences in bacteria were found in Pseudobutyrivibrio and several members of the Lachnospiraceae. Functional prediction indicated that "Amino acid metabolism" and "Lipid metabolism" were mainly enriched in females, whereas "Carbohydrate metabolism" and "Glycan biosynthesis and metabolism" were enriched in males (P<0.05). RDA analysis highlighted butyrate as a key factor influencing the rumen bacterial community. NK4A214_group and Ruminococcus were positively correlated with butyrate, while Prevotella and Pseudobutyrivibrio were negatively correlated with butyrate (P<0.05). We observed a significant improvement in the diversity and stability of rumen microbiota as age increased. Ruminococcus, NK4A214_group, and Prevotella were likely contributors to variations in energy utilization and fat deposition between male and female Qinchuan cattle.

Effects of Formaldehyde-Treated Feed on Rumen Metabolism and Blood Biochemistry in Lambs: A Review

This review evaluates the impact of formaldehyde treatment on feed for lambs, focusing on its effects on rumen metabolism and blood biochemical indicators. Formaldehyde is commonly used as a feed additive to improve nutritional efficiency and preserve feed quality. This review synthesizes data from various studies to assess how formaldehyde-treated feed influences rumen fermentation parameters, including volatile fatty acid (VFA) production, rumen pH, and microbial activity. Additionally, the review examines the effects of formaldehyde treatment on key blood biochemical markers such as glucose, urea nitrogen, and liver enzymes. Studies indicate that formaldehyde treatment can enhance the stability and digestibility of feed, potentially improving nutrient utilization and overall animal performance. The preservation of protein and reduction in feed spoilage are highlighted as significant benefits, contributing to more consistent rumen function and metabolic efficiency. However, the impact on rumen microbial populations and VFA profiles shows mixed results, with some studies reporting improved microbial efficiency and others noting minimal changes. The review also discusses potential adverse effects, including alterations in blood biochemical parameters. While formaldehyde treatment generally maintains or improves key indicators like blood glucose and protein levels, excessive use may lead to concerns such as elevated urea nitrogen levels and potential liver enzyme disruptions, the review concludes that formaldehyde-treated feed can be a valuable tool in optimizing feed efficiency and lamb health, provided it is used judiciously. Future research is recommended to further elucidate the long-term effects on rumen microbiota and metabolic processes, ensuring balanced benefits without compromising animal welfare.

Effects of spent substrate of oyster mushroom (Pleurotus ostreatus) on ruminal fermentation, microbial community and growth performance in Hu sheep.

The study aimed to evaluate the effects of Pleurotus Spent Mushroom Substrate (P.SMS) on the rumen microbiota, encompassing bacteria and fungi, as well as their interactions in Hu sheep. A total of forty-five 3-month-old Hu sheep were randomly assigned to five groups. Each group was fed diets in which whole-plant corn silage (WPCS) was substituted with P.SMS at varying levels: 0% (CON), 5% (PSMS5), 10% (PSMS10), 15% (PSMS15), or 20% (PSMS20). The results indicated that higher proportions of P.SMS during the experimental period might have a detrimental effect on feed utilization efficiency, kidney function, and blood oxygen-carrying capacity. Notably, moderate levels of P.SMS, specifically below 15%, were associated with improvements in rumen NH3-N levels and absorption capacity. The results indicated that (1) PSMS20 exhibited a significantly higher feed-to-gain ratio compared to CON (P < 0.05); (2) PSMS15 showed a significantly higher NH3-N content than CON, PSMS5, and PSMS20. Additionally, PSMS10 and PSMS20 had elevated concentrations of NH3-N compared to CON and PSMS5 (P < 0.05); (3) The length and width of rumen papillae were significantly greater in PSMS20 compared to CON and PSMS5 (P < 0.05); (4) Creatinine levels were significantly higher in PSMS20 than in CON, PSMS5, and PSMS10 (P < 0.05); (5) By the conclusion of the experiment, hemoglobin concentration in PSMS20 showed a significant increase compared to CON (P < 0.05). Furthermore, the addition of P.SMS influenced microorganisms at both the phylum and genus levels: (1) At the phylum level, the prevalence of Patescibacteria was significantly lower in PSMS20 compared to the other groups; (2) PSMS15 exhibited significantly higher relative abundances of Basidiomycota compared to CON and PSMS10, while PSMS20 also demonstrated significantly higher relative abundances compared to CON (P < 0.05); (3) At the genus level, the prevalence of Candidatus_Saccharimonas in PSMS20 was significantly lower than in PSMS5, PSMS10, and PSMS15. Conversely, the prevalence of Phanerochaete in PSMS15 was notably higher than in CON and PSMS10, and it was also significantly elevated in PSMS20 compared to CON (P < 0.05); (4) Correlation analysis indicated no significant correlation between changes in the structure of bacterial and fungal communities. Considering these findings, a high percentage of P.SMS negatively impacted feed utilization efficiency, blood oxygen carrying capacity, and kidney function, while a moderate percentage of P.SMS promotes rumen absorption capacity, indicating that feeding 10% P.SMS is optimal.

Comparative study on slaughter performance, meat quality, and rumen microbiota of Hainan Dong goat and its hybrid with Nubian goat.

The Hainan Dong goat (DG) is a local meat breed widely raised in Hainan, China because of its good adaptability to local hot and humid weather. However, the growth rate of these DG is much slower than that of commercialised breeds improved in European countries, resulting in poor carcase characteristics, including smaller slaughter weight and carcase weight, which have become increasingly prominent. In recent decades, Nubian goats have been continuously imported into China to improve the production performance of local breeds. In this study, the effects of breed on growth performance, carcase and meat quality, and ruminal microbiota were analysed in 40 goats, including 20 DGs and 20 hybrid F3 offspring generated by crossing the DG and Nubian hybrids (NH). All the goats were averagely aged 90 days and weighed at 11 ± 1.34 kg. They were assigned to two treatments, with three replicates per treatment. The two groups were fed the same diet for 90 days before slaughter. The results showed that the average daily gain, F/G ratio, slaughter weight, and carcase weight of the NH group were higher than those of the DG group (p < 0.05). However, tube circumference, meat-to-bone ratio, and eye muscle pH were lower in the NH group than in the DG group (p < 0.05). The NH group showed a smaller fibre crosssectional area and fibre diameter, but a larger fibre density than the DG group (p < 0.05). Bacteroidetes and Firmicutes were the most dominant phyla in the two groups; however, the two breeds had different ruminal microbial communities. In the present study, the differences in growth performance between two groups of goats under the same feeding environment and feed conditions were compared. The correlation between feed sources and rumen flora has been demonstrated, and the results of this study show that the same diet has similar effects on rumen microorganisms, which in turn have related effects on growth and production performance. In summary, hybrids can improve the growth and slaughter performance of local breeds, which may be related to changes in the rumen microorganisms. This study revealed that crossbreeding of Nubian goats with Dong goats has the potential to be used in a wide range of applications owing to its effectiveness in increasing production efficiency.

Different sources of alfalfa hay alter the composition of rumen microbiota in mid-lactation Holstein cows without affecting production performance.

Alfalfa hay is a commonly used and important feed ingredient in dairy production. To better expand the alfalfa supply market, it is of great significance to explore the impact of alfalfa hay from different sources on dairy cow production performance. This study compared the effects of imported alfalfa hay from America (AAH) and Spain (SAH) on lactation performance and rumen microbiota of cows. Three hundred and sixty healthy mid-lactation Holstein cows with similar body weight, milk yield, and parity were randomly divided into two groups fed diets based on AAH or SAH for a 70-day experimental period. Each group was composed of four pens, with 45 cows in each pen. Daily records were kept for MY per cow and dry matter intake per pen. Twelve randomly selected cows per group were sampled to collect milk, feces, rumen fluid, and blood. The findings revealed no significant differences between the two groups in terms of production performance, nutrient apparent digestibility, serum biochemical indices, or rumen fermentation parameters. However, rumen microbial composition differed significantly between the two groups of cows based on β-diversity. On the genus level, the relative abundance of Prevotella, Succinivibrionaceae_UCG-002 increased while that of NK4A214_group, Ruminococcus, norank_f_F082 and Lachnospiraceae_NK3A20_group decreased in the SAH group compared with AAH group. There was no significant correlation between these core differential bacteria and the molar proportions of acetate and propionate, the concentration of total volatile fatty acids, and milk yield. In conclusion, the feeding effects of SAH were similar to those of AAH. These findings provided a reference for the application of alfalfa hay from different sources and for the improvement of the economic benefit of dairy farms.