Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep

BACKGROUND

Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.

RESULTS

The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.

CONCLUSIONS

In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.

High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance

BACKGROUND

Compelling evidence has established a strong link between the gut microbiota and host reproductive health. However, the specific regulatory roles of individual bacterial species on reproductive performance are not well-understood. In the present study, Jinhua sows with varying reproductive performances under the same diet and management conditions were selected to explore potential mechanisms on the intricate relationship between the gut microbiome and host reproductive performance using 16S rRNA sequencing, metagenomics and serum metabolomics.

RESULTS

Our findings revealed that the KEGG pathways for base excision repair and DNA replication were enriched, along with gene-level enhancements in spore formation, in sows with higher reproductive performance, indicating that the gut microbiome experiences stress. Further analysis showed a positive correlation between these changes and litter size, indicating that the host acts as a stressor, reshaping the microbiome. This adaptation allows the intestinal microbes in sows with high reproductive performance to enrich specific serotonin-related bacteria, such as Oxalobacter formigenes, Ruminococcus sp. CAG 382, Clostridium leptum, and Clostridium botulinum. Subsequently, the enriched microbiota may promote host serotonin production, which is positively correlated with reproductive performance in our study, known to regulate follicle survival and oocyte maturation.

CONCLUSION

Our study provides a theoretical basis for understanding the interactions between gut microbes and the host. It highlights new insights into reassembling gut microbiota in sows with higher litter sizes and the role of serotonin-related microbiota and serotonin in fertility.

Ruminal microbiome-host metabolome crosstalk in the synthesis of unsaturated fatty acids in buffalo milk

Interactions between rumen microorganisms and their metabolites contribute to milk yield and milk fat content in dairy cows. However, whether rumen microbes and host metabolism affect fatty acid synthesis in milk is unknown. In this study, we investigated the potential regulatory mechanisms affecting the unsaturated fatty acid content of Binglangjiang buffalo by using macrogenomics and metabolomics. Macrogenomic analysis showed that Bacteroides was significantly more abundant in the high UFA group (HF), contributing to the improvement of functions related to fatty acid synthesis. Then, we found that the rumen microbiota of the HF group was enriched in 2 important pathways involved in lipid metabolism (i.e., fatty acid biosynthesis and fatty acid metabolism), suggesting that more fatty acids were synthesized in the HF group. Metabolomics analyses showed that most of the UFA were more abundant in the HF group, which was also confirmed by the quantification of related metabolic pathways in milk fatty acids, suggesting that the HF group has a higher capacity to synthesize MUFA and PUFA. Correlation analysis of rumen lipid metabolic pathways and metabolites revealed that metabolic pathways such as fatty acid biosynthesis, fatty acid metabolism, metabolic pathways, and peroxisome proliferator-activated receptor (PPAR) signaling pathway, which were significantly enriched in the HF group compared with the low UFA group, were significantly and positively correlated with multiple UFA . The synthesis of UFA is mainly influenced by Bacteroides, Prevotella, and Bacteroidaceae, and regulated by fatty acid biosynthesis, fatty acid metabolism, and PPAR signaling pathways, which together influence the synthesis of UFA in buffaloes.

Graduate Student Literature Review: Concepts and challenges of amino acid supply and nitrogen metabolism in dairy cattle

Nitrogen utilization in dairy cows is crucial for maximizing production efficiency and minimizing environmental impacts. Ruminants possess a unique digestive system filled with microorganisms that work synergically to degrade feed particles and provide nutrients for both the microorganism and host metabolism. Dietary N, supplied as true protein and NPN, undergoes different degradation processes: a portion is degraded in the rumen, and another portion escapes ruminal degradation (i.e., RUP). Rumen-degraded protein is essential for microbial growth, contributing to the formation of microbial CP (MCP). Amino acids present in MCP and RUP that are digested and absorbed into the bloodstream and become available for animal metabolism (e.g., maintenance, growth, and production) constitute MP. Accurately assessing protein degradability and AA availability remains a challenge due to the limitations of current evaluation methods. In situ techniques are the most commonly used technique for this purpose, but they are not meant to predict MCP, RUP, and consequently the metabolizable AA supply of feed ingredients, which compromises diet formulation. Microbial CP growth is enhanced when both fermentable energy and N is available in the rumen. However, the extent of N recycling in sustaining microbial growth under low-protein diets is not adequately captured by MCP prediction models. Due to these limitations, several biases are added to protein models, resulting in protein overfeeding in an attempt to supply MP requirements and increasing both costs and N overload to the environment. Therefore, this review aims to synthesize fundamental information on the complex interplay of factors influencing ruminal protein degradation, MCP synthesis, AA supply, N metabolism, and N efficiency, and highlight the knowledge gaps that must be addressed to improve the accuracy of prediction models of AA supply in dairy cattle.

Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights

Fledgling broiler ducks vary in body weight and growth rate. The aim of this study was to investigate the relationship between serum metabolites and the intestinal microbiota in Cherry Valley broiler ducks with different finishing weights and to reveal differences in their metabolic regulation and microbial composition. Serum and cecum content samples were collected from Cherry Valley broiler ducks of different finishing weights. Metabolites were identified and compared using untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics and bioinformatics. Six key findings emerged. First, serum biochemical parameters showed that AST and ALT levels were significantly lower in the high weight group (Group H) than in the low weight group (Group L), and serum immunoglobulin IgG levels were significantly higher in group H. Second, the chorionic height to crypt depth ratio of the duodenum was significantly higher in group H than in group L. Third, the gut microbial community diversity or abundance was lower in broiler ducks in group L. Fourth, LEfSe analysis showed that the biomarker for group L was Streptococcus, whereas for group H it was Faecalibacterium. Fifth, a total of 127 differential metabolites were identified (49 up-regulated and 78 down-regulated). Finally, Spearman's correlation analysis showed that Spearman's correlation analyses showed that the Lipid-related serum metabolites were higher in low-body recombinant broiler ducks, mainly Lathosterol, Cholesterol, Cynaratriol and Leukotriene B4. In addition to lipid-associated serum metabolites in high-body recombination, The water-soluble vitamin-like metabolite Pantothenate and the antibiotic-like metabolite Tylosin were high. The cecum microbiota is strongly associated with metabolites, especially Faecalibacterium, unclassified Tannerellaceae, Subdoligranulum, Alistipes, and [Ruminococcus] torques_group, with which it exhibits strong Correlation. Broiler ducks with higher body weights have a better intestinal villous structure, enhanced digestion and absorption, higher levels of immunoglobulin secretion and superior growth performance. Broiler ducks with different body weights differed in plasma metabolites and cecum flora. Spearman's correlation analyses showed that the Correlation between differential metabolites and differential gut microbial genera.

Enhancing Holstein steers growth performance: oregano essential oil's impact on rumen development, functionality and microorganism

BACKGROUND

Dietary supplementation with oregano essential oil (OEO), a natural plant extracts, is an effective and acceptable method to improve growth, beef quantity and quality, but the undergoing mechanism in rumen has not yet been reported in Holstein steers. This study investigated the effects of oregano essential oil (OEO) on growth performance, fermentation parameters, digestive enzymes activity, rumen development and microbiota in Holstein steers. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CCK) or the same diet supplemented with 20 g/(d·head) OEO (CEO) for 270 days.

RESULTS

OEO increased the rumen contents of volatile fatty acids (VFA, acetate (P = 0.011), propionate (P = 0.008), butyrate (P = 0.018)) and digestive enzymes activity (cellulase (P = 0.018), protease and β-glucosidase (P < 0.001)), and improved rumen development (papillae width (P = 0.008) and micropapillary density (P = 0.001)), which reasons contribute to increase body weight (BW, P = 0.022), average daily gain (ADG, P = 0.021), carcass weight (P = 0.001), dressing percentage (P < 0.001), and net meat production (P = 0.001) of steers. Meanwhile, metagenomic and metabolomic analysis revealed OEO significantly reduced abundance of rumen microorganisms, especially methanogenic archaea and viruses while beneficial bacteria (Bifidobacterium) and virulence factors were not affected. KEGG analysis revealed that OEO significantly reduces the host risk of disease, improves the digestive system, and reduces the energy basic metabolism level. A correlation analysis indicated fourteen kinds key microbiome and six downregulated metabolites interfere with each other and together influence the growth performance of steers.

CONCLUSION

These results suggest that feed with 20 g/(d·head) OEO in steers diets could improve growth performance, and reduces virus abundance and disease risk. And the findings provide fundamental insights into OEO, as an alternative source of natural bioactive compounds, how effect on rumen development, composition and function of microorganisms.

Integrated multi-omics to elucidate the interplay between rumen microorganisms and host metabolism in Hu sheep supplemented with herbal preparations

The aim of this experiment was to study the effects of herbal preparations on serum metabolites, rumen microorganisms, and their metabolites, and the relationship between them. Hu sheep ram lambs with an average initial weight of (19.57 ± 1.56 kg) at 3 months of age were selected and randomly divided into three groups of six lambs each. The groups were as follows: the control group (Con), which was fed the basic diet; Test I, which was fed a diet with 0.5% herbal preparations added to the concentrate; and Test II, which was fed a diet with 1% herbal preparations added to the concentrate. Also, the main component of herbal medicine is polysaccharide. The pre-experimental period was 10 days and the experimental period was 90 days. The results of the study showed that the addition of herbal preparations resulted in differences in species, abundance, and metabolic functions of rumen microorganisms. The abundance of rumen-dominant bacteria, such as Firmicutes and Proteobacteria, increased after the addition of herbal preparation, which was more conducive to rumen development. In addition, after the addition of 0.5% herbal preparation, there was an increase in the abundance of fermenting carbohydrate (CHO) and fiber-degrading bacteria (e.g., Ruminococcus and Prevotella). Herbal preparations significantly altered rumen microorganisms and serum metabolite compositions. Metabolites such as bile acids, L-glutamine, cytosine, and choline, which contribute to the antiviral and anti-inflammatory effects, nutrient metabolism, and immune responses, and increased rumen microbial activity, were increased in the rumen of the experimental group with the addition of the herbal preparations. The increase in serum metabolites, such as L-tryptophan, and the pathways of tryptophan metabolism and glutathione metabolism in animals were also significantly higher than those in Con. Prevotella and Ruminococcus were significantly positively correlated with histamine and L-arginine. The uncultured_rumen_bacterium was significantly negatively correlated with serum metabolites testosterone and guanine, but Prevotella and Ruminococcus were significantly positively correlated with both metabolite testosterone and guanine.

IMPORTANCE

In this study, we investigated the changes in rumen microbes after supplementation with herbal preparations. We used 16S sequencing and metabolomics approaches to explore changes in rumen contents and serum metabolites and their interrelationships. Our findings revealed marked changes in rumen microbial profiles, including changes in species composition, abundance levels, and metabolic activities induced by herbal supplementation. The increased abundance of beneficial bacteria (e.g., fixative and proteobacteria) in the rumen was more favorable for their survival and colonization of the rumen. In addition, a surge in the abundance of fermenting carbohydrate and fiber-degrading bacteria was observed. It was also found that the addition of herbal preparations enhanced antiviral and anti-inflammatory responses, nutrient metabolism, immune function, and stimulation of rumen microbial activity as well as facilitated the acceleration of body metabolism in Hu sheep.

Associations of rumen and rectum bacteria with the sustained productive performance of dairy cows

The gut bacterial community is essential for maintaining lifelong health and productivity in ruminants, but the relationship between the gut microbiota and the sustained productivity of ruminants remains inadequately understood. In this study, we selected long-lived dairy cows in mid-lactation (≥5 parities) with different levels of milk production (n = 10). Significant differences were observed in the rumen bacterial structures between the two groups of dairy cows, whereas no significant differences were detected in the rectum bacterial communities. Additionally, there were no significant differences in serum oxidative stress biomarkers, inflammatory markers, or immunological markers between the long-lived high-yield (LH) and long-lived low-yield (LL) dairy cows. Furthermore, the concentrations of propionate (Pr) in the rumen and butyrate (Bu) in the rectum were elevated in the high-yield group. Spearman correlation and microbial co-occurrence network analyses revealed that several rumen-enriched bacteria, such as Syntrophococcus, Lachnospira, Shuttleworthia, Erysipelotrichaceae_UCG-2, and Roseburiaare associated with rumen propionate (Pr) production. In the rectum, the reduced abundance of Christensenellaceae_R-7_group and Moryella favors butyrate production. Furthermore, Random Forest machine learning analysis demonstrated that six bacterial taxa in the rumen combined with one serum biomarker, as well as three bacterial taxa in the rectum combined with three serum biomarkers, can serve as potential biomarkers for distinguishing between LH and long- LL dairy cows, achieving prediction accuracies of 92 and 99%, respectively. The findings of this study indicate that rumen and rectum bacteria are associated with the milk production phenotypes of dairy cows with sustained productivity. The rumen microbes are closely linked to the long-term productive capacity of dairy cows and represent a key target for the development of gut microbiota-based interventions. The unique bacterial communities of the rumen and rectum of long-lived high-yielding dairy cows contribute to maintaining their productive capacity.

A genome-wide association study on rumination time in first-lactation dairy cattle

Rumination time (RT) in dairy cattle is a crucial indicator of health, production, reproduction, and greenhouse gas emissions. With moderate heritability estimates for RT, there is potential for further analyses regarding the genetic architecture of the trait. To identify genomic regions associated with RT, we conducted a GWAS on SNPs in a cohort of 452 mid-first-lactation Canadian Holstein cows, followed by the annotation of genes and enrichment analyses of quantitative trait loci (QTL). Animals were genotyped using a medium-density SNP panel (50 K). Quality control measures were used to remove markers residing on nonautosomal chromosomes or with minor allele frequencies <5%, and SNP or animals with call rates lower than 90%. The SNP effects were estimated using single-step genomic BLUP. Significant markers were identified using a chromosome-wise modified Bonferroni correction, based on the expected number of independent chromosome segments. We identified 35 SNPs significantly associated with RT, mapping 34 genes within a 50-kbp interval up and downstream from these SNPs. Additionally, 19 QTL were found enriched in these genomic regions. Notably, genes such as ATP2B4, LDB3,WARS2, and PTPRO were identified, suggesting potential links to muscle fiber activity and milk solids percentage. The enriched QTL were associated with traits related to fat and protein synthesis and deposition in both milk and muscle tissues. Gene Ontology analysis highlighted terms related to muscle contraction and neuronal communication, consistent with the physiological processes underlying RT. Our findings offer new insights into the genetic architecture of RT, advancing the understanding of the physiological mechanisms governing this complex trait.

Dietary L-leucine supplementation improves ruminal fermentation parameters and epithelium development in fattening Angus beef cattle

BACKGROUND

In this study, the effects of L-leucine (Leu) on rumen fermentation parameters, rumen epithelium development, amino acid composition, rumen bacterial communities and rumen metabolites in beef cattle were investigated. Twenty-four fattening Angus females of similar initial weight (575.5 ± 22.1 kg) were randomly assigned to 2 treatments with 4 replicate pens (3 cattle per pen). They were fed either a basal diet or a basal diet supplemented with 6.0 g L-Leu/100 kg BW/d for 120 d.

RESULTS

(1) Leu increased the ruminal concentrations of total volatile fatty acid (VFA) (P = 0.017), propionate (P = 0.023), isovalerate (P = 0.001), and branched-chain volatile fatty acid (BCVFA) (P = 0.01) at 4 h post-feeding. It also tended to increase acetate (P = 0.083) and decrease the ammonia-N (NH3-N) concentration (P = 0.055), but it did not affect ruminal pH (P > 0.1). Leu also increased microbial crude protein (MCP) (P = 0.026) at 4 h post-feeding, but decreased MCP at 8 h post-feeding (P = 0.010). (2) Supplementation with L-Leu increased the ruminal concentrations of phenylalanine (P = 0.011), lysine (P = 0.034), and tyrosine (P = 0.033), while decreasing the cystine concentration (P = 0.010). (3) Leu increased the thickness of the stratum spinosum and basal (P < 0.05), while decreasing the thickness of the stratum granulosum (P < 0.05). (4) Leu upregulated the relative mRNA abundance of genes involved in tight junction proteins (P < 0.05) and VFA absorption and metabolism (P < 0.01) in the rumen epithelium. This upregulation was positively correlated with the concentrations ruminal isovalerate and BCVFA (P < 0.01). (5) L-Leu did not affect the diversity and richness of ruminal microbes (P > 0.05), but differential bacterial biomarkers (LEfSe, LDA > 2) were either positively or negatively correlated with ruminal MCP, NH3-N, and BCVFA concentrations (P < 0.001). Additionally, differential bacterial metabolites (OPLS-DA, VIP > 1.5) were primarily enriched in the amino acid metabolism pathway and the cofactors and vitamins metabolism pathway (P < 0.05).

CONCLUSIONS

Dietary supplementation with L-Leu altered rumen fermentation parameters and patterns, improved rumen epithelial morphology, and enhanced the expression of genes related to VFA absorption and metabolism in the rumen epithelium of beef cattle.

Rumen microbes affect the somatic cell counts of dairy cows by modulating glutathione metabolism

Healthy mammary glands are essential for high-quality milk production in the dairy industry. The relationship between somatic cell counts (SCCs), rumen fermentation, and microbiota interactions remains unclear. This study integrated physiological indicators, high-throughput 16S rRNA gene sequencing, and metagenomics data analysis to investigate the mechanisms linking rumen microbes and mastitis and to evaluate the changes in milk production and serum cytokine levels in cows with low (L-SCC) and high (H-SCC) somatic cell counts. Compared with the L-SCC group, the H-SCC group exhibited significantly lower lactose and fat contents in milk, reduced rumen fermentation product levels, and increased abundances of Bacteroidetes, Firmicutes, Lachnospiraceae, Prevotella, and Rumiclostridium. Elevated serum levels of IgG2, IgM, IL-1β, IL-6, and TNF-ɑ in the H-SCC group indicated inflammation and rumen microbiota dysbiosis. Functional analysis of microbial communities revealed significant enrichment in pathways related to glutathione metabolism, thyroid hormone synthesis, hypertrophic cardiomyopathy (HCM), the phosphotransferase system (PTS), the P53 signaling pathway, and the Jak-STAT signaling pathway. Correlation network analysis showed that changes in bacterial families, such as Rikenellaceae, Muribaculaceae, and Prevotellaceae, were associated with cytokines, rumen fermentation, and milk quality. The study highlights the interaction between rumen microbiota homeostasis and mammary gland health, indicating that rumen fermentation status influences serum inflammation and milk quality. Modulating rumen fermentation to enhance mammary gland immune function presents a viable strategy for sustainable dairy industry development with long-lived, highly productive cows.IMPORTANCEHigh somatic cell counts (SCCs) are a key biomarker of mastitis and are associated with decreased milk production and significant economic losses in dairy farming. This study systematically examines the relationship between elevated SCCs, rumen microbial dysbiosis, and host inflammatory responses, shedding light on the intricate interplay between microbial ecosystems and host physiology. The findings highlight the potential for microbiota-targeted interventions to reduce inflammation, improve milk composition, and enhance dairy cow productivity. Rather than presuming a direct causative link between SCC-associated dysbiosis and inflammation, this research focuses on their interdependent dynamics, offering a nuanced understanding of the complex biological mechanisms involved. This work advances knowledge of host-microbiota interactions in livestock, providing practical insights for the development of innovative strategies to manage mastitis and improve overall herd health. By adhering to One Health principles, this study underscores the significance of sustainable agricultural practices that prioritize animal welfare, environmental stewardship, and food security. These findings establish a robust foundation for future research into microbiota-driven solutions aimed at enhancing the health and productivity of dairy cattle.

Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics

BACKGROUND

This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS

A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS

Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER

Not applicable.

Associations among body condition score, body weight, and serum biochemistry in dairy cows

Body condition score and BW yield insights into body tissue reserves and diet, and serum biochemical measures reflect the metabolic status of cows. Associations between body composition measures and biochemistry are unclear and investigation may reveal important information on the metabolic and physiological status of cattle with varying levels of labile tissue reserves. Cohorts of 739 nonlactating, late-pregnancy, dry cows (26.9 d prepartum, SD = 12.4) and 690 peak-milk cows (58.0 DIM, SD = 14.5) were selected by stratified (parity: 1, 2, 3, >3) random sampling from 30 farms (15 pasture, 15 TMR) in this cross-sectional study. A single serum, BCS (1-5 scale), BW, and milk-production datum was collected per cow, per cohort between November 2022 and July 2023. Eleven analytes were collected, analyzed, and standardized within group (cohort/breed per farm). Mixed linear models for BCS and BW were specified, with the random effect of group. A 6-point, unordered, categorical body-group classification that combined BCS (greater, equal to, or less than group median; as high, median, or low BCS) and BW (greater or less than group median; as high or low BW) was analyzed by polytomous logistic regression. Effect sizes are listed for a 1 SD increase in the specified analyte, keeping other covariables at their mean value. Dry BCS was positively associated with albumin (0.075 BCS ± 0.014 SE), urea (0.038 BCS ± 0.014 SE), and glucose (0.052 BCS ± 0.014 SE), and negatively with the interaction between cholesterol and days precalving. Dry BW positively associated with albumin (11.03 kg ± 2.48 SE) and negatively with cholesterol (-8.47 kg ± 2.57 SE). Peak-milk BCS was positively associated with albumin (0.47 BCS ± 0.015 SE), BHB (0.048 BCS ± 0.015 SE), and glucose (0.051 BCS ± 0.015 SE). Peak-milk BW was positively associated with albumin (6.94 kg ± 2.35 SE) and negatively with Ca (-7.02 kg ± 2.33 SE). Increasing BW and decreasing BCS was associated with increasing parity, except in dry second-parity cows that had low BCS. The dry polytomous model associated a 1 SD increase in albumin with a 4.89% ± 1.56 SE decreased risk of being low BCS/low BW and 5.87% ± 1.46 SE increased risk of high BCS/high BW. Risk change associated with 1 SD of glucose was -5.61% ± 1.58 SE for low BCS/high BW and 3.17% ± 1.58 SE for high BCS/high BW. For the peak-milk cohort, change in risk was associated with albumin for low BCS/low BW -3.67% ± 1.56 SE, low BCS/high BW -3.22% ± 1.53 SE. Risk change with 1 SD of BHB was -3.36% ± 1.47 SE for median BCS/low BW, 2.86% ± 1.44 SE for high BCS/low BW, and 2.69% ± 1.37 SE for high BCS/high BW. Risk of low BCS/low BW was greatest in second-parity cows, and high BCS/high BW was greatest in dry cows with greater than third parity and third-parity cows in peak milk. There were no interactions between parity and analytes. Albumin was consistently associated with BCS and BW, potentially reflecting innate differences in protein metabolism of cows.

Effects of glycyrrhetinic acid on production performance, serum biochemical indexes, ruminal parameters, and rumen microflora of beef cattle

This research was carried out to assess the impact of supplementing with glycyrrhetinic acid (GA) on production performance, serum biochemical indexes, ruminal parameters, and rumen bacterial flora of beef cattle. Twenty-four Simmental bulls were randomly assigned to two dietary treatments (n = 12 per treatment): the control treatment (basal ration, CON) and the GA treatment (basal ration supplemented with GA at 0.1% DM). After an 87-day feeding trial (7-day adaptation period and 80-day period dedicated to data and sample collection), feces, blood, and rumen fluid samples were collected on day 87. The GA addition significantly increased the average daily gain of beef cattle (p < 0.05). The GA treatment exhibited significantly greater apparent digestibility of crude protein, neutral detergent fiber, and acid detergent fiber than the control treatment (p < 0.05). Total volatile fatty acid concentration, microbial protein concentration, and propionic acid concentration in the rumen fluid were significantly increased by GA addition (p < 0.05). Compared with the control group, the interleukin-4 concentration was significantly higher in GA treatment (p < 0.05). The indices, including operational taxonomic units (OTUs), Sobs, Shannon, Ace, and Chao1, were found to be greater in the GA treatment. At the phyla level, GA addition (p < 0.05) significantly decreased the relative abundance of Bacteroidetes and increased the relative abundance of Firmicutes, while also significantly decreasing the Bacteroidetes:Firmicutes ratios. At the genera level, the relative abundance of Prevotella, NK4A214_group, norank_f_UCG-011, Prevotellaceae_UCG-003, Christensenellaceae_R-7_treatment, Prevotellaceae_UCG-001, norank_f_Bacteroidales_UCG-001, Pseudobutyrivibrio, and Butyrivibrio significantly differed due to GA addition (p < 0.05). Carbohydrate and amino acid transport and metabolism, as well as energy production and conversion, were significantly enriched in the GA treatment (p < 0.05). In summary, the findings indicated that adding glycyrrhetinic acid to the diet could improve growth performance and modify the rumen microbial composition and diversity of beef cattle.

The rumen microbiome and its metabolome together with the host metabolome regulate the growth performance of crossbred cattle

BACKGROUND

Although it has been demonstrated that gastrointestinal microorganisms greatly influence livestock performance, the effect of gastrointestinal microorganisms on the growth performance of crossbred cattle remains unclear. Due to their superior production characteristics, understanding the impact of gastrointestinal microorganisms on the growth performance of crossbred beef cattle is of significant importance for improving farming efficiency.

RESULT

In this study, healthy Simmental with similar birth date and weight were selected as dams, Simmental (Combination I), Belgian Blue (Combination II) and Red Angus (Combination III) were used as parents for crossbreeding. The progeny of the three combination crosses were measured for growth performance under identical conditions from birth rearing to 18 months of age (n = 30). Rumen fluid and plasma were collected for macro-genomic and non-targeted metabolomic analysis (n = 8). The results showed that Combination II was superior to Combination I and Combination III in body weight (BW) and body height (BH) (P < 0.05). Mycoplasma, Succinivibrio, Anaerostipes, Methanosphaera, Aspergillus, and Acidomyces were significantly increased in the rumen of Combination II (P < 0.05), whereas differentially expressed metabolites (DEMs) 9,10,13-Trihome (11), 9,12,13-Trihome and 9(10)-Epome, and 9(S)-Hpode were reduced in abundance. In addition, plasma DEM PC (14:0/P-18:1(11Z)), PC (16:0/0:0), and PC (17:0/0:0) were down-regulated in combination II. Correlation analysis revealed that Anaerostipes, Methanosphaera, and Succinivibrio were associated with PC (14:0/P-18:1(11Z)), 9(10)-Epome, 9,10,13-Trihome (11), 9(S)-Hpode, 9,10,13-Trihome, PC (17:0/0:0), and PC (16:0/0:0). Growth traits were significantly positively correlated with the three dominant genera, Anaerostipes, Methanosphaera, and Succinivibrio, while significantly negatively correlated with key rumen metabolites and plasma metabolites (P < 0.05).

CONCLUSIONS

Our study reveals the role of rumen microorganisms and its metabolites with host metabolism in the regulation of growth performance of crossbred cattle, which will contribute to the development of modern cattle breeding.

Under heat stress conditions, selenium nanoparticles promote lactation through modulation of rumen microbiota and metabolic processes in dairy goats

This study aimed to investigate the effects of dietary supplementation with Selenium nanoparticles (SeNPs) on lactation performance, rumen microbial communities, and metabolism in dairy goats under heat stress conditions. Twenty Guanzhong dairy goats with the same parity, similar lactation period (120 ± 15 days), and similar milk yield (1.20 ± 0.16 kg/day) were randomly divided into two groups, with 10 replicates in each group. The control group was fed a standard diet, while the experimental group was supplemented with 0.5 mg SeNPs/kg DM based on the standard diet. The pretrial period lasted for seven days, followed by a 30-day trial period. The results showed that dietary supplementation with SeNPs significantly increased milk yield, milk fat and lactose content in dairy goats, under heat stress conditions. SeNPs significantly altered the composition of the rumen microbiota, increasing the relative abundance of Prevotella and Ruminococcus while decreasing the relative abundance of Succiniclasticum. This enhanced the rumen's ability to degrade starch and fiber under heat stress conditions. Non-targeted metabolomic analysis revealed a total of 119 differential metabolites between the two groups, indicating changes in rumen metabolism. Further correlation analysis indicated that Rumen bacterium R-21 was positively correlated with propionate, while Ralstonia insidiosa was negatively correlated with γ-glutamylcysteine. Additionally, several differential microbes, including Succinivibrio dextrinosolvens, Rummeliibacillus pycnus, Ralstonia insidiosa, and Prevotella sp BP1-56, were significantly correlated with milk composition. In conclusion, dietary supplementation with SeNPs can positively impact milk yield, milk components, and metabolism in dairy goats by improving the composition of the rumen microbiota under heat stress conditions.

Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores

Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥  3, n =  16) and thin (BCS <  3, n =  16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.

Multi-Omics Analysis Revealed the Molecular Mechanisms Affecting Average Daily Gain in Cattle

The average daily gain (ADG) is a critical index for evaluating growth rates in cattle and is closely linked to the economic benefits of the cattle industry. Heredity is one of the factors affecting the daily gain of cattle. However, the molecular mechanisms regulating ADG remain incompletely understood. This study aimed to systematically unravel the molecular mechanisms underlying the divergence in ADG between high average daily gain (HADG) and low average daily gain (LADG) Angus cattle through integrated multi-omics analyses (microbiome, metabolome, and transcriptome), hypothesizing that the gut microbiota-host gene-metabolism axis is a key regulatory network driving ADG divergence. Thirty Angus cattle were classified according to their HADG and LADG. Fecal and serum samples were collected for 16S, fecal metabolome, and blood transcriptome analysis. The results showed that compared with the LADG group, the abundance of Firmicutes increased in the HADG group, while the abundance of Bacteroidetes and Proteobacteria decreased. Metabolomics and transcriptomic analysis revealed that KEGG pathways associated with differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) were enriched in bile acid metabolism. Spearman correlation analysis showed that Oscillospira was positively correlated with ZBTB20 and negatively correlated with RADIL. ZBTB20 was negatively correlated with dgA-11_gut_group. This study analyzed the regulatory mechanism of average daily gain of beef cattle from genetic, metabolic, and microbial levels, providing a theoretical basis for analyzing the mechanism of differential daily gain of beef cattle, and has important significance for improving the production performance of beef cattle. The multi-omics network provides biomarker foundations for machine learning-based ADG prediction models, offering potential applications in precision breeding. While these biomarkers show promise for precision breeding, their causal roles require further validation. The conclusions are derived from a single breed (Angus) and gender (castrated males). Future studies should include females and diverse breeds to assess generalizability.

Gut Microbiota of Ruminants and Monogastric Livestock: An Overview

The diversity and composition of the gut microbiota are widely recognized as fundamental factors influencing the well-being and productivity of domestic animals. Advancements in sequencing technologies have revolutionized studies in this research field, allowing for deeper insights into the composition and functionality of microbiota in livestock. Ruminants and monogastric animals exhibit distinct digestive systems and microbiota characteristics: ruminants rely on fermentation, while monogastrics use enzymatic digestion, and monogastric animals have simpler stomach structures, except for horses and rabbits, where both processes coexist. Understanding the gut microbiota's impact and composition in both animal types is essential for optimizing production efficiency and promoting animal health. Following this perspective, the present manuscript review aims to provide a comprehensive overview of the gut microbiota in ruminants (such as cattle, sheep, and goats) and monogastric animals (including horses, pigs, rabbits, and chickens).

Effects of Yeast Culture on Lamb Growth Performance, Rumen Microbiota, and Metabolites

The effects of incorporating yeast culture (YC) into pelleted feeds on sheep production and the potential impact on rumen microbial populations, microbial metabolism, and fermentation have not been extensively studied. This study aimed to evaluate the effect of YC on growth performance, rumen tissue development, rumen fermentation, and rumen microflora in sheep and to explore the potential microbial mechanisms involved. Fifty healthy 3-month-old male lambs of small-tailed Han sheep, with an average weight of 28.44 ± 0.63 kg, were randomly divided into five groups: control (0% YC), 3% YC, 6% YC, 9% YC, and 12% YC. The pre-feeding period lasted for 15 days, followed by an official feeding period of 60 days. On the last day of the formal feeding period, six lambs that exhibited the best growth performance were randomly selected from the control group and the 9% YC group. These sheep were slaughtered, then the rumen epithelial tissue and rumen contents were collected for the measurement of rumen fermentation, microbial populations, and metabolites. Compared to the control group, the YC-treated groups showed higher daily and final body weight gains, as well as increased levels of propionic acid, butyric acid, and total volatile fatty acids (p < 0.05). YC supplementation also enhanced rumen papilla length and width (p < 0.05). Additionally, YC increased the relative abundance of certain microbial species (p < 0.05). These results suggest that supplementing 9% YC in pelleted diets for small-tailed Han sheep may enhance growth performance and improve the rumen environment.

Hydroxy-selenomethionine helps cows to overcome heat stress by enhancing antioxidant capacity and alleviating blood-milk barrier damage

Heat stress can lead to decreased feed intake, apoptosis of mammary epithelial cells, and decreased milk yield and quality. Selenium is an important element in the composition of at least 25 selenoproteins. Hydroxy-selenomethionine (HMSeBA) is a novel organic selenium that has been shown to have a better deposition effect. However, whether HMSeBA alleviates damage to the mammary gland blood-milk barrier caused by heat stress and how this affects the performance of dairy cows remain largely unexplored. Therefore, 32 healthy Holstein cows with similar gestation days (150.41 ± 20.07 d), milk yield (36.15 ± 3.02 kg) and parity (3.25 ± 0.51) were selected and randomly divided into two total mixed rations with different selenium (Se) sources: sodium selenite (SSe) and HMSeBA. This study evaluated the outcomes of HMSeBA on antioxidant capacity, immunity, and blood-milk barrier damage in dairy cows during heat stress by collecting the samples of blood, rumen fluid and mammary gland biopsy. The experiment was conducted over 35 d, including a 5-day pre-feeding period and a 30-day experimental period. The temperature and humidity index (THI) were all above 80 throughout the experiment period. The results showed that HMSeBA decreased the respiratory rate (P < 0.001) and the content of inflammatory cytokines in the serum and increased the content of immune factors and antioxidant capacity (P < 0.05). In addition, HMSeBA reduced the expression of inflammatory cytokines and heat shock proteins in mammary gland (P < 0.05). Hematoxylin-eosin-stained pathological sections showed massive thickening of acinar walls and severe destruction of glandular structures in the SSe group, but the structure of the acinar mammary gland in the HMSeBA group was intact. Furthermore, HMSeBA promoted the expression of the phosphatidylinositol 3-kinase (PI3K, P < 0.001)/protein kinase B (AKT, P = 0.011)/mammalian target of rapamycin (mTOR, P = 0.008) pathway and improved the expression of zonula occludens-1 (ZO-1, P = 0.014) and occluding (OCLN, P = 0.012) in the mammary gland, suggesting less damage caused by heat stress to the blood-milk barrier. Our results demonstrated that HMSeBA can improve the antioxidant capacity and immunity of dairy cows and the expression of tight junction proteins in mammary gland to help alleviate the blood-milk barrier damage by heat stress, which could reduce the damage of heat stress on milk yield.

A comparative study of the composition of microorganisms and metabolites in different β-casein genetic types of dairy cows based on metagenomics and non-targeted metabolomics

β-Casein is the main component of cow's milk protein, with A1 and A2 β-casein being the most common. Of these, A1 β-casein hydrolysate produces BCM-7, which can cause lactose intolerance, while A2 β-casein milk is more gentle on the gut. However, there is limited research on the composition of rumen microbiota, metabolites, and host metabolites in different genotype cows using metagenomics and metabolomics. In this study, we used multi-omics analysis techniques to perform enrichment analysis of differential metabolites, identifying three key metabolic pathways in all three groups: Arachidonic acid metabolism and Tryptophan metabolism. The metabolites in these pathways exhibited unique metabolic characteristics within each group. We then used random forests and ROC to predict key metabolites in these pathways, identifying that the signature metabolites in the A2A2 group were predominantly anti-inflammatory substances, including 12-HETE, PGD2-4d, and Arachidonic Acid. The signature metabolites in the A1A2 group and A2A2 group were Indoleacetaldehyde. The AUC of these signature metabolites was greater than 0.85. Macrogenic linear discriminant analysis (LDA > 2.5) found that the microorganisms with greater contribution were concentrated in the A2A2 group. Compared with the other two groups, g_Bacteroides and g_Parabacteroides were mainly enriched in the A1A2 group. In group A2A2, g_Xanthomonas and g_Acetobacter are mainly enriched. Then, the key microorganisms in A1A2 group were identified by correlation analysis as g_Bacteroides and g_Parabacteroides. The key microorganisms in group A2A2 were g_Acetobacter, g_Xanthomonas and g_Mannheimia, which were consistent with the results of LEfSe analysis. These microorganisms mainly affect the degradation of fiber in the diet, host metabolism and the occurrence of inflammation. In conclusion, our results provide theoretical basis and data support for the study of dairy cows with different genotypes of β-casein, and help to determine the potential biological functions of different genotypes of casein in dairy products and their effects on human health.

Effects of partial silage replacement with corn stover pellets on the rumen microbiota and serum metabolome of breeding cows

Introduction

Straw pellet ration replacing part of silage is of great significance for farmers to save farming costs and solve the lack of feed resources. A comprehensive analysis of rumen microbial and serum metabolite compositions is conducted to promote the development of the modern breeding cows-feeding industry.

Methods

In this study, 18 healthy 2-year-old Simmental breeding cows weighing 550 ± 20 kg were selected and randomly divided into two groups. They were fed under the same feeding conditions for 70 days, of which 8 in the control (CON) group were fed 65% roughage (100% silage) + 35% concentrate, and 10 in the treatment (TRT) group were fed 65% roughage (50% corn stover pellets +50% silage) + 35% concentrate, and milk quality, serum immunity indexes, serum metabolomes, rumen fermentation parameters, rumen Microorganisms.

Results

The results showed that there was no significant difference in production performance between the two groups of breeding cows fed hay and Corn stover pellet feed (p < 0.05); Immunoglobulin A (IgA) was significantly higher in TRT compared to CON (p < 0.05), and there was no significant difference in Immunoglobulin G (IgG) and Immunoglobulin M (IgM) between the two groups (p > 0.05); a total of 92 differential metabolites were screened out in the serum metabolomics analysis, among them, L-valine, L-leucine, L-arginine, L-cysteine, L-tyrosine, and L-tryptophan were up-regulated; In rumen fermentation parameters there was no significant difference between CON and TRT in rumen pH, rumen ammonia nitrogen (NH3-N) content, rumen Acetic/Propionic concentration (p > 0.05), and the concentration of Acetic, Propionic, butyric and Total volatile fatty acids (TVFA) in CON was significantly lower than that in TRT (p < 0.05). Among the rumen microorganisms, the dominant groups were Thick-walled Firmicutes, Bacteroidota, Prevotella and Ruminalococcus. In the correlation analysis between rumen fermentation parameters and rumen microorganisms, Propionic and TVFA showed a significant positive correlation with Prevotella (p < 0.05), butyric showed a highly significant positive correlation with Prevotella (p < 0.01), and propionic butyric, and TVFA showed a positive correlation with Bacteroides (p < 0.05); L-cysteine was significantly positively correlated with Prevotella and Anaeroplasma (p < 0.05) and Eubaterium in rumen microbial-serum metabolite correlation analysis (p < 0.01).

Conclusion

The microbial and metabolomic analyses provide us with essential data support to further provide a scientific basis for breeding cows feeding through the feeding pattern of straw pellets instead of silage, which will help breeding cows farming in future research.

SYISL Knockout Promotes Embryonic Muscle Development of Offspring by Modulating Maternal Gut Microbiota and Fetal Myogenic Cell Dynamics

Embryonic muscle fiber formation determines post-birth muscle fiber totals. The previous research shows SYISL knockout significantly increases muscle fiber numbers and mass in mice, but the mechanism remains unclear. This study confirms that the SYISL gene, maternal gut microbiota, and their interaction significantly affect the number of muscle fibers in mouse embryos through distinct mechanisms, as SYISL knockout alters maternal gut microbiota composition and boosts butyrate levels in embryonic serum. Both fecal microbiota transplantation and butyrate feeding significantly increase muscle fiber numbers in offspring, with butyrate inhibiting histone deacetylases and increasing histone acetylation in embryonic muscle. Combined analysis of RNA-seq between wild-type and SYISL knockout mice with ChIP-seq for H3K9ac and H3K27ac reveals that SYISL and maternal microbiota interaction regulates myogenesis via the butyrate-HDAC-H3K9ac/H3K27ac pathway. Furthermore, scRNA-seq analysis shows that SYISL knockout alone significantly increases the number and proportion of myogenic cells and their dynamics, independently of regulating histone acetylation levels. Cell communication analysis suggests that this may be due to the downregulation of signaling pathways such as MSTN and TGFβ. Overall, multiple pathways are highlighted through which SYISL influences embryonic muscle development, offering valuable insights for treating muscle diseases and improving livestock production.

Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet

The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.

Multi-Omics Insights into Rumen Microbiota and Metabolite Interactions Regulating Milk Fat Synthesis in Buffaloes

The present study was conducted to analyze the correlation between the milk fat content of Binglangjiang buffaloes and their microbial and host metabolites. The 10 buffaloes with the highest milk fat content (HF, 5.60 ± 0.61%) and the 10 with the lowest milk fat content (LF, 1.49 ± 0.13%) were selected. Their rumen fluid and plasma were collected for rumen microbiota and metabolome analysis. The results showed that the rumen bacteria abundance of Synergistota, Quinella, Selenomonas, and Fretibacterium was significantly higher in the HF buffaloes. The abundance of 14 rumen fungi, including Candida, Talaromyces, Cyrenella, and Stilbella, was significantly higher in the HF buffaloes. The analysis of the metabolites in the rumen and plasma showed that several metabolites differed between the HF and LF buffaloes. A total of 68 and 42 differential metabolites were identified in the rumen and plasma, respectively. By clustering these differential metabolites, most of those clustered in the HF group were lipid and lipid-like molecules such as secoeremopetasitolide B, lucidenic acid J LysoPE (0:0/18:2 (9Z, 12Z)), and 5-tetradecenoic acid. Spearman's rank correlations showed that Quinella, Fretibacterium, Selenomonas, Cyrenella, and Stilbella were significantly positively correlated with the metabolites of the lipids and lipid-like molecules in the rumen and plasma. The results suggest that rumen microbiota such as Quinella, Fretibacterium, Selenomonas, and Cyrenella may regulate milk fat synthesis by influencing the lipid metabolites in the rumen and plasma. In addition, the combined analysis of the rumen microbiota and host metabolites may provide a fundamental understanding of the role of the microbiota and host in regulating milk fat synthesis.

Rumen DNA virome and its relationship with feed efficiency in dairy cows

BACKGROUND

The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.

RESULTS

Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.

CONCLUSIONS

This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.

Ecological and Functional Changes in the Hindgut Microbiome of Holstein Cows at High Altitudes

The extreme environmental conditions of the Qinhai-Tibetan Plateau (QTP) challenge livestock survival and productivity, yet little is known about how high-altitude environments impact the gut microbiota of dairy cows. To fill this gap, we systematically investigated the differences in the hindgut microbiome between 87 plateau Holstein cows and 72 plain Holstein cows using 16S rRNA gene sequencing. Our analysis revealed that the hindgut microbiota of the plateau group exhibited lower species richness but higher evenness than that in the plain group. Additionally, significant separation in hindgut microbiota composition between the two groups was observed based on altitude, while parity, days in milk, and age did not show a comparable impact. Moreover, altitude had a lasting impact on bacterial communities and their co-occurrence networks, resulting in reduced microbial interactions and lower modularity in the plateau group. Furthermore, we identified four key microbial taxa, the Bacteroidaceae and Rikenellaceae families, as well as the Prevotella and Treponema genera, which were associated with the regulation of carbohydrate digestion and energy metabolism and might help the Holstein cows adapt to the plateau environment. Our findings provide insights into strategies for enhancing the adaptability of dairy cows to high-altitude environments through microbiota modulation, which could ultimately contribute to improving livestock management and sustainability in these extreme environments.

Effects of chili straw on rumen fermentation, meat quality, amino acid and fatty acid contents, and rumen bacteria diversity in sheep

Crop residues have shown promise as non-conventional feed sources to enhance animal health and growth. This study evaluated the effects of chili straw (CS) on rumen fermentation, meat quality, amino and fatty acid composition, and rumen microbial diversity in sheep. Fifty F1 Dorper×Hu lambs (29.58 ± 2.06 kg) were randomly assigned to five groups, fed pelleted feed with 0%, 5%, 10%, 15%, or 20% CS over a 63-day period, including a 7-day pre-test. Post-trial, rumen fluid was sampled to assess fermentation and microbial profiles, and slaughter performance and meat quality were evaluated. Key findings include: (1) No significant differences were observed in rumen pH, NH3-N, or acetic acid-to-propionic acid ratio across groups (P > 0.05). (2) Rumen microbial diversity indices did not vary significantly between groups (P > 0.05), though the relative abundance of Firmicutes and Proteobacteria increased, and Bacteroidota decreased in CS-fed groups, with specific genus-level changes. (3) Carcass weight decreased in the CS20% group (P < 0.01). (4) Cooking loss decreased in CS10%, 15%, and 20% groups (P < 0.05), and meat redness increased in CS15% and 20% groups (P < 0.01). (5) Saturated fatty acids decreased, while the PUFA/SFA ratio and amino acid profiles, including sulfur-containing amino acids (SAA), dibasic amino acids (DAA), essential amino acids (EAA), and total amino acids (TAA), increased with CS, with a significant rise in Gly content in the CS15% group (P < 0.05). In conclusion, incorporating CS into lamb diets can enhance meat quality without adversely affecting rumen fermentation, with recommended levels between 10% and 15%.

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.

Integrated analysis of rumen metabolomics and metataxonomics to understand changes in metabolic and microbial community in Korean native goats under heat stress

Heat stress (HS) is an impactful condition in ruminants that negatively affects their physiological and rumen microbial composition. However, a fundamental understanding of metabolomic and metataxonomic mechanisms in goats under HS conditions is lacking. Here, we analyzed the rumen metabolomics, metataxonomics, and serum metabolomics of goats (n = 10, body weight: 41.08 ± 1.83 kg) under optimum temperature period (OTP) (HS-free, temperature humidity index (THI): 57.13 ± 3.98) and high temperature period (HTP) (HS-exposed, THI: 80.27 ± 1.22) conditions, to identify changes in key metabolites and the rumen microbiome induced by HS. Compared to the OTP and HTP conditions, metabolomic analysis revealed significant changes in rumen metabolites related to energy and amino acid metabolism, with HTP goats showing potential rumen metabolic biomarkers, such as butyrate, isopropanol, phenylacetate, and 2-oxoisocaproate (P < 0.001). Serum analysis revealed significant changes in energy metabolism and immune response, with HTP goats showing potential metabolic biomarkers, including acetate, betaine, glucuronate, and kynurenine (P < 0.05). Metataxonomic analysis revealed that HS affected the alpha diversity measurements, including the Chao1 estimate (P < 0.05) and evenness (P < 0.05) between OTP and HTP groups. Through the metabolic association of the rumen microbiome with the metabolome, we found that Fibrobacter and Ruminococcus were enriched in HTP and positively correlated with ruminal microbial metabolites, such as acetate. In addition, Prevotellaceae UCG-003, which was denoted as the keynote genus in the HTP, co-occurred with acetate-producing bacteria such as Quinella and Ruminococcus. Furthermore, we identified that Oscillospiraceae UCG-002, an enriched bacterial genus in HTP, showed a positive correlation with functional features, such as biotin and sulfur metabolism. Our study provided fundamental insights into how HS affected the physiology and rumen microbial compositions of goats and how both microbiome and host-dependent mechanisms contributed to these changes. These findings could potentially suggest strategies for mitigating the adverse effects of HS, including changes in the microbial population and energy metabolism in goats.

Partially substituting roughage with traditional Chinese herbal medicine residues in the diet of goats improved feed quality, growth performance, hematology, and rumen microbial profiles

This study aimed to reveal the effect of traditional Chinese herbal medicine residues (TCHMR) on growth performance, hematology, ruminal microbiota, and economic benefits of Guizhou black male goats through the fermented total mixed ration (FTMR) diet technique. A total of 22 Guizhou black male goats with an initial weight of 21.77 ± 0.85 kg were randomly divided into 2 groups (n = 11), with 11 goats in each group. The control group (CON) was fed a traditional total mixed ration (TMR) diet without the TCHMR. The TCHMR group was fed an FTMR diet containing 40%TCHMR. Compared with the CON group, the results showed that the incorporation of TCHMR into goat diets reduced feeding costs and Feed conversion ratio (FCR). On the contrary, it improved (P < 0.01) feed quality, apparent digestibility of Dry matter (DM), Crude Protein (CP), Neutral detergent fiber (NDF), average daily gain (ADG), and dry matter intake. Interestingly, TCHMR also reduced (P < 0.01) acetate levels in the rumen of goats. Supplementally, TCHMR significantly increased (P < 0.01) the levels of GH, IgM, IgA (p < 0.05), and IFN-γ (P < 0.05), while significantly reducing (P < 0.01) the levels of IL-6, ALT, and AST in serum. Notably, at the phylum level, TCHMR significantly reduced (P < 0.01) the abundance of Bacteroidota and increased (P < 0.01) the abundance of Firmicutes. Moreover. at the genus level, TCHMR significantly reduced (P < 0.01) the abundance of Prevotella, F082, and Bacteroidales_RF16_group, while Muribaculaceae, Proteus, Lachnospiraceae_ND3007_group, and Ruminococcus were increased (P < 0.01). In conclusion, our current findings indicated that 40% TCHMR improved feed quality and the apparent digestibility of nutrients. Additionally, 40% TCHMR improved the growth performance and immunity of Guizhou black male goats, while also reorganizing the composition of ruminal microbiota. So far, under the conditions of this experiment, we have not found any negative effects of 40% TCHMR on goats. This study will be a new idea for developing feed resources, which will reduce environmental pollution and the cost of animal husbandry.

The dynamics of microbial community structure and metabolic function in different parts of cigar tobacco leaves during air-curing

Air-curing is the initial step in the processing of cigar tobacco leaves. However, the dynamics of microbial community and metabolic functions in different parts of tobacco leaves during this process remain largely unclear. In this study, amplicon-based high-throughput sequencing revealed that Pseudomonas (9.0 to 29.9%) and Sphingomonas (0.5 to 13.8%) were the dominant bacterial genera in the early stages of air-curing, while Pantoea (1.7-90.4%) became predominant after air-curing. Microbial community diversity analysis indicated that species richness and diversity were significantly higher during the fresh leaf and withering periods. Functional prediction based on PICRUSt2 suggested that the microbial communities in the middle leaves exhibited higher abundances of metabolic pathways related to carbohydrates and amino acids than those in the upper leaves, potentially leading to the formation of more flavor compounds. The volatile flavor compounds were detected during the air-curing process by HS-SPME-GC-MS, with alkaloids and esters being the most prominent, although their accumulation periods differed across leaf parts. Furthermore, based on PLS-DA, 17 and 38 significantly changed flavor components were identified in the upper and middle leaves, respectively. Finally, the potential relationships between characteristic microbes and flavor components were explored based on Spearman correlation coefficient. It was found that multiple bacteria such as Rhodanobacter, Gemmatimonas, and Ramlibacter present in the middle leaves exhibited significant positive correlations with multiple flavor compounds such as 3,3-dimethylacrylic acid, phenylacetone, 2,3-butanedione, and geranylacetone, potentially promoting the flavor formation of cigar tobacco leaves during air-curing process. This study provides scientific insights into the role of microorganisms during the air-curing process of cigar tobacco leaves and offers a scientific basis for screening of specific functional microorganisms to improve and stabilize cigar tobacco flavor in the future.

Rumen-mammary gland axis and bacterial extracellular vesicles: Exploring a new perspective on heat stress in dairy cows

Heat stress poses a significant threat to the global livestock industry, particularly impacting dairy cows due to their higher metabolic heat production and increased susceptibility. The rumen microbiota plays a crucial role in regulating heat stress in dairy cows. Moreover, the rumen-mammary gland axis has been recently unveiled, indicating that rumen bacteria and their metabolites can influence mammary gland health and function. Extracellular vesicles, cell-derived vesicles, are known to carry various biomolecules and mediate intercellular communication and immune modulation. This review proposes the hypothesis that heat stress poses a threat to dairy cows via the rumen-mammary gland axis by regulating rumen microbiota and their secreted extracellular vesicles. It summarizes existing knowledge on bacterial extracellular vesicles and the rumen-mammary gland axis, suggesting that targeting the rumen microbiota and their extracellular vesicles, while enhancing mammary gland health through this axis, could be a promising strategy for preventing and alleviating heat stress in dairy cows. The aim of this review is to offer new insights and guide future research and development efforts concerning heat stress in dairy cows, thereby contributing to a deeper understanding of its pathogenesis and potential interventions.

The dynamic distribution of the rectal microbiota in Holstein dairy calves provides a framework for understanding early-life gut health

The posterior intestinal microbiota plays a vital role in the growth and health of Holstein dairy calves. However, its establishment and dynamic changes during early development remain unclear. The aim of this study was to investigate microbial colonization and development in the rectum of calves within the first 70 d after birth. Here, 96 rectal content samples were collected from 8 Holstein dairy calves at 12 time points and analyzed using 16S rRNA gene sequencing. The microbial alpha diversity increased with age. The bacterial community displayed a distinct dynamic distribution. The phylum Proteobacteria was replaced by Firmicutes and Bacteroidetes after d 3. The colonization process of bacterial genera in the rectum of neonatal calves can be divided into 2 periods: the colonization period (stage 1: d 1 and stage 2: d 3) and the stable period (stage 3: d 7-14, stage 4: d 21-42, and stage 5: d 49-70). The fermentation pattern and metabolic function changed from propionate fermentation dominated by Shigella to lactic acid fermentation dominated by Lactobacillus, Blautia, and Oscillospira. The stable period was more comprehensive and complete than the colonization period. This study revealed the dynamic changes in the posterior intestinal microbiota of Holstein dairy calves during early development. The transition period (d 7-14) was identified as a key stage for early nutritional intervention, as the abundance of Lactobacillus increased and the abundance of harmful bacteria (such as Proteobacteria and Shigella) decreased. This study provides a framework for understanding early-life gut health and offers theoretical guidance for future research on host-microbe interactions and early nutritional interventions. It is suggested that nutritional interventions based on microbial characteristics at different stages be implemented to improve calf growth performance and immune function, which may contribute to the reduction of diarrhea and other gastrointestinal disorders during dairy production.

Invited review: Ruminal acidosis and its definition-A critical review

Ruminal acidosis occurs as a continuum of disorders, stemming from ruminal dysbiosis and disorders of metabolism, of varying severity. The condition has a marked temporal dynamic expression, resulting in cases expressing quite different rumen concentrations of VFA, lactic acid, ammonia, and rumen pH over time. Clinical ruminal acidosis is an important condition of cattle and subclinical ruminal acidosis (SRA) is very prevalent in many dairy populations, with estimates between 10% and 26% of cows in early lactation. Estimates of the duration of a case suggest that the lactational incidence of the condition may be as high as 500 cases per 100 cows in the first 100 d of lactation. Historical confusion about the etiology and pathogenesis of ruminal acidosis led to definitions that are not fit for purpose, as acidic ruminal conditions solely characterized by ruminal pH determination at a single point fail to reflect the complexity of the condition. Use of a model based on integrated ruminal measures, including VFA, ammonia, lactic acid, and pH, for evaluating ruminal acidosis is fit for purpose, as indicated by meeting postulates for assessing metabolic disease, but requires a method to simplify application in the field. Although it is likely that this model, which we have termed the Bramley acidosis model (BAM), will be refined, the critical value in the model is that it demonstrates that ruminal acidosis is much more than ruminal pH. Disease, milk yield, and milk composition are more associated with the BAM than rumen pH alone. Two single VFA, propionate and valerate, are sensitive and specific for SRA, especially when compared with rumen pH. Even with the use of such a model, astute evaluations of the condition, whether in experimental or field circumstances, will be aided by ancillary measures that can be used in parallel or in series to enhance diagnosis and interpretation. Sensing methods, including rumination detection, behavior, milk analysis, and passive analysis of rumen function, have the potential to improve the detection of SRA; however, these may advance more rapidly if SRA is defined more broadly than by ruminal pH alone.

Butyrate metabolism in rumen epithelium affected by host and diet regime through regulating microbiota in a goat model

The rumen is an important organ that enables ruminants to digest nutrients. However, the biological mechanism by which the microbiota and its derived fatty acids regulate rumen development is still unclear. In this study, 18 female Haimen goats were selected and slaughtered at d 30, 60, and 90 of age. Multi-omics analyses (rumen microbial sequencing, host transcriptome sequencing, and rumen epithelial metabolomics) were performed to investigate host-microbe interactions from preweaning to postweaning in a goat model. With increasing age, and after the introduction of solid feed, the increased abundances of Prevotella and Roseburia showed positive correlations with volatile fatty acid (VFA) levels and morphological parameters (P < 0.05). Epithelial transcriptomic analysis showed that the expression levels of hub genes, including 3-hydroxy-3-methylglutaryl-CoA synthase isoform 2 (HMGCS2), enoyl-CoA hydratase, short chain 1 (ECHS1), and peroxisome proliferator activated receptor gamma (PPARG), were positively associated with animal phenotype (P < 0.05). These hub genes were mainly correlated to VFA metabolism, oxidative phosphorylation, and the mammalian target of rapamycin (mTOR) and peroxisome proliferator activated receptor (PPAR) signaling pathways (P < 0.05). Moreover, the primary metabolites in the epithelium changed from glucose preweaning to (R)-3-hydroxybutyric acid (BHBA) and acetoacetic acid (ACAC) postweaning (P < 0.05). Diet and butyrate were the major factors shaping epithelial metabolomics in young ruminants (P < 0.05). Multi-omics analysis showed that the rumen microbiota and VFA were mainly associated with the epithelial transcriptome, and that alterations in gene expression influenced host metabolism. The "butanoate metabolism" pathway, which transcriptomic and metabolomic analyses identified as being upregulated with age, produces ketones that regulate the "oxidative phosphorylation" pathway, which could provide energy for the development of rumen papillae. Our findings reveal the changes that occur in the rumen microbiota, host transcriptome, and metabolome with age, and validate the role of microbiota-derived VFA in manipulating host gene expression and subsequent metabolism. This study provides insight into the molecular mechanisms of host-microbe interactions in goats and supplies a theoretical basis and guidance for precise nutritional regulation during the critical time window for rumen development of young ruminants.

Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle

Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.

Multiomics of yaks reveals significant contribution of microbiome into host metabolism

An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, while grazing yaks had higher methyl metabolites associated with methane production. These rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks' growth. Thus, an intensive feeding system altered the rumen microbiome and metabolism as well as host metabolism, resulting in improvements of yak growth.

Biofermentation of aquatic plants: Potential novel feed ingredients for dairy cattle production

The study assessed the impacts of aquatic plant silages on feeding efficiency and dairy cattle health as an alternative to conventional corn silage under high altitude conditions. Mid-lactation Holstein cows were assigned to treatment groups according to a randomized complete block design of parity, previous 105-d milk yield, and body weight. Cows (n = 8 per group) were fed with aquatic plant silage inoculated with Bacillus subtilis (BS), Yeast (YS), or conventional corn silage without inoculants (control) in addition to [standard grain feed] for 75 consecutive days. BS and YS had higher protein contents than control silage (111.20 ± 7.68, 112.10 ± 6.83 vs 76.94 ± 3.48 g/kg DM), while feeding efficiency was comparable between treatments (1.07, 0.99, and 0.90, respectively). In addition, the addition of aquatic plant silage in ruminant diets enhanced immunity and antioxidant capacity when compared with control group. Metagenomic analysis showed similar composition in rumen microbiota between YS and control groups, with higher enrichment for energy and nitrogen utilization pathways in YS-treated cows. This study highlights the use of aquatic plant silage as an alternative feed for dairy cattle with higher protein than corn silage. Our results suggest YS or BS could potentially boost immune and antioxidant functions, improving adaptation to high-altitudes and reducing demand for high input corn production on the Qinghai-Tibetan Plateau.

Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves

BACKGROUND

Long-distance road transportation is a common practice in the beef industry, frequently resulting in bovine respiratory disease (BRD) and compromised growth performance. However, a comprehensive investigation integrating clinical performance, physiological conditions, and nasopharyngeal microflora remains lacking.

METHODS

This study aimed to evaluate the respiratory health and immunometabolic status of 54 beef calves subjected to a 3000-km journey. The respiratory health of calves was monitored over 60 days post-arrival using a modified clinical scoring system. Nasopharyngeal microflora and venous blood samples were collected at 3 time points: before transportation (A), 30 days post-arrival (B), and 60 days post-arrival (C), for 16S rRNA microbiomics, whole-blood transcriptomics, serum metabolomics, and laboratory assays.

RESULT

Within the first week post-arrival, the appetite and mental scores of calves dropped to zero, while other respiratory-related scores progressively declined over the 60 days. The α-diversity of nasopharyngeal microflora in calves was similar at time points A and B, both significantly higher than at time point C. The structure of these microbial communities varied significantly across different time points, with a notably higher relative abundance of BRD-related genera, such as Pasteurella and Mannheimia, detected at time point A compared to B and C. The composition and gene expression profiles of circulating blood cells at time point A were significantly different from those at B and C. Specifically, higher expression levels of oxidative- and inflammatory-related genes, cytokines, and enzymes were observed at time point A compared to B and C. Higher levels of catabolism-related metabolites and enzymes were detected at time point A, while higher levels of anabolism-related metabolites and enzymes were observed at time points B and C. Additionally, significant correlations were found among microorganisms, genes, and metabolites with differing abundances, expression levels, and concentrations across time points. Stronger correlations were observed between calves' performance and nasopharyngeal microflora and immunometabolic status at time point A compared to B or C.

CONCLUSIONS

Collectively, these results confirm that 3000 km of road transportation significantly alters the composition and gene expression profiles of circulating white blood cells in calves, affects their metabolic processes, disrupts the balance of the respiratory microbial community, and leads to pronounced respiratory symptoms that persist for at least 60 days. During this period, the influenced composition and gene expression of circulating blood cells, metabolic processes, and nasopharyngeal microbial community gradually return to equilibrium, and the respiratory symptoms gradually diminish. This observational research indicates that transportation induces BRD in calves by disrupting the homeostasis of their immune function, metabolic processes, and nasopharyngeal microbial community. However, these results and their underlying molecular mechanisms warrant further validation through well-designed in vivo and in vitro confirmatory experiments with larger sample size. Video Abstract.

Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions

Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.

Regulation of Milk Fat Synthesis: Key Genes and Microbial Functions

Milk is rich in a variety of essential nutrients, including fats, proteins, and trace elements that are important for human health. In particular, milk fat has an alleviating effect on diseases such as heart disease and diabetes. Fatty acids, the basic units of milk fat, play an important role in many biological reactions in the body, including the involvement of glycerophospholipids and sphingolipids in the formation of cell membranes. However, milk fat synthesis is a complex biological process involving multiple organs and tissues, and how to improve milk fat of dairy cows has been a hot research issue in the industry. There exists a close relationship between milk fat synthesis, genes, and microbial functions, as a result of the organic integration between the different tissues of the cow's organism and the external environment. This review paper aims (1) to highlight the synthesis and regulation of milk fat by the first and second genomes (gastrointestinal microbial genome) and (2) to discuss the effects of ruminal microorganisms and host metabolites on milk fat synthesis. Through exploring the interactions between the first and second genomes, and discovering the relationship between microbial and host metabolite in the milk fat synthesis pathway, it may become a new direction for future research on the mechanism of milk fat synthesis in dairy cows.

The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.

Hydrogen-rich water 400ppb as a potential strategy for improving ruminant nutrition and mitigating methane emissions

The objective of this study was to evaluate the effects of different concentrations of hydrogen-rich water (HRW) on in vitro rumen fermentation characteristics and the dynamics of bacterial communities. The experiment included four treatment groups: a control (CON) and hydrogen-rich water (HRW) at 200, 400, and 800 ppb. Each group was analyzed at 12-hour (h) and 48-hour (h) time points with five replicates, totaling 40 samples. The experimental results highlighted the HRW800ppb group as the top production in terms of gas production and CH4 content. In contrast, the HRW200ppb group exhibited significantly lower methane levels at both 12 h and 48 h (P < 0.05). Regarding rumen fermentation, the HRW400ppb group significantly increased the levels of ammonia nitrogen (NH3-N) and microbial crude protein (MCP) at 12 h fermentation, but reduced the dry matter degradation rate (P < 0.05). After 48 h, the HRW400ppb group had highest MCP content (P < 0.05), but no significant differences in NH3-N and dry matter degradation rate compared with the CON group (P > 0.05). Although HRW did not significantly benefit the synthesis of total volatile fatty acids (TVFA) and individual VFA, the HRW800ppb group significantly increased the ratio of acetate to propionate (P < 0.05). Based on CH4 emissions and MCP synthesis, we selected the HRW400ppb group for subsequent bacterial community analysis. Bacterial community analysis showed that at 12 h, compared with the CON group, the Bacterial community analysis revealed that the HRW400ppb group had significant increases in the Simpson index, Firmicutes, Streptococcus, Schwartzia, Prevotellaceae_YAB2003_group, and Oribacterium, and decreases in Prevotella, Ruminobacter, Succinivibrio, unclassified_Succinivibrionaceae, and Prevotellaceae_UCG-003 (P < 0.05). At 48 h, the Prevotellaceae_YAB2003_group and Oribacterium abundances continued to rise significantly, while Rikenellaceae_RC9_gut_group and Succiniclasticum abundances fell in the HRW400ppb group (P < 0.05). Correlation analysis indicated a negative link between CH4 and Streptococcus, and a positive correlation between the abundance of Rikenellaceae_RC9_gut_group and CH4. Collectively, these results indicate that HRW can modulate rumen fermentation and microbial community structure to reduce methane emissions without significantly affecting VFA synthesis, highlighting its potential as drinking water for enhancing ruminant nutrition and mitigating the environmental impact of livestock farming.

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

BACKGROUND

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.

RESULTS

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).

CONCLUSION

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.

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

BACKGROUND

During 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.

METHODS

Dairy 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.

RESULTS

CPE 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.

CONCLUSIONS

Our 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.

Medium-chain fatty acid triglycerides improve feed intake and oxidative stress of finishing bulls by regulating ghrelin concentration and gastrointestinal tract microorganisms and rumen metabolites

BACKGROUND

As a feed additive, medium-chain fatty acids (MCFAs)/medium-chain fatty acid triglycerides (MCTs) have been used in ruminant production, but mostly added in the form of mixed esters. Studies have shown that MCTs may have a positive effect on feed intake or oxidative stress in animals, but it is unclear which MCT could play a role, and the mechanism has not been elucidated. In this study, the effects of individual MCT on growth performance, serum intake-related hormones, and oxidative stress indices in finishing bulls were investigated and further studied the effects of MCT supplementation on gastrointestinal tract bacteria and rumen fluid metabolomics.

RESULTS

Four ruminally fistulated Yanbian cattle (bulls) were selected in 4 × 4 Latin square designs and allocated to four treatment groups: a control group (CON) fed a basal diet (total mixed ration, TMR), three groups fed a basal diet supplemented with 60 g/bull/day glycerol monocaprylin (GMC, C8), glycerol monodecanoate (GMD, C10), and glycerol monolaurate (GML, C12), respectively. Compared with the CON group, GMD tended to increase the dry matter intake (DMI) of finishing bulls (P = 0.069). Compared with the CON group, GMD significantly increased the concentration of ghrelin O-acyl transferase (GOAT), total ghrelin (TG), acylated ghrelin (AG), and orexins (P < 0.05) and significantly decreased the concentrations of hydrogen peroxide (H2O2), malondialdehyde, reactive oxygen species (ROS), and lipopolysaccharides (LPS) in the serum of finishing bulls (P < 0.05). Compared with the CON group, GMD and GML significantly increased the concentrations of total antioxidant capacity (T-AOC), catalase, glutathione peroxidase (GSH-PX), glutathione reductase (GR), and nitric oxide (NO) in the serum of finishing bulls (P < 0.05). Compared with the CON group, there were 5, 14, and 6 significantly different bacteria in the rumen digesta in the C8, C10, and C12 groups, respectively; there were 3, 10, and 5 significantly different bacteria in the rumen fluid in the C8, C10, and C12 groups, respectively; and only one differential bacteria (genus level) in the feces among the four treatment groups. Compared with the CON group, there were 3, 14, and 15 significantly differential metabolites identified under positive ionization mode in the C8, C10, and C12 groups, respectively, while under negative ionization mode were 3, 11 and 14, respectively. Correlation analysis showed that there was a significant correlation between DMI, GOAT, AG, GSH-PX, LPS, gastrointestinal tract bacteria, and rumen fluid metabolites.

CONCLUSIONS

Our findings revealed that different types of MCTs have different application effects in ruminants. Among them, GMD may improve the feed intake of finishing bulls by stimulating the secretion of AG. GMD and GML may change gastrointestinal tract microorganisms and produce specific rumen metabolites to improve the oxidative stress of finishing bulls, and ghrelin may also be involved. This study enlightens the potential mechanisms by which MCT improves feed intake and oxidative stress in finishing bulls. Video Abstract.

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.

Whole-Genome Metagenomic Analysis of Functional Profiles in the Fecal Microbiome of Farmed Sows with Different Reproductive Performances

Recent studies suggested an association between the reproductive performance of sows and their gut microbiota. To understand how the gut microbiota affect the reproductive performances of sows, we conducted a whole-genome metagenomic analysis on the fecal microbial functional profiles of sows with high and low reproductive performances. We used 60 sows from six farms (10 sows/farm), including 30 sows from three farms with higher reproductive performances (the mean number of weaned piglets/sow/year) (group H) and 30 sows from three farms with lower performances (group L). Fecal microbial DNA was subjected to a whole-genome metagenomic analysis. Biomarker exploration analysis identified "carbohydrate transport and metabolism" as the most discriminative function enriched in group H. Further analysis of carbohydrate-active enzymes revealed that the fecal microbiome of group H had a greater capacity to degrade dietary fiber, specifically cellulose and pectin. Group H also exhibited higher fecal short-chain fatty acid (SCFA) concentrations than group L, with the abundances of cellulose- and pectin-degrading genes showing significant positive correlations with fecal SCFA concentrations. Taxonomic analysis indicated greater contributions of Prevotella, Treponema, Ruminococcus, and Fibrobacter to cellulose and pectin degradation in the fecal microbiome in group H. In conclusion, higher reproductive performances of sows were, at least in part, associated with a greater microbial capacity for degrading cellulose and pectin, resulting in a higher SCFA production in the hindgut.