Serum metabolome profiling revealed potential biomarkers for milk protein yield in dairy cows

Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits

Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.

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.

Integrating Metabolomics and Genomics to Uncover the Impact of Fermented Total Mixed Ration on Heifer Growth Performance Through Host-Dependent Metabolic Pathways

With the increasing demand for enhancing livestock production performance and optimizing feed efficiency, this study aimed to investigate the effects of fermented total mixed ration (FTMR) containing different proportions of rice straw and sheath and leaves of Zizania latifolia on systemic nutrient metabolism and oxidative metabolism under host genetic regulation and on growth performance of heifers. A total of 157 heifers aged 7-8 months were selected, and their hair was collected for whole-genome sequencing. They were randomly assigned into four groups of 18 to 21 cattle each and fed FTMR containing varying levels of rice straw (21% in LSF, 28% in MSF, 35% in HSF) or 31% sheath and leaves of Zizania latifolia (ZF) for a two-month period. At the end of trial, blood and urine samples were collected to measure biochemical indexes and metabolomics. The results showed that high rice straw content and ZF diets could increase blood glucose and non-protein nitrogen in heifers, that is, blood glucose and urea nitrogen levels in HSF and ZF groups were higher than those in LSF and MSF groups (p < 0.05). Meanwhile, the two diets could improve the antioxidant level of heifers. Urine metabolomics analysis between the groups identified three differential metabolic pathways, including 11 metabolites. Among them, l-homoserine and o-acetylserine had significant SNPs associated with them, which promoted glutathione metabolism. Although there was no significant effect of diet on heifers' average daily gain (ADG) in body weight (p > 0.05), there was substantial inter-individual variation in metabolites among all animals, as further correlation analyses illustrated. Twenty-eight metabolites were significantly associated with ADG (R > 0.3, p < 0.05). Four of them were identified as biomarkers, primarily regulating energy metabolism and oxidative balance. In conclusion, feeding HSF and ZF FTMR enhances glutathione metabolism and antioxidant capacity in heifers, positioning key metabolites as candidates for ADG markers. This integrative omics approach underscores the potential for enhancing livestock productivity and promoting sustainable agricultural practices.

Variations in the milk lipidomic profile of lactating dairy cows fed the diets containing alfalfa hay versus alfalfa silage

Alfalfa is primarily stored as silage or hay in livestock production. Previous research has shown that the storage method of grass significantly influences milk composition. This study aimed to investigate milk production performance and lipid composition in dairy cows fed diets consisting of alfalfa hay or alfalfa silage as roughage. Forty-two mid-lactation Holstein dairy cows were selected and randomly divided into three groups, each receiving a total mixed ration consisting of alfalfa hay (AH), 50% alfalfa silage + 50% alfalfa hay (AHAS), or alfalfa silage (AS). The results showed that milk fat content (P = 0.049) and milk fat yield (P < 0.001) were significantly higher in the AH and AHAS groups compared to the AH group. With increased supplementation of alfalfa silage in the diet, ω-3 polyunsaturated fatty acid content increased significantly (P < 0.001), while ω-6 polyunsaturated fatty acid content (P = 0.007) and the ratio of ω-6 to ω-3 polyunsaturated fatty acids decreased (P < 0.001). The contents of sphingomyelins, phosphatidylserines, phosphatidylethanolamines, and phosphatidylglycerols in the AHAS and AS samples were higher than in the AH samples, although the differences were not statistically significant. Additionally, the content of phosphatidylcholines was significantly higher in the AS group compared to the AH group (P = 0.032). In conclusion, feeding dairy cows a diet consisting of alfalfa silage can increase the major phospholipid content and polyunsaturated fatty acid composition in raw milk, which is more conducive to human health. These findings provide valuable insights into the benefits of alfalfa silage for dairy cows.

Metabolomics and amino acid profiling of plasma reveals the metabolite profiles associated with nitrogen utilisation efficiency in primiparous dairy cows

Nitrogen (N) utilisation efficiency (NUE, milk N yield [g/d]/N intake [g/d]) is an important performance indicator in dairy farming. Determining the NUE-associated blood metabolite profile will contribute to the optimisation of nutritional strategies to further improve NUE among dairy cows. Here, 20 primiparous lactating cows with days in milk ranging from 95 to 115 days were selected from a total of 1 221 cows. Each cow's N intake and milk N yield were measured for 7 days. Subsequently, blood samples were collected before morning feeding. Based on analysis and calculations, cows were retrospectively classified into two groups based on their NUE values, namely, a low NUE group (LNUE, NUE = 24.8 ± 1.6%, n = 10, mean ± SD) and a high NUE group (HNUE, NUE = 35.2 ± 1.7%, n = 10, mean ± SD). Plasma samples were selected from six cows in each group for metabolomics and amino acid profiling. Among the 41 differential metabolites (DMs) identified in the metabolomic analysis, sucrose, MG(0:0/22:1(13Z)/0:0), 2-amino-6-hydroxyhexanoic acid, and L-glutamine exhibited significant correlations with NUE, milk yield, and BW (P < 0.05). Moreover, the five differential amino acids and amino acid metabolites (DAAs) identified in the amino acid profiling and 5 of the 6 differential amino acids and amino acid conjugates identified by plasma metabolomics were found to be less abundant in the HNUE group (P < 0.05). Specifically, there was a 39.4% decrease in L-arginine content and a 29.2% decrease in L-glutamine content (P < 0.05). Pathway analysis indicated that the DMs and DAAs were mainly involved in arginine biosynthesis, glutathione metabolism, arginine and proline metabolism, and tryptophan metabolism (pathway impact > 0.1). These results provided new insights into the new blood metabolite profile associated with NUE in dairy cows. These new insights can provide foundational information for the formulation of new strategies to further enhance NUE in dairy cows.

Rapid authenticity assessment of PGI Hongyuan yak milk based on SICRIT-QTOF MS

Hongyuan (HY) yaks live in a pollution-free environment, making HY yak milk a green food, but their short milk production period and low milk yield make yak milk precious and expensive. The phenomenon of counterfeiting HY yak milk with ordinary milk from other origins has already occurred, so the authenticity assessment of HY yak milk is necessary. This study developed a rapid soft ionisation by chemical reaction in transfer quadrupole time-of-flight mass spectrometry (SICRIT-QTOF MS) for HY yak milk differences assessment. Principal component analysis and orthogonal least squares discriminant analysis showed differences between HY milk and the other three origins. Twenty-eight differential compounds were screened out by variable importance in projection, fold change, P-value, and database matching. Furthermore, six characteristic compounds (proline, 2-hydroxy-3-methylbutyric acid, and l-isoleucine, etc.) of HY samples were putatively identified. The study demonstrated that SICRIT-QTOF MS has great potential for rapidly distinguishing the milk origin.

Multi-omics reveals the mechanism of rumen microbiome and its metabolome together with host metabolome participating in the regulation of milk production traits in dairy buffaloes

Recently, it has been discovered that certain dairy buffaloes can produce higher milk yield and milk fat yield under the same feeding management conditions, which is a potential new trait. It is unknown to what extent, the rumen microbiome and its metabolites, as well as the host metabolism, contribute to milk yield and milk fat yield. Therefore, we will analyze the rumen microbiome and host-level potential regulatory mechanisms on milk yield and milk fat yield through rumen metagenomics, rumen metabolomics, and serum metabolomics experiments. Microbial metagenomics analysis revealed a significantly higher abundance of several species in the rumen of high-yield dairy buffaloes, which mainly belonged to genera, such as Prevotella, Butyrivibrio, Barnesiella, Lachnospiraceae, Ruminococcus, and Bacteroides. These species contribute to the degradation of diets and improve functions related to fatty acid biosynthesis and lipid metabolism. Furthermore, the rumen of high-yield dairy buffaloes exhibited a lower abundance of methanogenic bacteria and functions, which may produce less methane. Rumen metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, including lipids, carbohydrates, and organic acids, as well as volatile fatty acids (VFAs), such as acetic acid and butyric acid. Meanwhile, several Prevotella, Butyrivibrio, Barnesiella, and Bacteroides species were significantly positively correlated with these metabolites. Serum metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, mainly lipids and organic acids. Meanwhile, several Prevotella, Bacteroides, Barnesiella, Ruminococcus, and Butyrivibrio species were significantly positively correlated with these metabolites. The combined analysis showed that several species were present, including Prevotella.sp.CAG1031, Prevotella.sp.HUN102, Prevotella.sp.KHD1, Prevotella.phocaeensis, Butyrivibrio.sp.AE3009, Barnesiella.sp.An22, Bacteroides.sp.CAG927, and Bacteroidales.bacterium.52-46, which may play a crucial role in rumen and host lipid metabolism, contributing to milk yield and milk fat yield. The "omics-explainability" analysis revealed that the rumen microbial composition, functions, metabolites, and serum metabolites contributed 34.04, 47.13, 39.09, and 50.14%, respectively, to milk yield and milk fat yield. These findings demonstrate how the rumen microbiota and host jointly affect milk production traits in dairy buffaloes. This information is essential for developing targeted feeding management strategies to improve the quality and yield of buffalo milk.

Metabolic Changes in Serum and Milk of Holstein Cows in Their First to Fourth Parity Revealed by Biochemical Analysis and Untargeted Metabolomics

The performance of dairy cows is closely tied to the metabolic state, and this performance varies depending on the number of times the cows have given birth. However, there is still a lack of research on the relationship between the metabolic state of Holstein cows and the performance of lactation across multiple parities. In this study, biochemical analyses and metabolomics studies were performed on the serum and milk from Holstein cows of parities 1-4 (H1, N = 10; H2, N = 7; H3, N = 9; H4, N = 9) in mid-lactation (DIM of 141 ± 4 days) to investigate the link between performance and metabolic changes. The results of the milk quality analysis showed that the lactose levels were highest in H1 (p = 0.036). The total protein content in the serum increased with increasing parity (p = 0.013). Additionally, the lipase activity was found to be lowest in H1 (p = 0.022). There was no difference in the composition of the hydrolyzed amino acids in the milk among H1 to H4. However, the free amino acids histidine and glutamate in the serum were lowest in H1 and highest in H3 (p < 0.001), while glycine was higher in H4 (p = 0.031). The metabolomics analysis revealed that 53 and 118 differential metabolites were identified in the milk and serum, respectively. The differential metabolites in the cows' milk were classified into seven categories based on KEGG. Most of the differential metabolites in the cows' milk were found to be more abundant in H1, and these metabolites were enriched in two impact pathways. The differential metabolites in the serum could be classified into nine categories and enriched in six metabolic pathways. A total of six shared metabolites were identified in the serum and milk, among which cholesterol and citric acid were closely related to amino acid metabolism in the serum. These findings indicate a significant influence of blood metabolites on the energy and amino acid metabolism during the milk production process in the Holstein cows across 1-4 lactations, and that an in-depth understanding of the metabolic changes that occur in Holstein cows during different lactations is essential for precision farming, and that it is worthwhile to further investigate these key metabolites that have an impact through controlled experiments.

DNA methylation of GDF-9 and GHR genes as epigenetic regulator of milk production in Egyptian Zaraibi goat

BACKGROUND

DNA methylation is an epigenetic mechanism that takes place at gene promoters and a potent epigenetic marker to regulate gene expression.

OBJECTIVE

The study aimed to improve the milk production of Zaraibi goats by addressing the methylation pattern of two milk production-related genes: the growth hormone receptor (GHR) and the growth differentiation factor-9 (GDF-9).

METHODS

54 and 46 samples of low and high milk yield groups, respectively, were collected. Detection of methylation was assessed in two CpG islands in the GDF-9 promoter via methylation-specific primer assay (MSP) and in one CpG island across the GHR promoter using combined bisulfite restriction analysis (COBRA).

RESULTS

A positive correlation between the methylation pattern of GDF-9 and GHR and their expression levels was reported. Breeding season was significantly effective on both peak milk yield (PMY) and total milk yield (TMY), where March reported a higher significant difference in PMY than November. Whereas single birth was highly significant on TMY than multiple births. The 3rd and 4th parities reported the highest significant difference in PMY, while the 4th parity was the most effective one on TMY.

CONCLUSION

These results may help improve the farm animals' milk productive efficiency and develop prospective epigenetic markers to improve milk yield by epigenetic marker-assisted selection (eMAS) in goat breeding programs.

Metabolomics of natural samples: A tutorial review on the latest technologies

Metabolomics is the study of metabolites present in a living system. It is a rapidly growing field aimed at discovering novel compounds, studying biological processes, diagnosing diseases, and ensuring the quality of food products. Recently, the analysis of natural samples has become important to explore novel bioactive compounds and to study how environment and genetics affect living systems. Various metabolomics techniques, databases, and data analysis tools are available for natural sample metabolomics. However, choosing the right method can be a daunting exercise because natural samples are heterogeneous and require untargeted approaches. This tutorial review aims to compile the latest technologies to guide an early-career scientist on natural sample metabolomics. First, different extraction methods and their pros and cons are reviewed. Second, currently available metabolomics databases and data analysis tools are summarized. Next, recent research on metabolomics of milk, honey, and microbial samples is reviewed. Finally, after reviewing the latest trends in technologies, a checklist is presented to guide an early-career researcher on how to design a metabolomics project. In conclusion, this review is a comprehensive resource for a researcher planning to conduct their first metabolomics analysis. It is also useful for experienced researchers to update themselves on the latest trends in metabolomics.

The effects of polylactic acid bioplastic exposure on midgut microbiota and metabolite profiles in silkworm (Bombyx mori): An integrated multi-omics analysis

Polylactic acid (PLA) is a highly common biodegradable plastic and a potential threat to health and the environment. However, limited data are available on the effects of PLA exposure in the silkworm (Bombyx mori), a model organism used in toxicity studies. In this study, silkworms with or without PLA exposure (P1: 1 mg/L, P5: 5 mg/L, P25: 25 mg/L, and P0: 0 mg/L) for the entire 5th instar period were used to investigate the impact of PLA exposure on midgut morphology, larvae growth, and survival. Mitochondrial damage was observed in the P5 and P25 groups. The weights of the P25 posterior silk gland (5th day in the 5th instar), mature larvae and pupae were all significantly lower than those of the controls (P < 0.05). Dead worm cocoon rates and larva-pupa to 5th instar larvae ratios showed a positive and negative dose-dependent manner with respect to PLA concentrations, respectively. Additionally, reactive oxygen species levels and superoxide dismutase activity of the P25 midgut were significantly higher and lower when compared with controls, respectively (P < 0.05). The molecular mechanisms underlying the effects of PLA and associated physiological responses were also investigated. In the midgut metabolome, 127 significantly different metabolites (variable importance projection >1 and P < 0.05) were identified between the P0 and P25 groups and were mainly enriched for amino acid metabolism and energy supply pathways. The 16 S rDNA data showed that PLA altered microbial richness and structural composition. Microbiota, classified into 34 genera and 63 species, were significantly altered after 25 mg/L PLA exposure (P < 0.05). Spearman's correlation results showed that Bifidobacterium catenulatum and Schaalia odontolytica played potentially vital roles during exposure, as they demonstrated stronger correlations with the significantly different metabolites than other bacterial species. In sum, PLA induced toxic effects on silkworms, especially on energy- and protein-relevant metabolism, but at high concentrations (25 mg/L). This prospective mechanistic investigation on the effects of PLA on larval toxicity provides novel insight regarding the ecological risks of biodegradable plastics in the environment.

Differences in serum metabolome profile explain individual variation in growth performance of young goats

High growth rates and body weight are important traits of young dairy goats that can shorten generation intervals, improve animal performance, and increase economic benefits. In the present study, ninety-nine, 6-month-old, female goats were fed with the same diet and kept under the same management condition. The ten goats with highest average daily gain (ADG, HADG, 135.27 ± 4.59 g/d) and ten goats with lowest ADG (LADG, 87.74 ± 3.13 g/d) were selected to identify the key serum metabolites associated with ADG, and to investigate the relationships of serum metabolome profiles with digestive tract microbiota. The results showed that a total of 125 serum metabolites were significantly different between HADG and LADG. Of these, 43 serum metabolites were significantly higher levels in HADG, including D-ornithine, l-glutamine, L-histidine, carnosine, LysoPC (16:1(9Z)/0:0), DCTP and hydroxylysine, while, 82 serum metabolites were significantly higher levels in LADG, including P-salicylic acid and deoxycholic acid 3-glucuronide. Pathway analysis indicated that these different metabolites were mainly involved in amino acid and lipid metabolism. Furthermore, Spearman's rank correlation analysis revealed that these differential serum metabolites were correlated with ADG and ADG-related bacteria. Notably, serum hydroxylysine and L-histidine could be used as biomarkers for distinguishing HADG and LADG goats, with an accuracy of >92.0%. SIGNIFICANCE: Our study confirms that individual microbiota and metabolic differences contribute to the variations of growth rate in young goats. Some serum metabolites may be useful in improving the growth performance of young goats, which provides directions for developing further nutritional regulation in the goat industry to achieve healthy feeding and efficiency enhancement.

Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage

Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed at investigating the difference in the composition and functions of rumen microbiota as well as fermentation metabolites in Holstein cows with high and low milk protein concentrations. In this study, 20 lactating Holstein cows on the same diet were divided into two groups (10 cows each), high degree of milk protein group (HD), and low degree of milk protein (LD) concentrations based on previous milk composition history. Rumen content samples were obtained to explore the rumen fermentation parameters and rumen microbial composition. Shotgun metagenomics sequencing was employed to investigate the rumen microbial composition and sequences were assembled via the metagenomics binning technique. Metagenomics revealed that 6 Archaea genera, 5 Bacteria genera, 7 Eukaryota genera, and 7 virus genera differed significantly between the HD and LD group. The analysis of metagenome-assembled genomes (MAGs) showed that 2 genera (g__Eubacterium_H and g__Dialister) were significantly enriched (P < 0.05, linear discriminant analysis (LDA) > 2) in the HD group. However, the LD group recorded an increased abundance (P < 0.05, LDA > 2) of 8 genera (g__CAG-603, g__UBA2922, g__Ga6A1, g__RUG13091, g__Bradyrhizobium, g__Sediminibacterium, g__UBA6382, and g__Succinivibrio) when compared to the HD group. Furthermore, investigation of the KEGG genes revealed an upregulation in a higher number of genes associated with nitrogen metabolism and lysine biosynthesis pathways in the HD group as compared to the LD group. Therefore, the high milk protein concentration in the HD group could be explained by an increased ammonia synthesis by ruminal microbes which were converted to microbial amino acids and microbial protein (MCP) in presence of an increased energy source made possible by higher activities of carbohydrate-active enzymes (CAZymes). This MCP gets absorbed in the small intestine as amino acids and might be utilized for the synthesis of milk protein. KEY POINTS: • Rumen microbiota and their functions differed between cows with high milk protein % and those with low milk protein %. • The rumen microbiome of cows with high milk protein recorded a higher number of enriched genes linked to the nitrogen metabolism pathway and lysine biosynthesis pathway. • The activities of carbohydrate-active enzymes were found to be higher in the rumen of cows with high milk protein %.

Integrated meta-omics analyses reveal a role of ruminal microorganisms in ketone body accumulation and ketosis in lactating dairy cows

The extent to which a nutrition-related disorder such as ketosis alters the ruminal microbiota or whether microbiota composition is related to ketosis and potential associations with host metabolism is unknown. We aimed to evaluate variations occurring in the ruminal microbiota of ketotic and nonketotic cows in the early postpartum period, and how those changes may affect the risk of developing the disease. Data on milk yield, dry matter intake (DMI), body condition score, and blood β-hydroxybutyrate (BHB) concentrations at 21 d postpartum were used to select 27 cows, which were assigned (n = 9 per group) to a clinical ketotic (CK, 4.10 ± 0.72 mmol BHB/L, DMI 11.61 ± 0.49 kg/d, ruminal pH 7.55 ± 0.07), subclinical ketotic (SK, 1.36 ± 0.12 mmol BHB/L, DMI 15.24 ± 0.34 kg/d, ruminal pH 7.58 ± 0.08), or control (NK, 0.88 ± 0.14 mmol BHB/L, DMI 16.74 ± 0.67/d, ruminal pH 7.61 ± 0.03) group. Cows averaged 3.6 ± 0.5 lactations and a body condition score of 3.11 ± 0.34 at the time of sampling. After blood serum collection for metabolomics analysis (¹H nuclear magnetic resonance spectra), 150 mL of ruminal digesta was collected from each cow using an esophageal tube, paired-end (2 × 300 bp) sequencing of isolated DNA from ruminal digesta was performed via Illumina MiSeq, and sequencing data were analyzed using QIIME2 (v 2020.6) to measure the ruminal microbiota composition and relative abundance. Spearman correlation coefficients were used to evaluate relationships between relative abundance of bacterial genera and concentrations of serum metabolites. There were more than 200 genera, with approximately 30 being significant between NK and CK cows. Succinivibrionaceae UCG 1 taxa decreased in CK compared with NK cows. Christensenellaceae (Spearman correlation coefficient = 0.6), Ruminococcaceae (Spearman correlation coefficient = 0.6), Lachnospiraceae (Spearman correlation coefficient = 0.5), and Prevotellaceae (Spearman correlation coefficient = 0.6) genera were more abundant in the CK group and were highly positively correlated with plasma BHB. Metagenomic analysis indicated a high abundance of predicted functions related to metabolism (37.7%), genetic information processing (33.4%), and Brite hierarchies (16.3%) in the CK group. The 2 most important metabolic pathways for butyrate and propionate production were enriched in CK cows, suggesting increased production of acetyl coenzyme A and butyrate and decreased production of propionate. Overall, the combined data suggested that microbial populations may be related to ketosis by affecting short-chain fatty acid metabolism and BHB accumulation even in cows with adequate feed intake in the early postpartum period.

Plasma and milk metabolomics in lactating sheep divergent for feed efficiency

Enhancing the ability of animals to convert feed into meat or milk by optimizing feed efficiency (FE) has become a priority in livestock research. Although untargeted metabolomics is increasingly used in this field and may improve our understanding of FE, no information in this regard is available in dairy ewes. This study was conducted to (1) discriminate sheep divergent for FE and (2) provide insights into the physiological mechanisms contributing to FE through high-throughput metabolomics. The ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q/TOF-MS) technique was applied to easily accessible animal fluids (plasma and milk) to assess whether their metabolome differs between high- and low-feed efficient lactating ewes (H-FE and L-FE groups, respectively; 8 animals/group). Blood and milk samples were collected on the last day of the 3-wk period used for FE estimation. A total of 793 features were detected in plasma and 334 in milk, with 100 and 38 of them, respectively, showing differences between H-FE and L-FE. The partial least-squares discriminant analysis separated both groups of animals regardless of the type of sample. Plasma allowed the detection of a greater number of differential features; however, results also supported the usefulness of milk, more easily accessible, to discriminate dairy sheep divergent for FE. Regarding pathway analysis, nitrogen metabolism (either anabolism or catabolism) seemed to play a central role in FE, with plasma and milk consistently indicating a great impact of AA metabolism. A potential influence of pathways related to energy/lipid metabolism on FE was also observed. The variable importance in the projection plot revealed 15 differential features in each matrix that contributed the most for the separation in H-FE and L-FE, such as l-proline and phosphatidylcholine 20:4e in plasma or l-pipecolic acid and phosphatidylethanolamine (18:2) in milk. Overall, untargeted metabolomics provided valuable information into metabolic pathways that may underlie FE in dairy ewes, with a special relevance of AA metabolism in determining this complex phenotype in the ovine. Further research is warranted to validate these findings.

Untargeted metabolomics and lipidomics to assess plasma metabolite changes in dairy goats with subclinical hyperketonemia

Subclinical hyperketonemia (SCHK) is the major metabolic disease observed during the transition period in dairy goats, and is characterized by high plasma levels of nonesterified fatty acids (NEFA) and β-hydroxybutyrate (BHB). However, no prior study has comprehensively assessed metabolomic profiles of dairy goats with SCHK. Plasma samples were collected within 1 h after kidding from SCHK goats (BHB concentration >0.8 mM, n = 7) and clinically healthy goats (BHB concentration <0.8 mM, n = 7) with similar body condition score (2.75 ± 0.15, mean ± standard error of the mean) and parity (primiparous). A combination of targeted and untargeted mass spectrometric approaches was employed for analyzing the various changes in the plasma lipidome and metabolome. Statistical analyses were performed using the GraphPad Prism 8.0, SIMCA-P software (version 14.1), and R packages (version 4.1.3). Plasma aminotransferase, nonesterified fatty acids, and BHB concentrations were greater in the SCHK group, but plasma glucose concentrations were lower. A total of 156 metabolites and 466 lipids were identified. The analysis of untargeted metabolomics data by principal component analysis and orthogonal partial least squares discriminant analysis revealed a separation between SCHK and clinically healthy goats. According to the screening criteria (unpaired t-test, P < 0.05), 30 differentially altered metabolites and 115 differentially altered lipids were detected. Pathway enrichment analysis identified citrate cycle, alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine metabolism as significantly altered pathways. A greater concentration of plasma isocitric acid and cis-aconitic acid levels was observed in SCHK goats. In addition, AA such as lysine and isoleucine were greater, whereas alanine and phenylacetylglycine were lower in SCHK dairy goats. Dairy goats with SCHK also exhibited greater oleic acid, acylcarnitine, and phosphatidylcholine and lower choline and sphingomyelins. Acylcarnitines, oleic acid, and tridecanoic acid displayed positive correlations with several lipid species. Alanine, hippuric acid, and histidinyl-phenylalanine were negatively correlated with several lipids. Overall, altered metabolites in SCHK dairy goats indicated a more severe degree of negative energy balance. Data also indicated an imbalance in the tricarboxylic acid (TCA) cycle, lipid metabolism, and AA metabolism. The findings provide a more comprehensive understanding of the pathogenesis of SCHK in dairy goats.

Milk yield variation partially attributed to blood oxygen-mediated neutrophil activation in lactating dairy goats

Blood oxygen is an essential component for numerous biological processes of mammalian animals. Milk production of ruminants largely relies on the supply of nutrients, such as glucose, amino acids and fatty acids. To define the regulatory role of blood oxygen availability in regard to milk production, seventy-five healthy Guanzhong dairy goats with similar body weight, days in milk and parities were selected. For each animal, milk yield was recorded and milk sample was collected to determine compositions. Milk vein blood was collected to determine parameters including blood gas, physio-biochemistry and haematology. Another blood sample was prepared for transcriptome and RT-qPCR. Results showed that both pressure of oxygen (pO₂) in the milk vein (positively) and numbers of neutrophils in mammary vein (negatively) were associated with milk yield of the animals. To learn the role of pO₂ in blood cell functionality, twelve animals (six with higher yield (H-group) and six with lower yield (L-group)) from seventy-five goats were selected. Compared with animals in L-group, goats in H-group were higher in pO₂ but lower in pCO₂, lactate, lactate dehydrogenase activity and neutrophil abundance in milk vein, compared with L-group. The blood transcriptome analysis suggested that compared with L-group, animals in H-group were depressed in functionality including neutrophil activation and metabolic pathways including glycolysis, NF-κB and HIF-1. Our result revealed that lower milk production could be associated with neutrophil activation responding to low pO₂ in the mammary vein. In the meantime, we highlighted the potential importance of blood oxygen as a milk yield regulator.

Characteristics of ruminal microbiota and metabolome in Holstein cows differing in milk protein concentrations

The rumen is a vital organ containing vast amounts of microbes that play a key role in the digestion of nutrients and affect the production performance of ruminants. However, few studies have focused on the characterization of the ruminal microbiota composition and function in cows with long-term difference milk protein concentrations, and the relationship between milk protein concentration and ruminal microbiota remains elusive. In this study, we collected the data of milk protein concentrations of 1,025 Holstein cows for 10 mo on a commercial farm. Based on the milk protein concentrations, 30 cows were selected and divided into three groups (n = 10 per group): low milk protein group (LMP, milk protein concentration < 3.1%), medium milk protein group (MMP, 3.1% ≤ milk protein concentration < 3.4%), and high milk protein group (HMP, milk protein concentration ≥ 3.4%). The ruminal microbiome, metabolome, VFA concentrations and proportions, and amino acid profiles of the three groups were analyzed. The data showed that free amino acid (FAA) levels were lower in the rumen and higher in the plasma of HMP cows (P < 0.05). In addition, lower NH3 concentrations were observed in the rumen, plasma, and milk of the HMP cows (P < 0.05). Protease activity and isobutyric acid molar proportion in the rumen were lower in the HMP group (P < 0.05). Microbiome analysis showed that HMP cows had lower microbial diversity (represented as Shannon and Simpson indices) than LMP cows. At the genus level, lower relative abundances of Prevotella_1 and Ruminococcaceae_UCG_005 were observed in the HMP group (P < 0.05). At the operational taxonomic unit (OTU) level, a lower relative abundance of OTU3 (Prevotella ruminicola) was observed in the HMP group (P < 0.05). We found that the relative abundances of ruminal Prevotella_1 and OTU3 (Prevotella ruminicola) were negatively correlated with milk protein concentration (P < 0.05). These findings suggested that the cows with long-term high milk protein concentrations had lower microbial diversity and weaker protein degradation ability in the rumen. Furthermore, our observations identified a correlation between the milk protein concentration and ruminal microbiota.

Heritable and Nonheritable Rumen Bacteria Are Associated with Different Characters of Lactation Performance of Dairy Cows

Recent studies have reported that some rumen microbes are heritable. However, it is necessary to clarify the functions and specific contributions of the heritable rumen microbes to cattle phenotypes (microbiability) in comparison with those that are nonheritable. This study aimed to identify the distribution and predicted functions of heritable and nonheritable bacterial taxa at species level in the rumen of dairy cows and their respective contributions to energy-corrected milk yield, protein content and yield, and fat content and yield in milk. Thirty-two heritable and 674 nonheritable bacterial taxa were identified at species level, and the functional analysis revealed that predicted microbial functions for both groups were mainly enriched for energy, amino acid, and ribonucleotide metabolism. The mean microbiability (to reflect a single taxon's contribution) of heritable bacteria was found to range from 0.16% to 0.33% for the different milk traits, whereas the range for nonheritable bacteria was 0.03% to 0.06%. These findings suggest a strong contribution by host genetics in shaping the rumen microbiota, which contribute significantly to milk production traits. Therefore, there is an opportunity to further improve milk production traits through attention to host genetics and the interaction with the rumen microbiota. IMPORTANCE Rumen bacteria produce volatile fatty acids which exert a far-reaching influence on hepatic metabolism, mammary gland metabolism, and animal production. In the current study, 32 heritable and 674 nonheritable bacterial taxa at species level were identified, and shown to have different microbiability (overall community contribution) and mean microbiability (the average of a single taxon's contribution) for lactation performance. The predicted functions of heritable and nonheritable bacterial taxa also differed, suggesting that targeted nutritional and genetic breeding approaches could be used to manipulate them to improve dairy cow performance.

The physiological dissimilarities of Holstein dairy cows with different milk yields

BACKGROUND

Even if breed, parity, dietary and environmental management are same, dairy cows still have notable differences in milk yield that may be underpinned by physiologic differences.

OBJECTIVES

This study aimed to investigate the physiological dissimilarities of dairy cows with different milk yields.

METHODS

Thirty cows were sorted into high milk-yielding cows (group H: 58.93±2.31 kg/day), moderate milk-yielding cows (group M: 44.99±0.54 kg/day), and low milk-yielding cows (group L: 24.99±6.83 kg/day) according to milk yield. Blood was collected and serum parameters were assessed. Rumen fluid was collected for the evaluation of rumen fermentation parameters (RFPs) and bacterial community composition (BCC).

RESULTS

Serum prolactin, growth hormone, glutathione peroxidase, immunoglobulin A and non-esterified fatty acid had a significantly positive correlation with milk yield (p < 0.05), whereas serum glucagon and total antioxidant capacity had a significantly negative correlation with milk yield (p < 0.05). The concentration of valeric acid and the ratio of acetic acid to propionic acid in the rumen fluid in group H was significantly lower than that in group L (p < 0.05). The concentration of acetic acid and butyric acid in group H was significantly lower than that in groups M and L (p < 0.05). The relative abundances of Ruminococcaceae_NK4A214_group, Prevotella_1, Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group, Muribaculaceae, and Ruminococcus_2 were negatively correlated with milk yield, whereas the relative abundance of Succinivibrionaceae_UCG-001, Lachnospiraceae_NK3A20_group, Shuttleworthia and Dialister were positively correlated with milk yield (p < 0.05).

CONCLUSIONS

This study indicates that dairy cows with different milk yields have clear divergence in serum indicators, RFPs, BCC and rumen microbial metabolism.

Identification of Potential Biomarkers and Metabolic Pathways of Different Levels of Heat Stress in Beef Calves

Heat stress (HS) damages the global beef industry by reducing growth performance causing high economic losses each year. However, understanding the physiological mechanisms of HS in Hanwoo calves remains elusive. The objective of this study was to identify the potential biomarkers and metabolic pathways involving different levels of heat stress in Hanwoo calves. Data were collected from sixteen Hanwoo bull calves (169.6 ± 4.6 days old, BW of 136.9 ± 6.2 kg), which were maintained at four designated ranges of HS according to the temperature−humidity index (THI) including: threshold (22 to 24 °C, 60%; THI = 70 to 73), mild (26 to 28 °C, 60%; THI = 74 to 76), moderate (29 to 31 °C, 80%; THI = 81 to 83), and severe (32 to 34 °C, 80%; THI = 89 to 91) using climate-controlled chambers. Blood was collected once every three days to analyze metabolomics. Metabolic changes in the serum of calves were measured using GC-TOF-MS, and the obtained data were calculated by multivariate statistical analysis. Five metabolic parameters were upregulated and seven metabolic parameters were downregulated in the high THI level compared with the threshold (p < 0.05). Among the parameters, carbohydrates (ribose, myo-inositol, galactose, and lactose), organic compounds (acetic acid, urea, and butenedioic acid), fatty acid (oleic acid), and amino acids (asparagine and lysine) were remarkably influenced by HS. These novel findings support further in-depth research to elucidate the blood-based changes in metabolic pathways in heat-stressed Hanwoo beef calves at different levels of THI. In conclusion, these results indicate that metabolic parameters may act as biomarkers to explain the HS effects in Hanwoo calves.

Multi-tissue metabolomic profiling reveals potential mechanisms of cocoon yield in silkworms (Bombyx mori) fed formula feed versus mulberry leaves

Use of formula feed (FF) for silkworms for all instars, has promoted transformation and progress in traditional sericulture. However, the cocoon yield of FF silkworms has failed to reach that of silkworms fed mulberry leaves (ML). The biological mechanisms underlying this phenomenon have not been well described. This study aimed to identify metabolic mechanisms and potential biomarkers relating to the poor cocoon yield of FF silkworms. In this study, silkworms received treatments of either ML (ML group) or FF (FF group) for all instars. At the 3rd day of the 5th instar, the midgut (MG), hemolymph (HL) and posterior silk gland (PSG) were collected for the metabolome profiles detection. The remaining silkworms were fed ML or FF until cocooning for investigation. The whole cocoon yield (WCY) was significantly higher in the FF group than the ML group (p < 0.05), whereas the cocoon shell weight (CSW) and cocoon shell rate (CSR) were significantly lower in the FF group (p < 0.05). A total of 845, 867 and 831 metabolites were qualified and quantified in the MG, HL and PSG of the FF silkworms, respectively. Correspondingly, 789, 833 and 730 metabolites were quantified in above three tissues of the ML group. Further, 230, 249 and 304 significantly different metabolites (SDMs) were identified in the MG, HL and PSG between the FF and ML group, respectively. Eleven metabolic pathways enriched by the SDMs were mutual among the three tissues. Among them, cysteine and methionine metabolism, arginine biosynthesis, and arginine and proline metabolism were the top three pathways with the highest impact value in the PSG. Six biomarkers were obtained through biomarker analysis and Pearson correlation calculation. Among them, homocitrulline, glycitein, valyl-threonine, propyl gallate and 3-amino-2,3-dihydrobenzoic acid were positively correlated with WCY, but negatively correlated with CSW and CSR (p < 0.05). An opposite correlation pattern was observed between 3-dimethylallyl-4-hydroxyphenylpyruvate and the three cocoon performance traits. Overall, three key metabolic pathways and six biomarkers associated with cocoon yield were interpreted, and should provide directions for formula feed optimization in factory-raised silkworms.

Effects of Heavy Metal Exposure from Leather Processing Plants on Serum Oxidative Stress and the Milk Fatty Acid Composition of Dairy Cows: A Preliminary Study

This study investigated whether unsaturated fatty acids in milk and the oxidative status of cows are affected by heavy metal exposure due to leather processing. The blood lead (Pb) concentrations in cows from two farms in the polluted area were 16.27 ± 8.63 μg/L, respectively, which were significantly (p < 0.05) higher than the blood Pb concentrations in cows from an unpolluted farm (6.25 ± 3.04 μg/L). There were significantly (p < 0.05) lower levels of glutathione S-transferase (GST), glutathione peroxidase (GPX), and glutathione (GSH) in the serum of cows from the polluted area compared to the levels in cows from an unpolluted area. The linoleic acid (C18:2n6c) content in milk from the polluted area was 15% lower than in the control area. There was a significant correlation between linoleic acid in milk with the blood Pb and serum GSH levels. Heavy metals can alter fatty acid synthesis through oxidative stress, which may be the mechanism by which heavy metals affect fatty acid synthesis in milk.

Metagenomic and Metabolomic Insights Into the Mechanism Underlying the Disparity in Milk Yield of Holstein Cows

This study was conducted to investigate the metabolic mechanism underlying the disparity in the milk yield of Holstein cows. Eighteen lactating Holstein cows in their second parity and 56 (±14.81 SD) days in milking (DIM) were selected from 94 cows. Based on the milk yield of the cows, they were divided into two groups of nine cows each, the high milk yield group (HP) (44.57 ± 2.11 kg/day) and the low milk yield group (LP) (26.71 ± 0.70 kg/day). The experimental cows were fed the same diet and kept under the same management system for more than 60 days. Rumen metagenomics revealed that two Archaea genera, one Bacteria genus, eight Eukaryota genera, and two Virus genera differ between the HP and LP groups. The analysis of metabolites in the rumen fluid, milk, and serum showed that several metabolites differed between the HP and LP groups. Correlation analysis between the predominant microbiota and milk yield-associated metabolites (MP-metabolites) revealed that four Bacteria and two Eukaryota genera have a positive relationship with MP-metabolites. Pathway enrichment analysis of the differential metabolites revealed that five pathways were enriched in all the samples (two pathways in the milk, two pathways in the serum, and one pathway in the rumen fluid). Further investigation revealed that the low milk yield observed in the LP group might be due to an upregulation in dopamine levels in the rumen fluid and milk, which could inhibit the release of prolactin or suppress the action of oxytocin in the udder resulting in reduced milk yield. On the other hand, the high milk yield in the HP group is attributed to an upregulation in citrulline, and N-acetylornithine, which could be used as substrates for energy metabolism in the citric acid cycle and ultimately gluconeogenesis.

Ruminal bacterial community is associated with the variations of total milk solid content in Holstein lactating cows

Total milk solid (TMS) content directly reflects the quality of milk. Rumen bacteria ferment dietary components, the process of which generates the precursors for the synthesis of milk solid, therefore, the variation in rumen bacterial community could be associated with milk solid in dairy cows. In this study, 45 healthy mid-lactation Holstein dairy cows with the similar body weight, lactation stage, and milk yield were initially used for the selection of 10 cows with high TMS (HS) and 10 cows with low TMS (LS). All those animals were under the same feeding management, and the individual milk yield was recorded for 14 consecutive days before milk and rumen fluid were sampled. Rumen fluid was used to determine bacterial community by 16S rRNA gene sequencing technique. The HS cows had significantly greater feed intake and milk TMS, fat, protein content than LS cows (P < 0.05). Among the volatile fatty acids (VFA), propionic acid and valeric acid concentrations were significantly greater in HS cows than those in LS cows (P < 0.05). There was no significant difference in the concentrations of acetate, butyrate, isobutyrate, valerate, and the total VFA (P > 0.05), nor was the acetate-to-propionate ratio, pH value, ammonia nitrogen and microbial crude protein concentrations (P > 0.05). Significant differences in the relative abundances of some bacterial genera were found between HS and LS cows. Spearman’s rank correlation analysis revealed that TMS content was correlated positively with the abundances of Ruminococcaceae UCG-014, Ruminococcaceae NK4A214 group, Prevotellaceae UCG-001, Butyrivibrio 2, Prevotellaceae UCG-003, Candidatus Saccharimonas, Ruminococcus 2, Lachnospiraceae XPB1014 group, probable genus 10, Eubacterium ventriosum group, but negatively correlated with Pyramidobacte. In addition, Ruminococcaceae UCG-014, Ruminococcus 2, Ruminococcaceae UCG001, probable genus 10 and Eubacterium ventriosum group might boost the total VFA production in the rumen. In conclusion, the dry matter intake of dairy cows and some special bacteria in rumen were significantly associated with TMS content, which suggests the potential function of rumen bacteria contributing to TMS content in dairy cows.

Heat Stress Induces Shifts in the Rumen Bacteria and Metabolome of Buffalo

Exposure to the stress (HS) negatively affects physiology, performance, reproduction and welfare of buffalo. However, the mechanisms by which HS negatively affects rumen bacteria and its associated metabolism in buffalo are not well known yet. This study aimed to gain insight into the adaption of bacteria and the complexity of the metabolome in the rumen of six buffalo during HS using 16S rDNA and gas chromatography metabolomics analyses. HS increased respiratory rate (p < 0.05) and skin temperature (p < 0.01), and it decreased the content of acetic acid (p < 0.05) and butyric acid (p < 0.05) in the rumen. Omics sequencing revealed that the relative abundances of Lachnospirales, Lachnospiraceae, Lachnospiraceae_NK3A20_group and Clostridia_UCG-014 were significantly (p < 0.01) higher under HS than non-heat stress conditions. Several bacteria at different levels, such as Lactobacillales, Streptococcus, Leuconostocaceae and Leissella, were significantly (p < 0.05) more abundant in the rumen of the non-heat stress than HS condition. Thirty-two significantly different metabolites closely related to HS were identified (p < 0.05). Metabolic pathway analysis revealed four key pathways: D-Alanine metabolism; Lysine degradation, Tropane; piperidine and pyridine alkaloid biosynthesis; and Galactose metabolism. In summary, HS may negatively affected rumen fermentation efficiency and changed the composition of rumen community and metabolic function.

N-Carbamoylglutamate Supplementation on the Digestibility, Rumen Fermentation, Milk Quality, Antioxidant Parameters, and Metabolites of Jersey Cattle in High-Altitude Areas

This study aimed to assess the impact of the dietary supplementation of N-carbamoylglutamate (NCG) on nutrient digestibility, rumen fermentation, milk quality, oxidative stress, and metabolites in the plasma and feces of Jersey cattle under high altitude with the hypoxic condition. A total of 14 healthy lactating Jersey dairy cows with similar body conditions were selected and randomly divided into 2 groups. The control group (CON group, N = 6 replicates) was fed with a conventional complete diet, whereas the experimental group (NCG group, N = 8 replicates) received 20 g/d per head NCG supplementation. The experiment lasted for 60 days, the adaptation period was 12 days, and the formal experiment period was 48 days. Except that the NCG group showed an upward trend in dry matter intake (DMI) (p = 0.09) and the fermentation parameters, the molar proportion of butyric acid tended to decrease (p = 0.08); the two groups had no significant differences (p > 0.05) in nutrients digestibility, plasma immunity, and antioxidant ability. However, compared with the CON group, the milk fat rate and blood oxygen saturation of the NCG group showed an upward trend (p = 0.09). For indexes associated with altitude stress, the contents of thyroxine, transferrin, and endothelin both decreased significantly (p < 0.05) in the NCG group. Meanwhile, heat shock protein (p = 0.07) and aldosterone (p = 0.06) also showed a downward trend. A total of 114 different metabolites were identified from feces and plasma, 42 metabolites were derived from plasma that mainly included 5 kinds of Super Class, and 72 metabolites were derived from feces that mainly included 9 kinds of Super Class. The significantly increased plasma differential metabolites were 2,5-dihydroxybenzoate and salicyluric acid, and the significantly increased fecal differential metabolites were Butenafine (fold change > 2). Pathway analysis showed that after applying NCG as a feed additive, the changes of the Jersey dairy cows mainly focused on amino acid metabolism and lipid metabolism. These results indicated that adding NCG to the diet can prevent the hypoxic stress state of lactating Jersey cows in high-altitude areas and has a tendency to improve milk quality.

Nutritional Modulation, Gut, and Omics Crosstalk in Ruminants

Simple Summary

Over the last decade, animal nutrition science has been significantly developed, supported by the great advancements in molecular technologies. For scientists, the present "feedomics and nutrigenomics" era continues to evolve and shape how research is designed, performed, and understood. The new omics interpretations have established a new point of view for the nutrition–gene interaction, integrating more comprehensive findings from animal physiology, molecular genetics, and biochemistry. In the ruminant model, this modern approach addresses rumen microbes as a critical intermediate that can deepen the studies of diet–gut interaction with host genomics. The present review discusses nutrigenomics’ and feedomics’ potential contribution to diminishing the knowledge gap about the DNA cellular activities of different nutrients. It also presents how nutritional management can influence the epigenetic pathway, considering the production type, life stage, and species for more sustainable ruminant nutrition strategies.

Abstract

Ruminant nutrition has significantly revolutionized a new and prodigious molecular approach in livestock sciences over the last decade. Wide-spectrum advances in DNA and RNA technologies and analysis have produced a wealth of data that have shifted the research threshold scheme to a more affluent level. Recently, the published literature has pointed out the nutrient roles in different cellular genomic alterations among different ruminant species, besides the interactions with other factors, such as age, type, and breed. Additionally, it has addressed rumen microbes within the gut health and productivity context, which has made interpreting homogenous evidence more complicated. As a more systematic approach, nutrigenomics can identify how genomics interacts with nutrition and other variables linked to animal performance. Such findings should contribute to crystallizing powerful interpretations correlating feeding management with ruminant production and health through genomics. This review will present a road-mapping discussion of promising trends in ruminant nutrigenomics as a reference for phenotype expression through multi-level omics changes.

Contribution of Ruminal Bacteriome to the Individual Variation of Nitrogen Utilization Efficiency of Dairy Cows

High nitrogen utilization efficiency (NUE) is important for increasing milk protein production and decreasing the feed nitrogen cost and nitrogen emission to the environment. Currently, there is a limited whole picture of the relationship between ruminal bacteriome and the NUE of dairy cows, even though some information has been revealed about the bacteriome and milk or milk protein production of dairy cows. The purpose of this study was to compare the rumen bacterial community in dairy cows with different nitrogen utilization efficiency under the same diet. The natural abundance of 15N between the animal proteins and diet (Δ15N) was used as a simple, non-invasive, and accurate biomarker for NUE in ruminants to mark the individual variation. Dairy cows with high NUE (HE_HP, n = 7), medium NUE (ME_MP, n = 7), and low NUE (LE_LP, n = 7) were selected from 284 Holstein dairy cows with the same diet. Measurement of the rumen fermentation indices showed that the proportion of propionate was higher in HE_HP cows and ME_MP cows than in LE_LP cows (P < 0.05). The diversity of rumen bacterial community was higher in LE_LP cows than in ME_MP cows and HE_HP cows by 16S rRNA sequencing analysis (P < 0.05). Moreover, at the genus level, the relative abundances of Succinivibrionaceae_UCG_001, uncultured_Selenomonadaceae, and Acidaminococcus were higher in HE_HP cows than in LE_LP cows (P < 0.05). Interestingly, we found that these bacteria were positively correlated with milk protein yield and negatively correlated with Δ15N (P < 0.05). However, Clostridia_UCG_014, Saccharofermentans, Bacilli_RF39, and Desulfovibrio were lower in HE_HP cows and ME_MP cows than in LE_LP cows (P < 0.05), which were negatively correlated with milk protein yield and positively correlated with Δ15N (P < 0.05). In conclusion, the study showed that the diversity and relative abundances of rumen bacteria differed among different NUE cows, indicating that rumen bacteriome contributes to nitrogen metabolism in dairy cows.

Comparative metabolomics analysis of milk components between Italian Mediterranean buffaloes and Chinese Holstein cows based on LC-MS/MS technology

Buffalo and cow milk have a very different composition in terms of fat, protein, and total solids. For a better knowledge of such a difference, the milk metabolic profiles and characteristics of metabolites was investigated in Italian Mediterranean buffaloes and Chinese Holstein cows were investigated by liquid chromatography tandem-mass spectrometry (LC-MS/MS) in this study. Totally, 23 differential metabolites were identified to be significantly different in the milk from the two species of which 15 were up-regulated and 8 down-regulated in Italian Mediterranean buffaloes. Metabolic pathway analysis revealed that 4 metabolites (choline, acetylcholine, nicotinamide and uric acid) were significantly enriched in glycerophospholipid metabolism, nicotinate and nicotinamide metabolism, glycine, serine and threonine metabolism, as well as purine metabolism. The results provided further insights for a deep understanding of the potential metabolic mechanisms responsible for the different performance of Italian Mediterranean buffaloes' and Chinese Holstein cows' milk. The findings will offer new tools for the improvement and novel directions for the development of dairy industry.

Metabolic Profiling Analysis of Liver in Landes Geese During the Formation of Fatty Liver via GC-TOF/MS

Fatty liver production results from the process of overfeeding geese, inducing a dramatic increase in de novo liver lipogenesis. To investigate the alteration of liver metabolites by overfeeding, especially lipid metabolites, and the potential pathways causing these changes, 60 Landes geese at 65 days old were raised in three groups with 20 geese per group, namely, the D0 group (free from gavage), D7 group (overfeeding for 7 days), and D25 group (overfeeding for 25 days). At 90 days old, segments of liver tissue were collected from 10 geese of each group for gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) analysis. A large number of endogenous molecules in the livers of geese were altered dramatically by overfeeding. In the livers of overfed geese, the level of oleic acid was observed to continuously increase, while the levels of phenylalanine, methyl phosphate, sulfuric acid, and 3-hydroxybenzaldehyde were decreased. The most significantly different metabolites were enriched in amino acid, lipid, and nucleotide metabolism pathways. The present study further supports the idea that Landes geese efficiently produce fatty liver, and potential biomarkers and disturbed metabolic pathways during the process of forming fatty liver were identified. In conclusion, this study might provide some insights into the underlying mechanisms of fatty liver formation.

Supplementing N-carbamoylglutamate in late gestation increases newborn calf weight by enhanced placental expression of mTOR and angiogenesis factor genes in dairy cows

The objective of this study was to investigate whether supplementation with N-carbamoylglutamate (NCG) to cows during late gestation alters uteroplacental tissue nutrient transporters, calf metabolism and newborn weight. Thirty multiparous Chinese Holstein cows were used in a randomized complete block design experiment. During the last 28 d of pregnancy, cows were fed a diet without (CON) or with NCG (20 g/d per cow). The body weight of calves was weighed immediately after birth. Placentome samples were collected at parturition and used to assess mRNA expression of genes involved in transport of arginine, glucose, fatty acid and angiogenesis factors, as well as the mammalian target of rapamycin (mTOR) pathway. Blood samples of calves before colostrum consumption were also collected for the detection of plasma parameters, amino acids (AA) and metabolomics analysis. The newborn weight (P = 0.02) and plasma Arg concentration of NCG-calves was significantly higher (P = 0.05) than that of CON-calves, and the plasma concentrations of urea nitrogen tended to be lower (P = 0.10) in the NCG group. The mRNA abundance of genes involved in glucose transport (solute carrier family 2 member 3 [SLC2A3], P < 0.01), angiogenesis (nitric oxide synthase 3 [NOS3], P = 0.02), and mTOR pathway (serine/threonine-protein kinase 1 [AKT1], P = 0.10; eukaryotic translation initiation factor 4B pseudogene 1 [EIF4BP1], P = 0.08; EIF4EBP2, P = 0.04; and E74-like factor 2 [ELF2], P = 0.03) was upregulated in the placentome of NCG-supplemented cows. In addition, 17 metabolites were significantly different in the placentome of NCG-supplemented cows compared to non-supplemented cows, and these metabolites are mainly involved in arginine and proline metabolism, alanine, aspartate and glutamate metabolism, and citrate cycle. In summary, the increased body weight of newborn calves from the NCG supplemented dairy cows may be attributed to the increased angiogenesis and uteroplacental nutrient transport and to the activated mTOR signal pathway, which may result in the increased nutrient supply to the fetus, and improved AA metabolism and urea cycle of the fetus.

Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle

Metabolomics has been applied to measure the dynamic metabolic responses, to understand the systematic biological networks, to reveal the potential genetic architecture, etc., for human diseases and livestock traits. For example, the current published results include the detected relevant candidate metabolites, identified metabolic pathways, potential systematic networks, etc., for different cattle traits that can be applied for further metabolomic and integrated omics studies. Therefore, summarizing the applications of metabolomics for economic traits is required in cattle. We here provide a comprehensive review about metabolomic analysis and its integration with other omics in five aspects: (1) characterization of the metabolomic profile of cattle; (2) metabolomic applications in cattle; (3) integrated metabolomic analysis with other omics; (4) methods and tools in metabolomic analysis; and (5) further potentialities. The review aims to investigate the existing metabolomic studies by highlighting the results in cattle, integrated with other omics studies, to understand the metabolic mechanisms underlying the economic traits and to provide useful information for further research and practical breeding programs in cattle.

Characterization of Short-Term Heat Stress in Holstein Dairy Cows Using Altered Indicators of Metabolomics, Blood Parameters, Milk MicroRNA-216 and Characteristics

Simple Summary

In this study, we characterize the influence of short-term (4 days) heat stress on Holstein cows during early lactation. The use of indicators, such as production performance, physiological variables, blood parameters, micro-RNA expression, and metabolomes, in heat-stressed cows during early lactation—which is a high-stress phase—may provide insights into how to deal with the level of damage to dairy cows, through appropriate nutritional and management strategies. We identify that short-term heat stress has a negative effect, to some extent, on feed and water intake, rectal temperature, heart rate, blood hematology and metabolites, milk characteristics, miRNA expression in milk, and metabolomics in blood.

Abstract

This study aims to characterize the influence of short-term heat stress (HS; 4 day) in early lactating Holstein dairy cows, in terms of triggering blood metabolomics and parameters, milk yield and composition, and milk microRNA expression. Eight cows (milk yield = 30 ± 1.5 kg/day, parity = 1.09 ± 0.05) were homogeneously housed in environmentally controlled chambers, assigned into two groups with respect to the temperature humidity index (THI) at two distinct levels: approximately ~71 (low-temperature, low-humidity; LTLH) and ~86 (high-temperature, high-humidity; HTHH). Average feed intake (FI) dropped about 10 kg in the HTHH group, compared with the LTLH group (p = 0.001), whereas water intake was only numerically higher (p = 0.183) in the HTHH group than in the LTLH group. Physiological parameters, including rectal temperature (p = 0.001) and heart rate (p = 0.038), were significantly higher in the HTHH group than in the LTLH group. Plasma cortisol and haptoglobin were higher (p < 0.05) in the HTHH group, compared to the LTLH group. Milk yield, milk fat yield, 3.5% fat-corrected milk (FCM), and energy-corrected milk (ECM) were lower (p < 0.05) in the HTHH group than in the LTLH group. Higher relative expression of milk miRNA-216 was observed in the HTHH group (p < 0.05). Valine, isoleucine, methionine, phenylalanine, tyrosine, tryptophan, lactic acid, 3-phenylpropionic acid, 1,5-anhydro-D-sorbitol, myo-inositol, and urea were decreased (p < 0.05). These results suggest that early lactating cows are more vulnerable to short-term (4 day) high THI levels—that is, HTHH conditions—compared with LTLH, considering the enormous negative effects observed in measured blood metabolomics and parameters, milk yield and compositions, and milk miRNA-216 expression.

Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits

BACKGROUND

Antimicrobial resistance is one of the most urgent threat to global public health, as it can lead to high morbidity, mortality, and medical costs for humans and livestock animals. In ruminants, the rumen microbiome carries a large number of antimicrobial resistance genes (ARGs), which could disseminate to the environment through saliva, or through the flow of rumen microbial biomass to the hindgut and released through feces. The occurrence and distribution of ARGs in rumen microbes has been reported, revealing the effects of external stimuli (e.g., antimicrobial administrations and diet ingredients) on the antimicrobial resistance in the rumen. However, the host effect on the ruminal resistome and their interactions remain largely unknown. Here, we investigated the ruminal resistome and its relationship with host feed intake and milk protein yield using metagenomic sequencing.

RESULTS

The ruminal resistome conferred resistance to 26 classes of antimicrobials, with genes encoding resistance to tetracycline being the most predominant. The ARG-containing contigs were assigned to bacterial taxonomy, and the majority of highly abundant bacterial genera were resistant to at least one antimicrobial, while the abundances of ARG-containing bacterial genera showed distinct variations. Although the ruminal resistome is not co-varied with host feed intake, it could be potentially linked to milk protein yield in dairy cows. Results showed that host feed intake did not affect the alpha or beta diversity of the ruminal resistome or the abundances of ARGs, while the Shannon index (R² = 0.63, P < 0.01) and richness (R² = 0.67, P < 0.01) of the ruminal resistome were highly correlated with milk protein yield. A total of 128 significantly different ARGs (FDR < 0.05) were identified in the high- and low-milk protein yield dairy cows. We found four ruminal resistotypes that are driven by specific ARGs and associated with milk protein yield. Particularly, cows with low milk protein yield are classified into the same ruminal resistotype and featured by high-abundance ARGs, including mfd and sav1866.

CONCLUSIONS

The current study uncovered the prevalence of ARGs in the rumen of a cohort of lactating dairy cows. The ruminal resistome is not co-varied with host feed intake, while it could be potentially linked to milk protein yield in dairy cows. Our results provide fundamental knowledge on the prevalence, mechanisms and impact factors of antimicrobial resistance in dairy cattle and are important for both the dairy industry and other food animal antimicrobial resistance control strategies.

The use of metabolomics to reveal differences in functional substances of milk whey of dairy buffaloes raised at different altitudes

Buffalo milk is nutrient-rich and contains less cholesterol than cow milk. Dairy buffaloes are widely distributed at different altitudes in the Yunnan Province, China; however, the impacts of altitude on the whey-derived functional metabolites of buffalo milk whey are not well understood. Here, we used non-targeted and targeted metabolomics to evaluate the differential metabolites in the milk whey of buffaloes raised at low altitudes (LA), medium altitudes (MA), and high altitudes (HA). ANOVA statistical test was performed to acquire differential metabolites using IBM SPSS statistics 22 software. The results showed that LA- and MA-milk whey had higher levels of amino acids (glutamine and pyroglutamic acid) and vitamin B6 than HA-milk whey. LA-milk whey had higher levels of the carbohydrates involved in galactose, amino sugar, and nucleotide sugar metabolism than MA- and HA-milk whey, but HA-milk whey showed significantly higher levels of free fatty acids. In conclusion, owing to the biological functions of their most abundant components, LA-milk is more suitable for the production of functional milk with high levels of amino acids, vitamin B6, and carbohydrates; while HA-milk is suitable as raw milk for the production of dairy products with high free fatty acid content.

A Serum Metabolic Profiling Analysis During the Formation of Fatty Liver in Landes Geese via GC-TOF/MS

During the process of fatty liver production by overfeeding, the levels of endogenous metabolites in the serum of geese would change dramatically. This study investigated the effects of overfeeding on serum metabolism of Landes geese and the underlying mechanisms using a metabolomics approach. Sixty Landes geese of the same age were randomly divided into the following three groups with 20 replicates in each group: D0 group (free from gavage); D7 group (overfeeding for 7 days); D25 group (overfeeding for 25 days). At the end of the experiment, 10 geese of similar weight from each group were selected for slaughter and sampling. The results showed that overfeeding significantly increased the body weight and the liver weight of geese. Serum enzymatic activities and serum lipid levels were significantly enhanced following overfeeding. Gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) was employed to explore the serum metabolic patterns, and to identify potential contributors to the formation of fatty liver and the correlated metabolic pathways. Relative to overfeeding for 7 days, a large number of endogenous molecules in serum of geese overfed for 25 days were altered. Continuous elevated levels of pyruvic acid, alanine, proline and beta-glycerophosphoric acid and reduced lactic acid level were observed in the serum of overfed geese. Pathway exploration found that the most of significantly different metabolites were involved in amino acids, carbohydrate and lipid metabolism. The present study exhibited the efficient capability of Landes geese to produce fatty liver, identified potential biomarkers and disturbed metabolic pathways in liver steatosis. These findings might reveal the underlying mechanisms of fatty liver formation and provide some theoretical basis for the diagnosis and treatment of liver diseases.

Rumen and Serum Metabolomes in Response to Endophyte-Infected Tall Fescue Seed and Isoflavone Supplementation in Beef Steers

Fescue toxicosis impacts beef cattle production via reductions in weight gain and muscle development. Isoflavone supplementation has displayed potential for mitigating these effects. The objective of the current study was to evaluate isoflavone supplementation with fescue seed consumption on rumen and serum metabolomes. Angus steers (n = 36) were allocated randomly in a 2 × 2 factorial arrangement of treatments including endophyte-infected (E+) or endophyte-free (E−) tall fescue seed, with (P+) or without (P−) isoflavones. Steers were provided a basal diet with fescue seed for 21 days, while isoflavones were orally administered daily. Following the trial, blood and rumen fluid were collected for metabolite analysis. Metabolites were extracted and then analyzed by UPLC-MS. The MAVEN program was implemented to identify metabolites for MetaboAnalyst 4.0 and SAS 9.4 statistical analysis. Seven differentially abundant metabolites were identified in serum by isoflavone treatment, and eleven metabolites in the rumen due to seed type (p < 0.05). Pathways affected by treatments were related to amino acid and nucleic acid metabolism in both rumen fluid and serum (p < 0.05). Therefore, metabolism was altered by fescue seed in the rumen; however, isoflavones altered metabolism systemically to potentially mitigate detrimental effects of seed and improve animal performance.

Inhibition of enteric methanogenesis in dairy cows induces changes in plasma metabolome highlighting metabolic shifts and potential markers of emission

There is scarce information on whether inhibition of rumen methanogenesis induces metabolic changes on the host ruminant. Understanding these possible changes is important for the acceptance of methane-reducing practices by producers. In this study we explored the changes in plasma profiles associated with the reduction of methane emissions. Plasma samples were collected from lactating primiparous Holstein cows fed the same diet with (Treated, n = 12) or without (Control, n = 13) an anti-methanogenic feed additive for six weeks. Daily methane emissions (CH₄, g/d) were reduced by 23% in the Treated group with no changes in milk production, feed intake, body weight, and biochemical indicators of health status. Plasma metabolome analyses were performed using untargeted [nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC–MS)] and targeted (LC–MS/MS) approaches. We identified 48 discriminant metabolites. Some metabolites mainly of microbial origin such as dimethylsulfone, formic acid and metabolites containing methylated groups like stachydrine, can be related to rumen methanogenesis and can potentially be used as markers. The other discriminant metabolites are produced by the host or have a mixed microbial-host origin. These metabolites, which increased in treated cows, belong to general pathways of amino acids and energy metabolism suggesting a systemic non-negative effect on the animal.

Metabolomics and gene expressions revealed the metabolic changes of lipid and amino acids and the related energetic mechanism in response to ovary development of Chinese sturgeon (Acipenser sinensis)

Captive breeding has been explored in Chinese sturgeon (Acipenser sinensis) for species protection. However, gonad development from stage II to IV of cultured female broodstocks is a handicap. This study aimed to explore the physiological and metabolic changes during the ovary development from stage II to IV of female Chinese sturgeon and the related energy regulatory mechanism, which may be helpful to address the developmental obstacle. The results showed that the oocyte volume increased and the muscle lipid content decreased with the ovary development. Ovarian RNA levels of most genes related to lipid and amino acid metabolism were higher in stage II and III than in stage IV. Serum contents of differential metabolites in arginine, cysteine, methionine, purine, tyrosine, lysine, valine, leucine and isoleucine metabolism pathways peaked at stage III, while the contents of sarcosine, alanine and histidine, as well as most oxylipins derived from fatty acids peaked at stage IV. These results indicated the more active amino acids, lipid metabolism, and energy dynamics of fish body in response to the high energy input of ovary developing from stage II to III, and the importance of alanine, histidine, taurine, folate and oxylipins for fish with ovary at stage IV.

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

BACKGROUND

Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and management condition, a potential new trait that can be used to increase high-quality milk production. It is unknown to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to MPY. Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels.

RESULTS

Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis. In addition, the rumen microbiome of high-MPY cows had lower relative abundances of organisms with methanogen and methanogenesis functions, suggesting that these cows may produce less methane. Metabolomics analysis revealed that the relative concentrations of rumen microbial metabolites (mainly amino acids, carboxylic acids, and fatty acids) and the absolute concentrations of volatile fatty acids were higher in the high-MPY cows. By associating the rumen microbiome with the rumen metabolome, we found that specific microbial taxa (mainly Prevotella species) were positively correlated with ruminal microbial metabolites, including the amino acids and carbohydrates involved in glutathione, phenylalanine, starch, sucrose, and galactose metabolism. To detect the interactions between the rumen microbiome and host metabolism, we associated the rumen microbiome with the host serum metabolome and found that Prevotella species may affect the host's metabolism of amino acids (including glycine, serine, threonine, alanine, aspartate, glutamate, cysteine, and methionine). Further analysis using the linear mixed effect model estimated contributions to the variation in MPY based on different omics and revealed that the rumen microbial composition, functions, and metabolites, and the serum metabolites contributed 17.81, 21.56, 29.76, and 26.78%, respectively, to the host MPY.

CONCLUSIONS

These findings provide a fundamental understanding of how the microbiome-dependent and host-dependent mechanisms contribute to varied individualized performance in the milk production quality of dairy cows under the same management condition. This fundamental information is vital for the development of potential manipulation strategies to improve milk quality and production through precision feeding. Video Abstract.

Analysis of Astragalus Polysaccharide Intervention in Heat-Stressed Dairy Cows' Serum Metabolomics

This experiment was conducted to investigate the effects of astragalus polysaccharides (APS) on serum metabolism of dairy cows under heat stress. Thirty healthy Holstein dairy cows were randomly divided into three groups (10 cows in each group). In the experimental group, 30 mL/d (Treatment I) and 50 mL/d (Treatment II) of APS injection were injected into the neck muscle respectively. Each stage was injected with APS for 4 days (8:00 a.m. every day) and stopped for 3 days. Serum hormone and antioxidant indexes of dairy cows were investigated. Through repeated measurement analysis of variance, the results have shown that cortisol (COR) (F = 6.982, p = 0.026), triiodothyronine (T3) (F = 10.005, p = 0.012) and thyroxine (T4) (F = 22.530, p = 0.002) at different time points were significantly different. COR showed a downward trend, T3 and T4 showed an upward trend. At each time point, different concentrations of APS have significant effects on COR (F = 30.298, p = 0.000 < 0.05), T3 (F = 18.122, p = 0.001), and T4 (F = 44.067, p = 0.000 < 0.05). However, there were no significant differences in serum insulin (INS), glucagon (GC) and heat shock protein 70 (HSP70) between different time points (p > 0.05) and at each time point (p > 0.05). Additionally, the results have also shown that there were also no significant differences in serum Superoxide dismutase (SOD), malondialdehyde (MDA) and lactate dehydrogenase (LDH) between different time points (p > 0.05) and at each time point (p > 0.05). However, the injection of APS had a significant impact on glutathione peroxidase (GSH-Px) (F = 9.421, p = 0.014) at different times, and showed a trend of rising first and then falling. At each time point, APS of different concentrations had no significant effect on GSH-Px (p > 0.05). Furthermore, we used gas chromatography-mass spectrometry (GC-MS) non-targeted metabolomics to determine the potential markers of APS for heat-stressed dairy cows. Twenty metabolites were identified as potential biomarkers for the diagnosis of APS in heat-stressed dairy cows. These substances are involved in protein digestion and absorption, glutathione metabolism, prolactin signaling pathway, aminoacyl-tRNA biosynthesis, pentose and glucuronate interconversions, and so on. Our findings suggest that APS have an effect on the serum hormones of heat-stressed dairy cows, and regulate the metabolism of heat-stressed dairy cows through glucose metabolism and amino acid metabolism pathways.

Effects of a blend of Saccharomyces cerevisiae-based direct-fed microbial and fermentation products on plasma carbonyl-metabolome and fecal bacterial community of beef steers

BACKGROUND

Previous studies have evaluated the metabolic status of animals fed direct-fed microbial (DFM) using enzyme-based assays which are time-consuming and limited to a few metabolites. In addition, little emphasis has been placed on investigating the effects of DFM on hindgut microbiota. We examined the effects of dietary supplementation of a blend of Saccharomyces cerevisiae-based DFM and fermentation products on the plasma concentrations of carbonyl-containing metabolites via a metabolomics approach, and fecal bacterial community, via 16S rRNA gene sequencing, of beef steers during a 42-day receiving period. Forty newly weaned steers were randomly assigned to receive a basal diet with no additive (CON; n = 20) or a basal diet supplemented with 19 g of Commence™ (PROB; n = 20) for a 42-day period. Commence™ (PMI, Arden Hills, MN) is a blend of 6.2 × 1011 cfu/g of S. cerevisiae, 3.5 × 1010 cfu/g of a mixture of Enterococcus lactis, Bacillus subtilis, Enterococcus faecium, and Lactobacillus casei, and the fermentation products of these aforementioned microorganisms and those of Aspergillus oryzae and Aspergillus niger. On d 0 and 40, rectal fecal samples were collected randomly from 10 steers from each treatment group. On d 42, blood was collected for plasma preparation.

RESULTS

A total number of 812 plasma metabolites were detected. Up to 305 metabolites [fold change (FC) ≥ 1.5, FDR ≤ 0.01] including glucose, hippuric acid, and 5-hydroxykynurenamine were increased by PROB supplementation, whereas 199 metabolites (FC ≤ 0.63, FDR ≤ 0.01) including acetoacetate were reduced. Supplementation of PROB increased (P ≤ 0.05) the relative abundance of Prevotellaceae UCG-003, Megasphaera, Dorea, Acetitomaculum, and Blautia. In contrast, the relative abundance of Elusimicrobium, Moheibacter, Stenotrophomonas, Comamonas, and uncultured bacterium belonging to family p-2534-18B5 gut group (phylum Bacteroidetes) were reduced (P ≤ 0.05).

CONCLUSIONS

The results of this study demonstrated that supplementation of PROB altered both the plasma carbonyl metabolome towards increased glucose concentration suggesting an improved energy status, and fecal bacterial community, suggesting an increased hindgut fermentation of the beef steers.

Nuclear magnetic resonance (NMR)-based metabolome profile evaluation in dairy cows with and without displaced abomasum

Background

Displaced abomasum (DA) is a condition of dairy cows that severely impacts animal welfare and causes huge economic losses.

Objective

To assess the metabolic status of the disease using metabolomics in serum, urine and liver samples aimed at both water soluble and lipid soluble fractions.

Methods

Fifty Holstein multiparous cows with DA (42 left, 8 right) and 20 clinically healthy Holstein multiparous cows were used. Left DA was associated with concomitant ketosis in 19 animals and right in two. NMR-based metabolomics approach and hematological and biochemical analyses were performed. Statistical analysis was carried out on ¹H-NMR data after they have been normalized using PQN method.

Results

Contrary to generated PCA score plots the OPLS-supervised method revealed differences between healthy animals and diseased ones based on serum water-soluble samples. While water and lipid soluble metabolites decreased in serum samples, fatty acid fractions and cholesterol were increased in liver samples in DA affected cows. The metabolomic and chemical profiles clearly revealed that cows with DA (especially with LDA) were at risk of ketosis and fatty liver. Serum hippuric acid concentration was significantly higher in healthy cows in comparison with LDA, whereas serum glycine concentration was reported higher for healthy when compared to RDA affected animals.

Conclusion

A biochemical network and pathway mapping revealed ‘valine, leucine and isoleucine biosynthesis’ and ‘phenylalanine, tyrosine and tryptophan biosynthesis’ as the most probable altered metabolic pathway in DA condition. Serum was advocated as the optimal biological matrix for the ¹H-NMR analysis.

Effects of mineral supplementation on reproductive performance of pregnant cross-breed Bonsmara cows: An experimental study

Minerals in animal feed occur in variable structures, most of which determine the uptake and usage in biological processes in the body. Effective chemical breakdown of minerals may ensure efficient utilization in metabolism. The aim this study was to evaluate the effects of mineral supplementation on reproduction in cows. A farm was selected for the experiment due to the fact that it previously experienced different reproductive conditions in the farm. The farm comprises cross‐breed cows with Bonsmara dominating in the farm. Twelve pregnant primiparous and multiparous cows of different ages, parity and weight, that had previously experienced reproductive conditions, were randomly selected for this study. The cows were then randomly sub‐divided into two groups (experimental and control group) of six. The experimental group was injected with MULTIMIN™ + Se + Cu at a dosage of 1 ml/45 kg BW and Calci 50 p.i. at a dosage of 100–150 ml/500 kg BW at an interval of 6 weeks (from June to October 2017). Blood samples were collected before every injection date. The t test was used to relate the mean weight gain and serum metabolite between the experimental and control groups. The body weight gain was significantly higher in the experimental group compared to the non‐supplemented group. Supplemented cows had significantly (p < .05) high levels of triglycerides and creatinine kinase. A case of retained placenta and dystocia among non‐supplemented cows were noted. Thus, mineral supplementation can be used to improve productivity and reproductive well‐being.

Supply of Methionine During Late-Pregnancy Alters Fecal Microbiota and Metabolome in Neonatal Dairy Calves Without Changes in Daily Feed Intake

To our knowledge, most studies demonstrating the role of manipulating maternal nutrition on hindgut (i.e., large intestine) microbiota in the offspring have been performed in non-ruminants. Whether this phenomenon exists in cattle is largely unknown. Therefore, the objectives of the current study were to evaluate the impact of maternal post-ruminal supply of methionine during late-pregnancy in dairy cows on fecal microbiota and metabolome in neonatal calves, and their association with body development and growth performance during the preweaning period. To achieve this, heifer calves, i.e., neonatal female offspring, born to Holstein cows receiving either a control (CON) diet (n = 13) or CON plus rumen-protected methionine (MET; Evonik Nutrition & Care GmbH) during the last 28 days of pregnancy were used. Fecal samples from heifers were collected from birth until 6 weeks of age, i.e., the preweaning period. Fecal microbiota was analyzed with QIIME 2 whereas fecal metabolites were measured using an untargeted LC-MS approach. At birth, MET heifers had greater (P ≤ 0.05) BW, HH, and WH. During the preweaning period, no differences between groups were detected for starter intake (P = 0.77). However, MET heifers maintained greater (P ≤ 0.05) BW, HH and tended (P = 0.06) to have greater WH and average daily gain (ADG) (P = 0.10). Fecal microbiota and metabolome profiles through 42 days of age in MET heifers indicated greater capacity for hindgut production of endogenous antibiotics and enhanced hindgut functionality and health. Enhancing maternal post-ruminal supply of methionine during late-gestation in dairy cows has a positive effect on hindgut functionality and health in their offspring through alterations in the fecal microbiota and metabolome without affecting feed intake. Those alterations could limit pathogen colonization of the hindgut while providing essential nutrients to the neonate. Together, such responses contribute to the ability of young calves to achieve better rates of nutrient utilization for growth.

Days-in-Milk and Parity Affected Serum Biochemical Parameters and Hormone Profiles in Mid-Lactation Holstein Cows

It is well known that serum biochemical parameters and hormones contribute greatly to the physiological and metabolic status of dairy cows. However, few studies have focused on the variation of these serum parameters in multiparous mid-lactation cows without the interference of diet and management. A total of 287 Holstein dairy cows fed the same diet and maintained under the same management regime were selected from a commercial dairy farm to evaluate the effects of days-in-milk (DIM) and parity on serum biochemical parameters and hormone profiles. Milk yield and milk protein content were affected by DIM and parity (p < 0.05). Milk protein yield showed a numerically decreasing trend with parity, and it was relatively constant in cows with parities between 2 and 4 but lower in cows with parity 6 (p = 0.020). Ten and five serum biochemical parameters related to protein status, energy metabolism, liver and kidney function, and oxidative stress were affected by DIM and parity, respectively (p < 0.05). Glucagon, insulin-like growth factor 1 concentration, and the revised quantitative insulin sensitivity check index were significantly different (p < 0.05) among cows with different DIM. Parity had no effect on hormone concentrations. An interaction between DIM and parity effect was only detected for glucagon concentration (p = 0.015), which showed a significantly increasing trend with DIM and overall decreasing trend with parity. In summary, DIM and parity played an important role in affecting the serum biochemical parameters and/or hormones of dairy cows, with serum parameters affected more by DIM than parity.

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health

Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.

Assessment of rumen bacteria in dairy cows with varied milk protein yield

The present study was conducted to assess rumen bacteria in lactating cows with different milk protein yield, aiming to understand the role of rumen bacteria in this trait. Cows with high milk protein yield (high milk yield and high milk protein content, HH; n = 20) and low milk protein yield (low milk yield and low milk protein content, LL; n = 20) were selected from 374 mid-lactation Holstein dairy cows fed a high-grain diet. Measurement of the rumen fermentation products showed that the concentrations of ruminal total volatile fatty acids, propionate, butyrate, and valerate and the proportion of isobutyrate were higher in the HH cows than in the LL cows. Amplicon sequencing analysis of the rumen bacterial community revealed that the richness (Chao 1 index) of rumen microbiota was higher in the LL cows than in the HH cows. Among the 10 predominant bacterial phyla (relative abundance being >0.10%, present in >60% of animals within each group), the relative abundance of Proteobacteria was 1.36-fold higher in the HH cows than in the LL cows. At the genus level, the relative abundance of Succinivibrio was significantly higher and that of Clostridium tended to be higher in the LL cows than in the HH cows. Sharpea was 2.28-fold enriched in the HH cows compared with the LL cows. Different relationships between the relative abundances of rumen microbial taxa and volatile fatty acid concentrations were observed in the HH and the LL animals, respectively. Succinivibrio and Prevotella were positively correlated with acetate, propionate, and valerate in the LL cows, whereas Sharpea was positively correlated with propionate and valerate concentrations in the HH cows. Collectively, our results revealed that rumen bacterial richness and the relative abundances of several bacterial taxa significantly differed between dairy cows with high and low milk protein yields, suggesting the potential roles of rumen microbiota contributing to milk protein yield in dairy cows.