Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids' metabolomics relationships in dairy cows

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.

Regulation of Milk Fat Synthesis: Key Genes and Microbial Functions

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

Milk metabolite composition of a semi-captive population of Asian elephants

Lack of maternal milk commonly leads to Asian elephant calves' death in captivity. Currently, available supplements seem inefficient. Hence, we aimed at characterizing the composition of Asian elephant milk to provide information on calves' nutritional needs. Seventy milk samples from 22 Asian elephants living in semi-captivity in their natural environment in Myanmar were collected. Samples were analysed through various techniques including liquid chromatography tandem mass spectrometry, gas chromatography-flame ionization detector, and bicinchoninic acid assay to determine total protein content and various metabolites. Associations with lactation stage (months postpartum) were investigated through repeated measure mixed models. We identified 160 compounds: 22 amino acids, 12 organic acids of the tricarboxylic acid cycle, 27 fatty acids, 15 acyl-carnitines and 84 phospholipids. The milk contained substantial amounts of free glutamate (median: 1727.9, interquartile range (IQR): 1278.4 µmol l-1) and free glycine (2541.7, IQR: 1704.1 µmol l-1). The fatty acid profile was mostly constituted by saturated fatty acids, particularly capric acid (40.1, IQR: 67.3 g l-1). Milk samples also contained high amounts of carnitines, phospholipids and organic acids. The wide array of metabolites identified and quantified, some of which present high concentrations in the milk from this species as opposed to other species, suggests underpinning physiological functions that might be crucial for the survival of Asian elephant calves.

A metabolomics analysis of interspecies and seasonal trends in ruminant milk: The molecular difference between bovine, caprine, and ovine milk

Ruminant milk composition can be affected by many factors, primarily interspecies differences, but also environmental factors (e.g., season, feeding system, and feed composition). Pasture-based feeding systems are known to be influenced by seasonal effects on grass composition. Spring pasture is rich in protein and low in fiber compared with late-season pasture, potentially inducing variability in the composition of some milk metabolites across the season. This study aimed to investigate interspecies and seasonal differences in the milk metabolome across the 3 major commercial ruminant milk species from factories in New Zealand: bovine, caprine, and ovine milk. Samples of bovine (n = 41) and caprine (n = 44) raw milk were collected monthly for a period of 9 mo (August 2016-April 2017), and ovine milk samples (n = 20) were collected for a period of 5 mo (August 2016-January 2017). Milk samples were subjected to biphasic extraction, and untargeted metabolite profiling was performed using 2 separate liquid chromatography high-resolution mass spectrometry analytical methods (polar metabolites and lipids). Major differences in the milk metabolome were observed between the 3 ruminant species, with 414 of 587 (71%) polar metabolite features and 210 of 233 (87%) lipid features being significantly different between species. Significant seasonal trends were observed in the polar metabolite fraction for bovine, caprine, and ovine milk (17, 24, and 32 metabolites, respectively), suggesting that the polar metabolite relative intensities of ovine and caprine milk were more susceptible to changes within seasons than bovine milk. We found no significant seasonal difference for the triglycerides (TG) species measured in bovine milk, whereas 3 and 52 TG species changed in caprine and ovine milk, respectively, across the seasons. In addition, 4 phosphatidylcholines and 2 phosphatidylethanolamines varied in caprine milk within the season, and 8 diglycerides varied in ovine milk. The interspecies and seasonal metabolite differences reported here provide a knowledge base of components potentially linked to milk physiochemical properties, and potential health benefits of New Zealand pasture-fed dairy ingredients.

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.

Self-Assembled Hyperbranched Gold Nanoarrays Decode Serum United Urine Metabolic Fingerprints for Kidney Tumor Diagnosis

Serum united urine metabolic analysis comprehensively reveals the disease status for kidney diseases in particular. Thus, the precise and convenient acquisition of metabolic molecular information from united biofluids is vitally important for clinical disease diagnosis and biomarker discovery. Laser desorption/ionization mass spectrometry (LDI-MS) presents various advantages in metabolic analysis; however, there remain challenges in ionization efficiency and MS signal reproducibility. Herein, we constructed a self-assembled hyperbranched black gold nanoarray (HyBrAuNA) assisted LDI-MS platform to profile serum united urine metabolic fingerprints (S-UMFs) for diagnosis of early stage renal cell carcinoma (RCC). The closely packed HyBrAuNA afforded strong electromagnetic field enhancement and high photothermal conversion efficacy, enabling effective ionization of low abundant metabolites for S-UMF collection. With a uniform nanoarray, the platform presented excellent reproducibility to ensure the accuracy of S-UMFs obtained in seconds. When it was combined with automated machine learning analysis of S-UMFs, early stage RCC patients were discriminated from the healthy controls with an area under the curve (AUC) > 0.99. Furthermore, we screened out a panel of 9 metabolites (4 from serum and 5 from urine) and related pathways toward early stage kidney tumor. In view of its high-throughput, fast analytical speed, and low sample consumption, our platform possesses potential in metabolic profiling of united biofluids for disease diagnosis and pathogenic mechanism exploration.

Untargeted Metabolomic Analysis of Lactation-Stage-Matched Human and Bovine Milk Samples at 2 Weeks Postnatal

Epidemiological data demonstrate that bovine whole milk is often substituted for human milk during the first 12 months of life and may be associated with adverse infant outcomes. The objective of this study is to interrogate the human and bovine milk metabolome at 2 weeks of life to identify unique metabolites that may impact infant health outcomes. Human milk (n = 10) was collected at 2 weeks postpartum from normal-weight mothers (pre-pregnant BMI < 25 kg/m2) that vaginally delivered term infants and were exclusively breastfeeding their infant for at least 2 months. Similarly, bovine milk (n = 10) was collected 2 weeks postpartum from normal-weight primiparous Holstein dairy cows. Untargeted data were acquired on all milk samples using high-resolution liquid chromatography-high-resolution tandem mass spectrometry (HR LC-MS/MS). MS data pre-processing from feature calling to metabolite annotation was performed using MS-DIAL and MS-FLO. Our results revealed that more than 80% of the milk metabolome is shared between human and bovine milk samples during early lactation. Unbiased analysis of identified metabolites revealed that nearly 80% of milk metabolites may contribute to microbial metabolism and microbe-host interactions. Collectively, these results highlight untargeted metabolomics as a potential strategy to identify unique and shared metabolites in bovine and human milk that may relate to and impact infant health outcomes.

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.

Metabolomic Analysis of Multiple Biological Specimens (Feces, Serum, and Urine) by 1H-NMR Spectroscopy from Dairy Cows with Clinical Mastitis

Due to huge economic losses to the dairy industry worldwide, mastitis can be considered as one of the most common diseases in dairy cows. This work aimed to study this disease by comparing multiple biological specimens (feces, serum, and urine) from individuals with or without clinical mastitis. This was performed by a single analytical platform, namely ¹H-NMR, through a multi-matrix strategy. Thanks to the high reproducibility of ¹H-NMR, we could characterize 120 molecules across dairy cow feces, serum, and urine. Among them, 23 molecules were in common across the three biofluids. By integrating the results of multi-matrix metabolomics, several pathways pertaining to energy metabolism and amino acid metabolism appeared to be affected by clinical mastitis. The present work wished to deepen the understanding of dairy cow mastitis in its clinical form. Simultaneous analysis of metabolome changes across several key biofluids could facilitate knowledge discovery and the reliable identification of potential biomarkers, which could be, in turn, used to shed light on the early diagnosis of dairy cow mastitis in its subclinical form.

NMR-based metabolomics of plasma from dairy calves infected with two primary causal agents of bovine respiratory disease (BRD)

Each year, bovine respiratory disease (BRD) results in significant economic loss in the cattle sector, and novel metabolic profiling for early diagnosis represents a promising tool for developing effective measures for disease management. Here, ¹H-nuclear magnetic resonance (¹H-NMR) spectra were used to characterize metabolites from blood plasma collected from male dairy calves (n = 10) intentionally infected with two of the main BRD causal agents, bovine respiratory syncytial virus (BRSV) and Mannheimia haemolytica (MH), to generate a well-defined metabolomic profile under controlled conditions. In response to infection, 46 metabolites (BRSV = 32, MH = 33) changed in concentration compared to the uninfected state. Fuel substrates and products exhibited a particularly strong effect, reflecting imbalances that occur during the immune response. Furthermore, ¹H-NMR spectra from samples from the uninfected and infected stages were discriminated with an accuracy, sensitivity, and specificity ≥ 95% using chemometrics to model the changes associated with disease, suggesting that metabolic profiles can be used for further development, understanding, and validation of novel diagnostic tools.

Milk metabolomics analyses of lactating dairy cows with divergent residual feed intake reveals physiological underpinnings and novel biomarkers

The opportunity to select for feed efficient cows has been limited by inability to cost-effectively record individual feed efficiency on an appropriate scale. This study investigated the differences in milk metabolite profiles between high- and low residual feed intake (RFI) categories and identified biomarkers of residual feed intake and models that can be used to predict residual feed intake in lactating Holsteins. Milk metabolomics analyses were undertaken at early, mid and late lactation stages and residual feed intake was calculated in 72 lactating dairy cows. Cows were ranked and grouped into high residual feed intake (RFI >0.5 SD above the mean, n = 20) and low residual feed intake (RFI <0.5 SD below the mean, n = 20). Milk metabolite profiles were compared between high residual feed intake (least efficient) and low residual feed intake (most efficient) groups. Results indicated that early lactation was predominantly characterized by significantly elevated levels of medium chain acyl carnitines and glycerophospholipids in high residual feed intake cows. Citrate cycle and glycerophospholipid metabolism were the associated pathways enriched with the significantly different metabolites in early lactation. At mid lactation short and medium chain acyl carnitines, glycerophospholipids and amino acids were the main metabolite groups differing according to residual feed intake category. Late lactation was mainly characterized by increased levels of amino acids in high residual feed intake cows. Amino acid metabolism and biosynthesis pathways were enriched for metabolites that differed between residual feed intake groups at the mid and late lactation stages. Receiver operating characteristic curve analysis identified candidate biomarkers: decanoylcarnitine (area under the curve: AUC = 0.81), dodecenoylcarnitine (AUC = 0.81) and phenylalanine (AUC = 0.85) at early, mid and late stages of lactation, respectively. Furthermore, panels of metabolites predicted residual feed intake with validation coefficient of determination (R ²) of 0.65, 0.37 and 0.60 at early, mid and late lactation stages, respectively. The study sheds light on lactation stage specific metabolic differences between high-residual feed intake and low-residual feed intake lactating dairy cows. Candidate biomarkers that distinguished divergent residual feed intake groups and panels of metabolites that predict individual residual feed intake phenotypes were identified. This result supports the potential of milk metabolites to select for more efficient cows given that traditional residual feed intake phenotyping is costly and difficult to conduct in commercial farms.

Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants

The RNA-Seq data provides new opportunities for the detection of transcriptome variants' single nucleotide polymorphisms (SNPs) in various species and tissues. Herein, milk samples from two sheep breeds and two cow breeds were utilized to characterize the genetic variation in the coding regions in three stages (before-peak (BP), peak (P), and after-peak (AP)) of the lactation process. In sheep breeds Assaf and Churra, 100,462 and 97,768, 65,996 and 62,161, and 78,656 and 39,245 variants were observed for BP, P, and AP lactation stages, respectively. The number of specific variants was 59,798 and 76,419, 11,483 and 49,210, and 104,033 and 320,817 in cow breeds Jersy and Kashmiri, respectively, for BP, P, and AP stages. Via the transcriptome analysis of variation in regions containing QTL for fat, protein percentages, and milk yield, we detected a number of pathways and genes harboring mutations that could influence milk production attributes. Many SNPs detected here can be regarded as appropriate markers for custom SNP arrays or genotyping platforms to conduct association analyses among commercial populations. The results of this study offer new insights into milk production genetic mechanisms in cow and sheep breeds, which can contribute to designing suitable breeding systems for optimal milk production.

Plasma Metabolomic Analysis Reveals the Relationship between Immune Function and Metabolic Changes in Holstein Peripartum Dairy Cows

Dairy cows undergo dynamic physiological changes from late gestation to early lactation, including metabolic changes and immune dysfunction. The aim of this study was to investigate the relationship between immune function and metabolic changes in peripartum dairy cows. Fifteen healthy Holstein dairy cows were enrolled 14 days prior to parturition, and plasma was collected on day −7, 0, 7, and 21 relative to calving. Plasma non-esterified fatty acids (NEFAs), glucose, β-hydroxybutyric acid (BHBA), immunoglobulin G (IgG), tumor necrosis factor alpha (TNF-α), and interleukin-2 levels were measured, and metabolic profiles were determined using ultra-high-performance liquid chromatography−quadrupole time-of-flight mass spectrometry. The data were analyzed using Tukey−Kramer adjustment for multiple comparisons, and multivariate and univariate statistical analyses were performed to screen for differential metabolites. The results showed that the concentrations of NEFAs, glucose, BHBA, and TNF-α in the plasma significantly increased and concentrations of IgG and interleukin-2 in plasma significantly decreased from −7 d to the calving day (p < 0.05). Additionally, the concentrations of glucose, IgG, and TNF-α significantly decreased from 0 to +7 d, and concentrations of NEFAs decreased significantly from +7 to +21 d (p < 0.05). The following six primary metabolic pathways were identified in all time point comparisons, and L-glutamate, linoleic acid, taurine, and L-tryptophan were involved in these major metabolic pathways. Correlation and pathway analyses indicated that a negative energy balance during the transition period adversely affects immune responses in cows, and L-tryptophan exerts immunomodulatory effects through the Trp-Kyn pathway, resulting in depletion of Trp and elevation of Kyn.

Evaluation of the metabolomic profile through 1H-NMR spectroscopy in ewes affected by postpartum hyperketonemia

Ketosis is one of the most important health problems in dairy sheep. The aim of this study was to evaluate the metabolic alterations in hyperketonemic (HYK) ewes. Forty-six adult Sardinian ewes were enrolled between 7 ± 3 days post-partum. Blood samples were collected from the jugular vein using Venosafe tubes containing clot activator from jugular vein after clinical examination. The concentration of β-hydroxybutyrate (BHB) was determined in serum and used to divide ewes into assign ewes into: Non-HYK (serum BHB < 0.80 mmol/L) and HYK (serum BHB ≥ 0.80 mmol/L) groups. Animal data and biochemical parameters of groups were examined with one-way ANOVA, and metabolite differences were tested using a t-test. A robust principal component analysis model and a heatmap were used to highlight common trends among metabolites. Over-representation analysis was performed to investigate metabolic pathways potentially altered in connection with BHB alterations. The metabolomic analysis identified 54 metabolites with 14 different between groups. These metabolites indicate altered ruminal microbial populations and fermentations; an interruption of the tricarboxylic acid cycle; initial lack of glucogenic substrates; mobilization of body reserves; the potential alteration of electron transport chain; influence on urea synthesis; alteration of nervous system, inflammatory response, and immune cell function.

Intramammary infusion of matrine-chitosan hydrogels for treating subclinical bovine mastitis -effects on milk microbiome and metabolites

Background

Bovine metabolism undergoes significant changes during subclinical mastitis, but the relevant molecular mechanisms have not been elucidated. In this study we investigated the changes in milk microbiota and metabolites after intramammary infusion of matrine-chitosan hydrogels (MCHs) in cows with subclinical mastitis.

Methods

Infusions were continued for 7 days, and milk samples were collected on days 1 and 7 for microbiome analysis by 16S rRNA gene sequencing and metabolite profiling by liquid chromatography-mass spectrometry.

Results

MCHs significantly decreased the somatic cell count on day 7 compared to day 1, and the Simpson index indicated that microbial diversity was significantly lower on day 7. The relative abundance of Aerococcus, Corynebacterium_1, Staphylococcus and Firmicutes was significantly decreased on day 7, while Proteobacteria increased. In the milk samples, we identified 74 differentially expressed metabolites. The MCHs infusion group had the most significantly upregulated metabolites including sphingolipids, glycerophospholipids, flavonoids and fatty acyls. The mammary gland metabolic pathways identified after MCHs treatment were consistent with the known antimicrobial and anti-inflammatory properties of matrine that are associated with glycerophospholipid metabolism and the sphingolipid metabolic signaling pathways.

Conclusion

These insights into the immunoregulatory mechanisms and the corresponding biological responses to matrine demonstrate its potential activity in mitigating the harmful effects of bovine mastitis.

Dynamic Changes in the Human Milk Metabolome Over 25 Weeks of Lactation

Human milk (HM) provides essential nutrition for ensuring optimal infant growth and development postpartum. Metabolomics offers insight into the dynamic composition of HM. Studies have reported the impact of lactation stage, maternal genotype, and gestational age on HM metabolome. However, the majority of the studies have considered changes within the first month of lactation or sampled with large intervals. This leaves a gap in the knowledge of progressing variation in HM composition beyond the first month of lactation. The objective of this study was to investigate whether the HM metabolome from mothers with term deliveries varies beyond 1 month of lactation, during the period in which HM is considered fully mature. Human milk samples (n = 101) from 59 mothers were collected at weeks 1-2, 3-5, 7-9, and 20-25 postpartum and analyzed using 1H nuclear magnetic resonance spectroscopy. Several metabolites varied over lactation and exhibited dynamic changes between multiple time points. Higher levels of HM oligosaccharides, cis-aconitate, O-phosphocholine, O-acetylcarnitine, gluconate, and citric acid were observed in early lactation, whereas later in lactation, levels of lactose, 3-fucosyllactose, glutamine, glutamate, and short- and medium-chain fatty acids were increased. Notably, we demonstrate that the HM metabolome is dynamic during the period of maturity.

Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle

Increasing the efficiency and sustainability of cattle production is an effective way to produce valuable animal proteins for a growing human population. Genetics and nutrition are the 2 major research topics in selecting cattle with beneficial phenotypes and developing genetic potentials for improved performance. There is an inextricable link between genetics and nutrition, which urgently requires researchers to uncover the underlying molecular mechanisms to optimize cattle production. Feedomics integrates a range of omic techniques to reveal the mechanisms at different molecular levels related to animal production and health, which can provide novel insights into the relationships of genes and nutrition/nutrients. In this review, we summarized the applications of feedomics techniques to reveal the effect of genetic elements on the response to nutrition and investigate how nutrients affect the functional genome of cattle from the perspective of both nutrigenetics and nutrigenomics. We highlighted the roles of rumen microbiome in the interactions between host genes and nutrition. Herein, we discuss the importance of feedomics in cattle nutrition research, with a view to ensure that cattle exhibit the best production traits for human consumption from both genetic and nutritional aspects.

Metabolomics Analysis Across Multiple Biofluids Reveals the Metabolic Responses of Lactating Holstein Dairy Cows to Fermented Soybean Meal Replacement

This experiment was performed to reveal the metabolic responses of dairy cows to the replacement of soybean meal (SBM) with fermented soybean meal (FSBM). Twenty-four lactating Chinese Holstein dairy cattle were assigned to either the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] or the FSBM group (the experimental TMR diet containing 5.55% FSBM), in a completely randomized design. The entire period of this trial consisted of 14 days for the adjustment and 40 days for data and sample collection, and sampling for rumen liquid, blood, milk, and urine was conducted on the 34th and 54th day, respectively. When SBM was completely replaced by FSBM, the levels of several medium-chain FA in milk (i.e., C13:0, C14:1, and C16:0) rose significantly (p < 0.05), while the concentrations of a few milk long-chain FA (i.e., C17:0, C18:0, C18:1n9c, and C20:0) declined significantly (p < 0.05). Besides, the densities of urea nitrogen and lactic acid were significantly (p < 0.05) higher, while the glucose concentration was significantly (p < 0.05) lower in the blood of the FSBM-fed cows than in the SBM-fed cows. Based on the metabolomics analysis simultaneously targeting the rumen liquid, plasma, milk, and urine, it was noticed that substituting FSBM for SBM altered the metabolic profiles of all the four biofluids. According to the identified significantly different metabolites, 3 and 2 amino acid-relevant metabolic pathways were identified as the significantly different pathways between the two treatments in the rumen fluid and urine, respectively. Furthermore, glycine, serine, and threonine metabolism, valine, leucine, and isoleucine biosynthesis, and cysteine and methionine metabolism were the three key integrated different pathways identified in this study. Results mainly implied that the FSBM replacement could enhance nitrogen utilization and possibly influence the inflammatory reactions and antioxidative functions of dairy cattle. The differential metabolites and relevant pathways discovered in this experiment could serve as biomarkers for the alterations in protein feed and nitrogen utilization efficiency of dairy cows, and further investigations are needed to elucidate the definite roles and correlations of the differential metabolites and pathways.

Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods

Simple Summary

In order to study the influence of RNA editing sites on lactation and mammary gland development process in yaks, we comprehensively characterized the RNA editome of the yak mammary gland during the lactation period and dry period by using the transcriptome and genome sequencing data. The results revealed 82,872 nonredundant RNA editing sites, 14,159 of which were differentially edited between the lactation period and dry period. Enrichment analysis showed that the genes harboring differential editing sites were mainly associated with mammary gland development-related pathways, such as MAPK pathway, PI3K-Akt pathway, FoxO signaling pathway, GnRH signaling pathway, and focal adhesion pathway. Our findings offer some novel insights into the RNA editing function in the mammary gland of yaks.

Abstract

The mammary gland is a complicated organ comprising several types of cells, and it undergoes extensive morphogenetic and metabolic changes during the female reproductive cycle. RNA editing is a posttranscriptional modification event occurring at the RNA nucleotide level, and it drives transcriptomic and proteomic diversities, with potential functional consequences. RNA editing in the mammary gland of yaks, however, remains poorly understood. Here, we used REDItools to identify RNA editing sites in mammary gland tissues in yaks during the lactation period (LP, n = 2) and dry period (DP, n = 3). Totally, 82,872 unique RNA editing sites were identified, most of which were detected in the noncoding regions with a low editing degree. In the coding regions (CDS), we detected 5235 editing sites, among which 1884 caused nonsynonymous amino acid changes. Of these RNA editing sites, 486 were found to generate novel possible miRNA target sites or interfere with the initial miRNA binding sites, indicating that RNA editing was related to gene regulation mediated by miRNA. A total of 14,159 RNA editing sites (involving 3238 common genes) showed a significant differential editing level in the LP when compared with that in the DP through Tukey’s Honest Significant Difference method (p < 0.05). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes that showed different RNA editing levels mainly participated in pathways highly related to mammary gland development, including MAPK, PI3K-Akt, FoxO, and GnRH signaling pathways. Collectively, this work demonstrated for the first time the dynamic RNA editome profiles in the mammary gland of yaks and shed more light on the mechanism that regulates lactation together with mammary gland development.

The Maternal Milk Microbiome in Mammals of Different Types and Its Potential Role in the Neonatal Gut Microbiota Composition

Maternal milk, a main source of nutrition for neonates in early life, has attracted attention. An increasing number of studies have found that maternal milk has a high microbial diversity, as well as factors that might influence this diversity. However, there is a lack of knowledge regarding the effects of host diet and phylogeny on maternal milk microbes and the contribution of the maternal milk microbiota to the neonatal gut microbiota. Here, we analyzed the maternal milk and fecal microbiota of nine species (lion, dog, panda, human, mouse, rhesus macaque, cow, goat, and rabbit) of mammals of three type groups (herbivore, omnivore, and carnivore) using 16S rRNA amplicon sequencing. Our study provided evidence of host diet and phylogeny on the maternal milk microbiota. Moreover, functional prediction revealed that the carnivores had a significantly higher percentage of base excision repair, glycerolipid metabolism, taurine and hypotaurine metabolism, inorganic ion transport and metabolism, and nucleotide metabolism; while arginine and proline metabolism showed enrichment in the herbivore group. Source-tracking analysis showed that the contributions of bacteria from maternal milk to the microbiota of neonates of different mammals were different at day 3 after neonatal birth. Overall, our findings provided a theoretical basis for the maternal milk microbiota to affect neonatal fecal microbiota at day 3 after neonatal birth.

The Improved Method for Determination of Orotic Acid in Milk by Ultra-Fast Liquid Chromatography with Optimized Photodiode Array Detection

Ultra-fast liquid chromatography (UFLC) with a photodiode array detector (DAD) for simple and rapid determination of orotic acid (OAc) in milk of sheep and cows is described. Milk samples are treated with acetonitrile (1:1, v/v) and then centrifuged at 4 °C. To 1 mL of the obtained supernatant 9 mL of ultrapure water was added. Subsequently, 0.5-6 µL of the resulting solution was injected into the UFLC-DAD system. Separation and quantification of OAc in milk samples was achieved using two Kinetex C18 columns (1.7 µm, 150 mm × 2.1 mm, i.d., 100 Å; Phenomenex) fitted with a pre-column of 4 mm × 2 mm, i.d. (Phenomenex) containing C₁₈ packing material. All separations were performed at a column temperature of 35 °C while the ambient temperature was 21-24 °C. Satisfactory separation of OAc from endogenous species of milk can be achieved using the binary gradient elution program and UV detection at wavelengths 278 nm. Our original procedure resulted in suitable separation and quantification of OAc in milk samples; OAc eluted at 6.44 ± 0.03 min. The total run time of OAc analysis (including re-equilibration) was 27 min. As expected, the OAc peak was absent from the blank when the proposed gradient elution program and UV detection at 278 nm was used. The average recoveries of OAc standards added to milk samples were satisfactory (96.7-105.3%). The low inter-and intra-assay coefficient of variation derived from the measurements of OAc in cow and ovine milk samples (i.e., 0.784%, 1.283% and 0.710%, 1.221%, respectively) and in O-Ac standards (i.e., 0.377% and 0.294%, respectively), as well as high recoveries of OAc added to ovine and cows' milk (~100%) and the low detection (0.04 ng) and quantification (0.12 ng) limits point to satisfactory accuracy, precision and sensitivity of the reported method. OAc concentrations in ovine milk samples were within the range from 25 to 36 mg/L, while OAc levels in cows' milk samples was found in the range of 32-36 mg/L. Our original procedure is suitable for routine quantification of OAc in milk of ewes and cows.

Effect of Heat Stress on Bovine Mammary Cellular Metabolites and Gene Transcription Related to Amino Acid Metabolism, Amino Acid Transportation and Mammalian Target of Rapamycin (mTOR) Signaling

Simple Summary

This study mainly employed metabolomics technology to determine changes of intracellular metabolite concentrations related to milk protein synthesis induced by heat stress (HS) in bovine mammary epithelial cells. HS was associated with significant differences in intracellular amino acid metabolism resulting in an increase in the intracellular amino acid concentrations. Moreover, HS promoted amino acid transportation and the activity of the mammalian target of rapamycin (mTOR) signaling pathway, which plays an important role as a central regulator of cell metabolism, growth, proliferation and survival. Greater expression of the alpha-S2-casein gene (CSN1S2) was also observed during HS. Overall, our study indicated that bovine mammary epithelial cells may have the ability to resist HS damage and continue milk protein synthesis partly through enhanced intracellular amino acid absorption and metabolism and by activating the mTOR signaling pathway during HS.

Abstract

Heat stress (HS) is one of the most serious factors to negatively affect the lactation performance of dairy cows. Bovine mammary epithelial cells are important for lactation. It was demonstrated that HS decreases the lactation performance of dairy cows, partly through altering gene expression within bovine mammary epithelial tissue. However, the cellular metabolism mechanisms under HS remains largely unknown. The objective of this study was to determine whether HS induced changes in intracellular metabolites and gene transcription related to amino acid metabolism, amino acid transportation and the mTOR signaling pathway. Immortalized bovine mammary epithelial cell lines (MAC-T cells, n = 5 replicates/treatment) were incubated for 12 h at 37 °C (Control group) and 42 °C (HS group). Relative to the control group, HS led to a greater mRNA expression of heat shock protein genes HSF1, HSPB8, HSPA5, HSP90AB1 and HSPA1A. Compared with the control group, metabolomics using liquid chromatography tandem–mass spectrometry identified 417 differential metabolites with p < 0.05 and a variable importance in projection (VIP) score >1.0 in the HS group. HS resulted in significant changes to the intracellular amino acid metabolism of glutathione, phenylalanine, tyrosine, tryptophan, valine, leucine, isoleucine, arginine, proline, cysteine, methionine, alanine, aspartate and glutamate. HS led to a greater mRNA expression of the amino acid transporter genes SLC43A1, SLC38A9, SLC36A1, and SLC3A2 but a lower mRNA expression of SLC7A5 and SLC38A2. Additionally, HS influenced the expression of genes associated with the mTOR signaling pathway and significantly upregulated the mRNA expression of mTOR, AKT, RHEB, eIF4E and eEF2K but decreased the mRNA expression of TSC1, TSC2 and eEF2 relative to the control group. Compared with the control group, HS also led to greater mRNA expression of the CSN1S2 gene. Overall, our study indicates that bovine mammary epithelial cells may have the ability to resist HS damage and continue milk protein synthesis partly through enhanced intracellular amino acid absorption and metabolism and by activating the mTOR signaling pathway during HS.

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.

Regulation of Milk Protein Synthesis by Free and Peptide-Bound Amino Acids in Dairy Cows

Milk protein (MP) synthesis in the mammary gland of dairy cows is a complex biological process. As the substrates for protein synthesis, amino acids (AAs) are the most important nutrients for milk synthesis. Free AAs (FAAs) are the main precursors of MP synthesis, and their supplies are supplemented by peptide-bound AAs (PBAAs) in the blood. Utilization of AAs in the mammary gland of dairy cows has attracted the great interest of researchers because of the goal of increasing MP yield. Supplying sufficient and balanced AAs is critical to improve MP concentration and yield in dairy cows. Great progress has been made in understanding limiting AAs and their requirements for MP synthesis in dairy cows. This review focuses on the effects of FAA and PBAA supply on MP synthesis and their underlying mechanisms. Advances in our knowledge in the field can help us to develop more accurate models to predict dietary protein requirements for dairy cows MP synthesis, which will ultimately improve the nitrogen utilization efficiency and lactation performance of dairy cows.

Application of Metabolomics in Diagnosis of Cow Mastitis: A Review

Cow mastitis, with high incidence rate and complex cause of disease, is one of the main diseases that affect the development of dairy industry in the world. Clinical mastitis and subclinical mastitis caused by Staphylococcus aureus, Escherichia coli, Streptococcus, and other pathogens have a huge potential safety hazard to food safety and the rapid development of animal husbandry. The economic loss caused by cow mastitis is billions of dollars every year in the world. In recent years, the omics technology has been widely used in animal husbandry with the continuous breakthrough of sequencing technology and the continuous reduction of sequencing cost. For dairy cow mastitis, the traditional diagnostic technique, such as histopathological screening, somatic cell count, milk pH test, milk conductivity test, enzyme activity test, and infrared thermography, are difficult to fully and comprehensively clarify its pathogenesis due to their own limitations. Metabolomics technology is an important part of system biology, which can simultaneously analyze all low molecular weight metabolites such as amino acids, lipids, carbohydrates under the action of complex factors including internal and external environment and in a specific physiological period accurately and efficiently, and then clarify the related metabolic pathways. Metabolomics, as the most downstream of gene expression, can amplify the small changes of gene and protein expression at the level of metabolites, which can more fully reflect the cell function. The application of metabolomics technology in cow mastitis can analyze the hetero metabolites, identify the related biomarkers, and reveal the physiological and pathological changes of cow mammary gland, so as to provide valuable reference for the prediction, diagnosis, and treatment of mastitis. The research progress of metabolomics technology in cow mastitis in recent years was reviewed, in order to provide guidance for the development of cow health and dairy industry safety in this manuscript.

Intensive lactation among women with recent gestational diabetes significantly alters the early postpartum circulating lipid profile: the SWIFT study

BACKGROUND

Women with a history of gestational diabetes mellitus (GDM) have a 7-fold higher risk of developing type 2 diabetes (T2D). It is estimated that 20-50% of women with GDM history will progress to T2D within 10 years after delivery. Intensive lactation could be negatively associated with this risk, but the mechanisms behind a protective effect remain unknown.

METHODS

In this study, we utilized a prospective GDM cohort of 1010 women without T2D at 6-9 weeks postpartum (study baseline) and tested for T2D onset up to 8 years post-baseline (n=980). Targeted metabolic profiling was performed on fasting plasma samples collected at both baseline and follow-up (1-2 years post-baseline) during research exams in a subset of 350 women (216 intensive breastfeeding, IBF vs. 134 intensive formula feeding or mixed feeding, IFF/Mixed). The relationship between lactation intensity and circulating metabolites at both baseline and follow-up were evaluated to discover underlying metabolic responses of lactation and to explore the link between these metabolites and T2D risk.

RESULTS

We observed that lactation intensity was strongly associated with decreased glycerolipids (TAGs/DAGs) and increased phospholipids/sphingolipids at baseline. This lipid profile suggested decreased lipogenesis caused by a shift away from the glycerolipid metabolism pathway towards the phospholipid/sphingolipid metabolism pathway as a component of the mechanism underlying the benefits of lactation. Longitudinal analysis demonstrated that this favorable lipid profile was transient and diminished at 1-2 years postpartum, coinciding with the cessation of lactation. Importantly, when stratifying these 350 women by future T2D status during the follow-up (171 future T2D vs. 179 no T2D), we discovered that lactation induced robust lipid changes only in women who did not develop incident T2D. Subsequently, we identified a cluster of metabolites that strongly associated with future T2D risk from which we developed a predictive metabolic signature with a discriminating power (AUC) of 0.78, superior to common clinical variables (i.e., fasting glucose, AUC 0.56 or 2-h glucose, AUC 0.62).

CONCLUSIONS

In this study, we show that intensive lactation significantly alters the circulating lipid profile at early postpartum and that women who do not respond metabolically to lactation are more likely to develop T2D. We also discovered a 10-analyte metabolic signature capable of predicting future onset of T2D in IBF women. Our findings provide novel insight into how lactation affects maternal metabolism and its link to future diabetes onset.

TRIAL REGISTRATION

ClinicalTrials.gov NCT01967030 .

Microbiome and Metabolic Changes of Milk in Response to Dietary Supplementation With Bamboo Leaf Extract in Dairy Cows

Bamboo leaf extracts, with high content of flavonoids and diverse biological activities, are used in animal husbandry. Increasing evidence has suggested an association between the bovine physiology and the udder microbiome, yet whether the microbiota and the metabolites of milk affect the mammary gland health or the milk quality remains unknown. In this study, we provide a potential mechanism for the effects of bamboo leaf extracts on milk microbiota and metabolites of dairy cows. Twelve multiparous lactating Chinese Holstein dairy cows were randomly separated into two groups: basal diet as the control group (CON, n = 6) and a diet supplemented with 30 g/d bamboo leaf extract per head as antioxidants of bamboo leaf (AOB) group (AOB, n = 6) for 7 weeks (2-week adaptation, 5-week treatment). Milk samples were collected at the end of the trial (week 7) for microbiome and associated metabolic analysis by 16S ribosomal RNA (rRNA) gene sequencing and liquid chromatography-mass spectrometry (LC-MS). The results showed that the milk protein was increased (p < 0.0001) and somatic cell count (SCC) showed a tendency to decrease (p = 0.09) with AOB supplementation. The relative abundance of Firmicutes was significantly decreased (p = 0.04) while a higher relative abundance of Probacteria (p = 0.01) was seen in the group receiving AOB compared to the CON group. The AOB group had a significantly lower relative abundance of Corynebacterium_1 (p = 0.01), Aerococcus (p = 0.01), and Staphylococcus (p = 0.02). There were 64 different types of metabolites significantly upregulated, namely, glycerophospholipids and fatty acyls, and 15 significantly downregulated metabolites, such as moracetin, sphinganine, and lactulose in the AOB group. Metabolic pathway analysis of the different metabolites revealed that the sphingolipid signaling pathway was significantly enriched, together with glycerophospholipid metabolism, sphingolipid metabolism, and necroptosis in response to AOB supplementation. Several typical metabolites were highly correlated with specific ruminal bacteria, demonstrating a functional correlation between the milk microbiome and the associated metabolites. These insights into the complex mechanism and corresponding biological responses highlight the potential function of AOB, warranting further investigation into the regulatory role of specific pathways in the metabolism.

SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing

Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk-producing Kashmiri cattle are being replaced by crossbreeding practices with Jersey cattle with the aim of improving milk production. However, crossbred animals are prone to infections and various other diseases resulting in unsustainable milk production. In this study, we tend to identify high-impact SNPs from Jersey and Kashmiri cows (utilizing RNA-Seq data) to delineate key pathways mediating milk production traits in both breeds. A total of 607 (442 SNPs and 169 INDELs) and 684 (464 SNPs and 220 INDELs) high-impact variants were found specific to Jersey and Kashmir cattle, respectively. Based on our results, we conclude that in Jersey cattle, genes with high-impact SNPs were enriched in nucleotide excision repair pathway, ABC transporter, and metabolic pathways like glycerolipid metabolism, pyrimidine metabolism, and amino acid synthesis (glycine, serine, and threonine). Whereas, in Kashmiri cattle, the most enriched pathways include endocytosis pathway, innate immunity pathway, antigen processing pathway, insulin resistance pathway, and signaling pathways like TGF beta and AMPK which could be a possible defense mechanism against mammary gland infections. A varied set of SNPs in both breeds, suggests a clear differentiation at the genomic level; further analysis of high-impact SNPs are required to delineate their effect on these pathways.

Exploration of metabolite profiles in the biofluids of dairy cows by proton nuclear magnetic resonance analysis

Studies that screen for metabolites produced in ruminants are actively underway. We aimed to evaluate the metabolic profiles of five biofluids (ruminal fluid, serum, milk, urine, and feces) in dairy cow by using proton nuclear magnetic resonance (1H-NMR) and provide a list of metabolites in each biofluid for the benefit of future research. We analyzed the metabolites in five biofluids from lactating cows using proton nuclear magnetic resonance imaging; 96, 73, 88, 118, and 128 metabolites were identified in the five biofluids, respectively. In addition, 8, 6, 9, and 17 metabolites were unique to ruminal fluid, serum, milk, and urine, respectively. The metabolites present at high concentrations were: acetate, propionate, and butyrate in ruminal fluid; lactate, glucose, and acetate in serum; and lactose, guanidoacetate, and glucitol in milk. In addition, the following metabolites were present at high concentrations: hippurate, urea, and trimethylamine N-oxide in urine and acetate, propionate, and butyrate in feces. The score plots of the principal component analysis did not show clear distinctions among the five biofluid samples. The purpose of this study was to verify the ability of our metabolomics approaches to identify metabolites in the biofluids of dairy cows.

Metabolomic and Proteomic Profiles Associated With Ketosis in Dairy Cows

Ketosis is a common metabolic disease in dairy cows during early lactation. However, information about the metabolomic and proteomic profiles associated with the incidence and progression of ketosis is still limited. In this study, an integrated metabolomics and proteomics approach was performed on blood serum sampled from cows diagnosed with clinical ketosis (case, ≥ 2.60 mmol/L plasma β-hydroxybutyrate; BHBA) and healthy controls (control, < 1.0 mmol/L BHBA). Samples were taken 2 weeks before parturition and 2 weeks after parturition from 19 animals (nine cases, 10 controls). All serum samples (n = 38) were subjected to Liquid Chromatography-Mass Spectrometry (LC-MS) based metabolomic analysis, and 20 samples underwent Data-Independent Acquisition (DIA) LC-MS based proteomic analysis. A total of 97 metabolites and 540 proteins were successfully identified, and multivariate analysis revealed significant differences in both metabolomic and proteomic profiles between cases and controls. We investigated clinical ketosis-associated metabolomic and proteomic changes using statistical analyses. Correlation analysis of statistically significant metabolites and proteins showed 78 strong correlations (correlation coefficient, R ≥ 0.7) between 38 metabolites and 25 proteins, which were then mapped to pathways using IMPaLA. Results showed that ketosis altered a wide range of metabolic pathways, such as metabolism, metabolism of proteins, gene expression and post-translational protein modification, vitamin metabolism, signaling, and disease related pathways. Findings presented here are relevant for identifying molecular targets for ketosis and biomarkers for ketosis detection during the transition period.

Untargeted metabolomic investigate milk and ruminal fluid of Holstein cows supplemented with Perilla frutescens leaf

Milk compounds are important for human nutrient requirements and health. The ruminal metabolic profile is responsible for dietary nutrition and determines milk production. Perilla frutescens leaf (PFL) is a commonly used medicinal herb due to its bioactive metabolites. This study elucidated the effects of PFL on the metabolome of two biofluids (rumen fluid and milk) of 14 cows fed a basic total mixed ration diet (CON, n = 7) and supplemented with 300 g/d PFL per cow (PFL, n = 7) by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. Milk PE-NMe (18:1(9Z)/18:1(9Z)) and DG (18:0/20:4(5Z,8Z,11Z,14Z)/0:0), oleanolic acid, and nucleotides were upregulated, and milk medium-chain fatty acids (2-hydroxycaprylic acid) were down-regulated in response to PFL. The supplementation of PFL increased the abundance of pyrimidine nucleotides both in rumen fluid and milk. The pathways of pyrimidine metabolism and biosynthesis of unsaturated fatty acids were enriched both in the rumen fluid and milk. We also found the milk 2-hydroxycaprylic acid was positively correlated with ruminal uridine 5-monophosphate, and was negatively correlated with ruminal deoxycytidine, and the milk thymidine was positively correlated with ruminal icosenoic acid. This study found that the supplementation of PFL could alter the ruminal metabolic profiles and milk synthesis through regulation of the pathways of pyrimidine metabolism and biosynthesis of unsaturated fatty acids. Our new findings provide comprehensive insights into the metabolomics profile of rumen fluid and milk, supporting the potential production of Perilla frutescens milk in dairy cows.

Microbiome and metabolic changes in milk in response to artemisinin supplementation in dairy cows

This study aimed to explore the effects of artemisinin (ART) on the milk microbiome and metabolites of dairy cow. A total of 12 mid-lactation Holstein dairy cows with similar parity, days in milk were randomly divided into 2 groups receiving either a total mixed ration (TMR) as the control group or this TMR and 120 g/d/head ART as the ART group. The milk samples were collected weekly to determine the contents, and end-of-trial (week 8) milk samples were used to identify microbial species and metabolite profiles by 16S rRNA sequencing and LC–MS analyses, respectively. We observed that the milk fat content significantly increased by ART treatment (P < 0.05). The bacterial community richness was significantly lower in the ART group (P < 0.05), while the diversity showed no difference (P > 0.05). Compared with its abundance in the control (CON) group, Firmicutes was significantly decreased, whereas Proteobacteria was significantly increased. Furthermore, in the ART group, the relative abundances of the genera Aerococcus, Staphylococcus, Corynebacterium_1 and Facklamia were significantly lower (P < 0.01). Metabolomics analysis revealed that ART significantly increasing the concentrations of glycerophospholipids, glycerolipids and flavonoids compared with those in the CON group. An enrichment analysis of the different metabolites showed that ART mainly affected glycerophospholipid metabolism and the pantothenate and CoA biosynthesis pathways. These findings revealed that ART supplementation could affect the milk microbiota and metabolites, that glycerophospholipids and glycerolipids could be potential biomarkers in the milk response to ART feed in dairy cows, and that ART changes substances in milk by maintaining lipid metabolism in the mammary gland.

Carbohydrate and amino acid metabolism and oxidative status in Holstein heifers precision-fed diets with different forage to concentrate ratios

Previous work led to the proposal that the precision feeding of a high-concentrate diet may represent a potential method with which to enhance feed efficiency (FE) when rearing dairy heifers. However, the physiological and metabolic mechanisms underlying this approach remain unclear. This study used metabolomics analysis to investigate the changes in plasma metabolites of heifers precision-fed diets containing a wide range of forage to concentrate ratios. Twenty-four half-sib Holstein heifers, with a similar body condition, were randomly assigned into four groups and precision fed with diets containing different proportions of concentrate (20%, 40%, 60% and 80% based on DM). After 28 days of feeding, blood samples were collected 6 h after morning feeding and gas chromatography time-of-flight/MS was used to analyze the plasma samples. Parameters of oxidative status were also determined in the plasma. The FE (after being corrected for gut fill) increased linearly (P < 0.01) with increasing level of dietary concentrate. Significant changes were identified for 38 different metabolites in the plasma of heifers fed different dietary forage to concentrate ratios. The main pathways showing alterations were clustered into those relating to carbohydrate and amino acid metabolism; all of which have been previously associated with FE changes in ruminants. Heifers fed with a high-concentrate diet had higher (P < 0.01) plasma total antioxidant capacity and superoxide dismutase but lower (P ≤ 0.02) hydroxyl radical and hydrogen peroxide than heifers fed with a low-concentrate diet, which might indicate a lower plasma oxidative status in the heifers fed a high-concentrate diet. Thus, heifers fed with a high-concentrate diet had higher FE and antioxidant capacity but a lower plasma oxidative status as well as changed carbohydrate and amino acid metabolism. Our findings provide a better understanding of how forage to concentrate ratios affect FE and metabolism in the precision-fed growing heifers.

MG-HCr, the Methylglyoxal-Derived Hydroimidazolone of Creatine, a Biomarker for the Dietary Intake of Animal Source Food

In the course of the Maillard reaction in vivo or in food, creatine reacts with the 1,2-dicarbonyl compound methylglyoxal to N-(4-methyl-5-oxo-1-imidazolin-2-yl)sarcosine (MG-HCr). We studied whether the urinary excretion of MG-HCr is affected by its intake with meat or by the intake of creatine and subsequent in vivo formation of MG-HCr. Therefore, 24 h urine of 30 subjects with different dietary habits was analyzed with HPLC-MS/MS. The daily MG-HCr excretion via urine varied between omnivores (0.39-9.67 μmol/day, n = 24), vegetarians (0.18-0.97 μmol/day, n = 19), and vegans (0.10-0.27 μmol/day, n = 8). An intervention study with 18 subjects demonstrated the bioavailability of MG-HCr (ca. 54%) from 200 g of heated meat and its quick excretion with urine. A creatine intervention of 0.44 g did not increase MG-HCr excretion. Thus, the differences in MG-HCr excretion between different diets are mainly caused by the dietary uptake of MG-HCr. We additionally found MG-HCr in milk and egg products, where it is formed during heat treatment. This partly explains differences in MG-HCr excretion of vegetarians and vegans. Hence, MG-HCr in urine is a short-term marker for the intake of heat-processed animal source food.

Analysis of Long Non-Coding RNAs and mRNAs Associated with Lactation in the Crop of Pigeons (Columba livia)

Pigeons have the ability to produce milk and feed their squabs. The genetic mechanisms underlying milk production in the crops of 'lactating' pigeons are not fully understood. In this study, RNA sequencing was employed to profile the transcriptome of lncRNA and mRNA in lactating and non-'lactating' pigeon crops. We identified 7066 known and 17,085 novel lncRNAs. Of these lncRNAs, 6166 were differentially expressed. Among the 15,138 mRNAs detected, 6483 were differentially expressed, including many predominant genes with known functions in the milk production of mammals. A GO annotation analysis revealed that these genes were significantly enriched in 55, 65, and 30 pathways of biological processes, cellular components, and molecular functions, respectively. A KEGG pathway enrichment analysis revealed that 12 pathways (involving 544 genes), including the biosynthesis of amino acids, the propanoate metabolism, the carbon metabolism and the cell cycle, were significantly enriched. The results provide fundamental evidence for the better understanding of lncRNAs' and differentially expressed genes' (DEGs) regulatory role in the molecular pathways governing milk production in pigeon crops. To our knowledge, this is the first genome-wide investigation of the lncRNAs in pigeon crop associated with milk production. This study provided valuable resources for differentially expressed lncRNAs and mRNAs, improving our understanding of the molecular mechanism of pigeon milk production.

Genetic analysis of orotic acid predicted with Fourier transform infrared milk spectra

Fourier transform infrared spectral analysis is a cheap and fast method to predict milk composition. A not very well studied milk component is orotic acid. Orotic acid is an intermediate in the biosynthesis pathway of pyrimidine nucleotides and is an indicator for the metabolic cattle disorder deficiency of uridine monophosphate synthase. The function of orotic acid in milk and its effect on calf health, health of humans consuming milk or milk products, manufacturing properties of milk, and its potential as an indicator trait are largely unknown. The aims of this study were to determine if milk orotic acid can be predicted from infrared milk spectra and to perform a large-scale phenotypic and genetic analysis of infrared-predicted milk orotic acid. An infrared prediction model for orotic acid was built using a training population of 292 Danish Holstein and 299 Danish Jersey cows, and a validation population of 381 Danish Holstein cows. Milk orotic acid concentration was determined with nuclear magnetic resonance spectroscopy. For genetic analysis of infrared orotic acid, 3 study populations were used: 3,210 Danish Holstein cows, 3,360 Danish Jersey cows, and 1,349 Dutch Holstein Friesian cows. Using partial least square regression, a prediction model for orotic acid was built with 18 latent variables. The error of the prediction for the infrared model varied from 1.0 to 3.2 mg/L, and the accuracy varied from 0.68 to 0.86. Heritability of infrared orotic acid predicted with the standardized prediction model was 0.18 for Danish Holstein, 0.09 for Danish Jersey, and 0.37 for Dutch Holstein Friesian. We conclude that milk orotic acid can be predicted with moderate to good accuracy based on infrared milk spectra and that infrared-predicted orotic acid is heritable. The availability of a cheap and fast method to predict milk orotic acid opens up possibilities to study the largely unknown functions of milk orotic acid.

Metabolome profiling in skeletal muscle to characterize metabolic alterations in over-conditioned cows during the periparturient period

The transition from late gestation to early lactation is associated with extensive changes in metabolic, endocrine, and immune functions in dairy cows. Skeletal muscle plays an important role in maintaining the homeorhetic adaptation to the metabolic needs of lactation. The objective of this study was to characterize the skeletal muscle metabolome in the context of the metabolic changes that occur during the transition period in dairy cows with high (HBCS) versus normal body condition (NBCS). Fifteen weeks antepartum, 38 pregnant multiparous Holstein cows were assigned to 1 of 2 groups, which were fed differently to reach the targeted BCS and back fat thickness (BFT) until dry-off at -49 d before calving (HBCS: >3.75 and >1.4 cm; NBCS: <3.5 and <1.2 cm). During the dry period and the subsequent lactation, both groups were fed identical diets. The differences in both BCS and BFT were maintained throughout the study. The metabolome was characterized in skeletal muscle samples (semitendinosus muscle) collected on d -49, 3, 21, and 84 relative to calving using a targeted metabolomics approach (AbsoluteIDQ p180 kit; Biocrates Life Sciences AG, Innsbruck, Austria), which allowed for the quantification of up to 188 metabolites from 6 different compound classes (acylcarnitines, amino acids, biogenic amines, glycerophospholipids, sphingolipids, and hexoses). On d -49, the concentrations of citrulline and hydroxytetradecadienyl-l-carnitine in muscle were higher in HBCS cows than in NBCS cows, but those of carnosine were lower. Over-conditioning did not affect the muscle concentrations of any of the metabolites on d 3. On d 21, the concentrations of phenylethylamine and linoleylcarnitine in muscle were lower in HBCS cows than in NBCS cows, and the opposite was true for lysophosphatidylcholine acyl C20:4. On d 84, the significantly changed metabolites were mainly long-chain (>C32) acyl-alkyl phosphatidylcholine and di-acyl phosphatidylcholine, along with 3 long-chain (>C16) sphingomyelin that were all lower in HBCS cows than in NBCS cows. These data contribute to a better understanding of the metabolic adaptation in skeletal muscle of dairy cows during the transition period, although the physiological significance and underlying molecular mechanisms responsible for the regulation of citrulline, hydroxytetradecadienyl-l-carnitine, carnosine, and phenylethylamine associated with over-conditioning are still elusive and warrant further investigation. The changes observed in muscle lysophosphatidylcholine and phosphatidylcholine concentrations may point to an alteration in phosphatidylcholine metabolism, probably resulting in an increase in membrane stiffness, which may lead to abnormalities in insulin signaling in the muscle of over-conditioned cows.

Microbiome and Metabolome Analyses of Milk From Dairy Cows With Subclinical Streptococcus agalactiae Mastitis-Potential Biomarkers

The microbial ecosystem in the udders of dairy cows directly influences the flavor and quality of milk. However, to our knowledge, no published research has analyzed the complex relationship between the udder microbiome and its associated metabolism in animals with subclinical mastitis. We identified the bacterial species and measured relative population numbers in the milk of cows with subclinical Streptococcus agalactiae mastitis (GBS) and compared this information to that from the milk of healthy cows. Metabolite profiles were determined to investigate correlations between the milk microbiota and metabolic factors in healthy vs. GBS dairy cows. Six milk samples from GBS cows and six from healthy cows were subjected to 16S rRNA gene sequencing to identify the microbial species using a MiSeq high-throughput sequencing apparatus. The metabolites present in the milk were identified by gas chromatography time-of-flight mass spectrometry. Both principal component analysis and orthogonal partial least squares discriminant analysis indicated that the metabolites were well-separated from each other in the milk samples from the two groups. GBS dramatically altered microbial diversity, and the GBS group had significantly fewer Proteobacteria, Actinobacteria, and Acidobacteria than the CON group, with greater relative abundance of Firmicutes (p < 0.01). Several bacterial genera, such as Streptococcus, were significantly more abundant in milk from the GBS group than in milk from the CON group, and there was a tendency for greater abundance of Turicibacter (p = 0.07) and Enterococcus spp. (p = 0.07) in the GBS group. The levels of five milk metabolites were significantly higher in the GBS group than in the CON group: phenylpyruvic acid, the homogentisic acid: 4-hydroxyphenylpyruvic acid ratio, the xanthine: guanine ratio, uridine and glycerol. Metabolic pathway analysis of the different metabolites revealed that the following were enriched in both groups: galactose metabolism; pentose and glucuronate interconversion; starch and sucrose metabolism; alanine, aspartate and glutamate metabolism; arginine biosynthesis; citrate cycle (TCA cycle); D-glutamine and D-glutamate metabolism; and the neomycin, kanamycin, and gentamicin biosynthesis pathways. Several typical metabolites were highly correlated with specific ruminal bacteria, such as Streptococcaceae, Lachnospiraceae, Lactobacillaceae and Corynebacteriaceae, demonstrating the functional correlations between the milk microbiome and associated metabolites. These findings revealed that the milk microbiota and metabolite profiles were significantly different between the two groups of cows, raising the question of whether the microbiota associated with the bovine mammary gland could be related to mammary gland health. There was also a relationship between milk quality and the presence of spoilage bacteria. Other bacterial taxa should be investigated, as related information may provide insights into how perturbations in milk metabolomics profiles relate to differences in milk synthesis between healthy cows and those with subclinical mastitis.

Metabolomic profiles in yak mammary gland tissue during the lactation cycle

The yak is one of the most important domestic animals in Tibetan life for providing basic resources such as milk, meat and transportation. Although yak milk production is not elevated, yak milk is superior to dairy cow milk in nutrient composition (protein and fat). However, the understanding of the metabolic mechanisms of yak mammary gland tissue during the lactation cycle remains elusive. In this study, GC-MS-based metabolomics was employed to study the metabolic variations in the yak mammary gland during the lactation cycle (pregnancy, lactation and dry period). Twenty-nine metabolites were up or downregulated during the lactation period. Compared to the dry period, during the lactation period the levels of oxalic acid were upregulated, while glycine and uridine were downregulated. Thirty-seven pathways were obtained when the 29 differential metabolites were imported into the KEGG pathway analysis. The most impacted pathways during the lactation cycle were glycine, serine and threonine metabolism; alanine, aspartate and glutamate metabolism; TCA cycle; glyoxylate and dicarboxylate metabolism; and pyrimidine metabolism. Our results provide important insights into the metabolic events involved in yak mammary gland development, lactogenesis and lactation, which can guide further research to improve milk yield and enhance the constituents of yak milk.

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.

Worldwide Variation in Human Milk Metabolome: Indicators of Breast Physiology and Maternal Lifestyle?

Human milk provides essential substrates for the optimal growth and development of a breastfed infant. Besides providing nutrients to the infant, human milk also contains metabolites which form an intricate system between maternal lifestyle, such as the mother's diet and the gut microbiome, and infant outcomes. This study investigates the variation of these human milk metabolites from five different countries. Human milk samples (n = 109) were collected one month postpartum from Australia, Japan, the USA, Norway, and South Africa and were analyzed by nuclear magnetic resonance. The partial least squares discriminant analysis (PLS-DA) showed separation between either maternal countries of origin or ethnicities. Variation between countries in concentration of metabolites, such as 2-oxoglutarate, creatine, and glutamine, in human milk, between countries, could provide insights into problems, such as mastitis and/or impaired functions of the mammary glands. Several important markers of milk production, such as lactose, betaine, creatine, glutamate, and glutamine, showed good correlation between each metabolite. This work highlights the importance of milk metabolites with respect to maternal lifestyle and the environment, and also provides the framework for future breastfeeding and microbiome studies in a global context.