NMR-metabolomics profiling of mammary gland secretory tissue and milk serum in two goat breeds with different levels of tolerance to seasonal weight loss

Goat mammary gland metabolism: An integrated Omics analysis to unravel seasonal weight loss tolerance

Seasonal weight loss (SWL), is a major limitation to animal production. In the Canary Islands, there are two dairy goat breeds with different levels of tolerance to SWL: Majorera (tolerant) and Palmera (susceptible). Our team has studied the response of these breeds to SWL using different Omics tools. The objective of this study was to integrate such results in a data driven approach and using dedicated tools, namely the DIABLO method. The outputs of our analysis mainly separate unrestricted from restricted goats. Metabolites behave as "hub" molecules, grouping interactions with several genes and proteins. Unrestricted goats upregulated protein synthesis, along with arginine catabolism and adipogenesis pathways, which are related with higher anabolic rates and a larger proportion of secretory tissue, in agreement with their higher milk production. Contrarily, restricted goats seemingly increased the synthesis of acetyl-CoA through serine and acetate conversion into pyruvate. This may have occurred to increase fatty acid synthesis and/or to use them as an energy source in detriment to glucose, which was more available in the diet of unrestricted goats. Lastly, restricted Palmera upregulated the expression of PEBP4 and GPD1 genes compared to all other groups, which might support their use as putative biomarkers for SWL susceptibility. SIGNIFICANCE: Seasonal weight loss (SWL) is a major issue influencing animal production in the tropics and Mediterranean. By studying its impact on the mammary gland of tolerant and susceptible dairy goat breeds, using Omics, we aim at surveying the tissue for possible biomarkers that reflect these traits. In this study, data integration of three Omics (transcriptomics, proteomics and metabolomics) was performed using bioinformatic tools, to relate putative biomarkers and evaluate all three levels of information; in a novel approach. This information can enhance selection programs, lowering the impact of SWL on food production systems.

Impact of dietary Chlorella vulgaris and feed enzymes on health status, immune response and liver metabolites in weaned piglets

In this study, we analysed the impact of dietary inclusion of Chlorella vulgaris and carbohydrases on general health, redox status, immune response, liver lipids and metabolites in weaned piglets. Forty-four male piglets were allocated into four diets: control (n = 11), CH (control diet with 5% CH, n = 10), CH+R (control diet with 5% CH plus 0.005% Rovabio Excel AP, n = 10), and CH+M (control diet with 5% CH plus 0.01% of a pre-selected four-CAZyme mixture, n = 11). After 15 days of trial, animals were slaughtered and samples of blood and liver collected. Spectrophotometry methods and commercial kits were used to determine blood parameters and gas and liquid chromatography for hepatic fatty acid and chlorophylls profiles, respectively. While total, LDL- and VLDL-cholesterol were increased by CH, the opposite was recorded for HDL-cholesterol (p < 0.001). Piglets fed CH-based diets presented an increase of IgG and a decrease of IgM (p < 0.001) which along with lymphocytes exacerbation contributed for piglets' survival after weaning. n-6 PUFA were reduced in piglets fed CH and the opposite occurred for n-3 PUFA (p < 0.001), thus benefiting n-6/n-3 ratio in the liver. Chlorophylls amount was not changed by the use of Rovabio or enzymatic mixture. The discriminant analysis applied to hepatic parameters revealed a clear separation between control and CH-based diets but failed to discriminate feed enzymes. Our findings indicate health promoting effects of CH as feed ingredient in piglets' nutrition at weaning, without negatively impacting on animals' performance.

Effect of dietary Spirulina (Arthrospira platensis) on the intestinal function of post-weaned piglet: An approach combining proteomics, metabolomics and histological studies

The effect of dietary Spirulina (Arthrospira platensis) and CAZyme supplementation was assessed on the gut of weaned piglets, using an integrated NMR-metabolomics approach combined with Tandem Mass Tag labelled proteomics. Thirty weaned male piglets were assigned to one of the three following diets (n = 10): cereal and soybean meal basal diet (Control), basal diet with 10% Spirulina inclusion (SP) and SP diet supplemented with 0.01% lysozyme (SP + L). The experiment lasted 4 weeks and, upon slaughter, small intestine samples were collected for histological, metabolomic and proteomic analysis. No significant differences were found for the histology and metabolomics analysis between the three experimental groups. Lactate, glutamate, glycine and myo-inositol were the most abundant metabolites. Proteomics results showed 1502 proteins identified in the intestine tissue. A total of 23, 78, 27 differentially abundant proteins were detected respectively for the SP vs. Control, SP + L vs. Control and SP + L vs. SP comparisons. The incorporation of Spirulina and supplementation of lysozyme in the piglet's diets is associated to intestinal proteomic changes. These include increased protein synthesis and abundance of contractile apparatus proteins, related with increased nutrient availability, which has beneficial (increased glucose uptake) and detrimental (increased digesta viscosity) metabolic effects. SIGNIFICANCE: The use of conventional feedstuffs becomes increasingly prohibitive due to its environmental toll. To increase the sustainability of the livestock sector, novel feedstuffs such as microalgae need to be considered. However, its recalcitrant cell wall has antinutritional effects that can inhibit high dietary inclusion levels. The supplementation with CAZymes is a possible solution to this issue. The small intestine is a central piece in monogastric digestion and of particular importance for the weaned piglet. Studying the effect of dietary Spirulina and CAZyme supplementation on its histomorphology, metabolome and proteome allows studying relevant physiological adaptations to these diets.

Extensive Sheep and Goat Production: The Role of Novel Technologies towards Sustainability and Animal Welfare

Simple Summary

New technologies have been recognized as valuable in controlling, monitoring, and managing farm animal activities. It makes it possible to deepen the knowledge of animal behavior and improve animal welfare and health, which has positive implications for the sustainability of animal production. In recent years, successful technological developments have been applied in intensive farming systems; however, due to challenging conditions that extensive pasture-based systems show, technology has been more limited. Nevertheless, awareness of the available technological solutions for extensive conditions can increase the implementation of their adoption among farmers and researchers. In this context, this review addresses the role of different technologies applied to sheep and goat production in extensive systems. Examples related to precision livestock farming, omics, thermal stress, colostrum intake, passive immunity, and newborn survival are presented; biomarkers of metabolic diseases and parasite resistance breeding are discussed.

Abstract

Sheep and goat extensive production systems are very important in the context of global food security and the use of rangelands that have no alternative agricultural use. In such systems, there are enormous challenges to address. These include, for instance, classical production issues, such as nutrition or reproduction, as well as carbon-efficient systems within the climate-change context. An adequate response to these issues is determinant to economic and environmental sustainability. The answers to such problems need to combine efficiently not only the classical production aspects, but also the increasingly important health, welfare, and environmental aspects in an integrated fashion. The purpose of the study was to review the application of technological developments, in addition to remote-sensing in tandem with other state-of-the-art techniques that could be used within the framework of extensive production systems of sheep and goats and their impact on nutrition, production, and ultimately, the welfare of these species. In addition to precision livestock farming (PLF), these include other relevant technologies, namely omics and other areas of relevance in small-ruminant extensive production: heat stress, colostrum intake, passive immunity, newborn survival, biomarkers of metabolic disease diagnosis, and parasite resistance breeding. This work shows the substantial, dynamic nature of the scientific community to contribute to solutions that make extensive production systems of sheep and goats more sustainable, efficient, and aligned with current concerns with the environment and welfare.

Analytical Methodology for a Metabolome Atlas of Goat's Plasma, Milk and Feces Using 1H-NMR and UHPLC-HRMS

Metabolomics has been increasingly used in animal and food sciences. Animal health is one of the most important factor that can also alter animal integrity and welfare. Some studies have already investigated the link between health and metabolic profile of dairy animals. These studies in metabolomics often consider a single type of sample using a single analytical platform (nuclear magnetic resonance or mass spectrometry). Only few studies with multi-platform approaches are also used with a single or a multi type of sample, but they mainly consider dairy cows’ metabolome although dairy goats present similar diseases, that it could be interesting to detect early to preserve animal health and milk production. This study aims to create a metabolic atlas of goat plasma, milk and feces, based on healthy animals. Our study describes a standard operating procedure for three goat matrices: blood plasma, milk, and feces using multiple platforms (NMR (¹H), UHPLC (RP)-MS and UHPLC (HILIC)-MS) that follows a unique sample preparation procedure for each sample type to be analyzed on multi-platforms basis. Our method was evaluated for its robustness and allowed a better characterization of goat metabolic profile in healthy conditions.

Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis

This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.

Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.

Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach

Background

Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional value. During the dry season, ruminants, particularly those raised in extensive production systems, lose around 30% of their body weight. Seasonal weight loss has important consequences on animal productive performance and health. In this study, RNA sequencing was used to characterize feed restriction effects in dairy goat of 2 breeds with different SWL tolerance: Majorera (tolerant) and Palmera (susceptible). Nine Majorera and ten Palmera goats were randomly distributed in a control and a restricted group: Majorera Control (adequately fed; MC; n = 4), Palmera Control (adequately fed; PC; n = 6), Majorera Restricted (feed restricted; ME; n = 5) and Palmera Restricted (feed restricted; PE; n = 4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis.

Results

From these samples, 24,260 unique transcripts were identified. From those, 82 transcripts were differentially expressed between MC and ME, 99 between PC and PE, twelve between both control groups and twenty-nine between both restricted groups.

Conclusions

Feed restriction affected several biochemical pathways in both breeds such as: carbohydrate and lipid transport; intracellular trafficking, RNA processing and signal transduction. This research also highlights the importance or involvement of the genes in tolerance (ENPP1, S-LZ, MT2A and GPNB) and susceptibility (GPD1, CTPS1, ELOVL6 and NR4A1) to SWL with respectively higher expression in the Majorera restriced group and the Palmera restricted group in comparison to the control groups. In addition, results from the study may be extrapolated to other dairy ruminant species.

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.

Urinary proteome and metabolome in dogs (Canis lupus familiaris): The effect of chronic kidney disease

Chronic kidney disease (CKD) is a progressive and irreversible disease. Although urine is an ideal biological sample for proteomics and metabolomics studies, sensitive and specific biomarkers are currently lacking in dogs. This study characterised dog urine proteome and metabolome aiming to identify and possibly quantify putative biomarkers of CKD in dogs. Twenty-two healthy dogs and 28 dogs with spontaneous CKD were selected and urine samples were collected. Urinary proteome was separated by SDS-PAGE and analysed by mass spectrometry, while urinary metabolome was analysed in protein-depleted samples by 1D ¹H NMR spectra. The most abundant proteins in urine samples from healthy dogs were uromodulin, albumin and, in entire male dogs, arginine esterase. In urine samples from CKD dogs, the concentrations of uromodulin and albumin were significantly lower and higher, respectively, than in healthy dogs. In addition, these samples were characterised by a more complex protein pattern indicating mixed glomerular (protein bands ≥65 kDa) and tubular (protein bands <65 kDa) proteinuria. Urine spectra acquired by NMR allowed the identification of 86 metabolites in healthy dogs, belonging to 49 different pathways mainly involved in amino acid metabolism, purine and aminoacyl-tRNA biosynthesis or tricarboxylic acid cycle. Seventeen metabolites showed significantly different concentrations when comparing healthy and CKD dogs. In particular, carnosine, trigonelline, and cis-aconitate, might be suggested as putative biomarkers of CKD in dogs. SIGNIFICANCE: Urine is an ideal biological sample, however few proteomics and metabolomics studies investigated this fluid in dogs and in the context of CKD (chronic kidney disease). In this research, applying a multi-omics approach, new insights were gained regarding the molecular changes triggered by this disease in canine urinary proteome and metabolome. In particular, the involvement of the tubular component was highlighted, suggesting uromodulin, trigonelline and carnosine as possible biomarkers of CKD in dogs.

Mineral profiling of muscle and hepatic tissues of Australian Merino, Damara and Dorper lambs: Effect of weight loss

Seasonal weight loss (SWL) is a major constraint to extensive animal production systems. The Australian sheep production is based on merino sheep, a European breed not tolerant to SWL. Tolerant alternative breeds such as the fat-tailed Damara and the Dorper have been increasingly used in Australia and elsewhere, due to their robustness. The aim of this study was to understand the mineral profile of muscle and liver tissues of Australian Merino, Damara and Dorper, when subjected to SWL in order to understand SWL-tolerance physiology. Twenty-four lambs were divided randomly between growing (control) and nutritionally restricted groups for each breed. The trial lasted 42 days. Animals were weighed bi-weekly and at the end of the trial, lambs were slaughtered. Liver and muscle samples were taken immediately after slaughter. Mineral assessment was carried out using inductively coupled plasma-optical emission spectrometry. Analysis of variance showed mineral concentrations were generally increased in the muscle of restricted animals, mainly because of fat tissue mobilization. An increase in Zn and Fe concentrations indicates an increase of enzymatic activity in the liver of restricted sheep as well as differential abundance of Fe-containing proteins. High concentrations of Cu in the liver of Dorper indicate higher ability to accumulate this element, even under SWL.

A blood metabolomics study of metabolic variations in Inner Mongolia white cashmere goats under shortened and natural photoperiod conditions

This study investigated metabolic variations by using gas chromatography – mass spectrometry (GC–MS)-based metabolomics in the blood of Inner Mongolia white cashmere goats under shortened and natural photoperiod conditions. Twenty-four female (non-pregnant) Inner Mongolia white cashmere goats aged 1–1.5 yr with similar live weights (mean, 20.36 ± 2.63 kg) were randomly allocated into two groups: a natural daily photoperiod group (NDPP group: 10–16 h light, n = 12) and a short daily photoperiod group (SDPP group: 7 h light:17 h dark, n = 12). In this study, we found that a SDPP promoted the blood metabolic perturbations based on the GC–MS-based metabolomics investigation, and nine metabolites were related to a SDPP. Compared with the NDPP group, the contents of serine, oxaloacetic acid, xylose, l-3,4-dihydroxyphenylalanine, and xanthosine significantly were up-regulated, whereas the contents of carnitine, 1,3-diaminopropane, indole-3-acetic acid, and l-kynurenine were significantly down-regulated in the SDPP group. The different metabolites could contribute to the regulation mechanisms of promoting cashmere growth of goats in the SDPP group.

Biomarkers of fitness and welfare in dairy animals: healthy living

Increased animal productivity has reduced animal fitness, resulting in increased susceptibility to infectious and metabolic diseases, locomotion problems and subfertility. Future animal breeding strategies should focus on balancing high production levels with health status monitoring and improved welfare. Additionally, understanding how animals interact with their internal and external environment is essential for improving health, fitness, and welfare. In this context, the continuous validation of existing biomarkers and the discovery and field implementation of new biomarkers will enable us to understand the specific physiological process and regulatory mechanisms used by the organism to adapt to different environmental conditions. Thus, biomarkers may be used to monitor welfare and improve management and breeding strategies. In this article, we describe major achievements in the establishment of biomarkers in dairy cows and small ruminants. This review mainly focuses on the physiological biomarkers used to monitor animal responses to, and recovery from, environmental perturbations. We highlight future avenues for research in this field and present a timely positioning document to the scientific community.

Dairy science and health in the tropics: challenges and opportunities for the next decades

In the next two decades, the world population will increase significantly; the majority in the developing countries located in the tropics of Africa, Asia, Latin America, and the Caribbean. To feed such a population, it is necessary to increase the availability of food, particularly high-value animal protein foods produced locally, namely meat and dairy products. Dairy production in tropical regions has a lot of growth potential, but also poses a series of problems, particularly as dairy production systems were developed in temperate countries and in most cases are difficult to implement in the tropics. Drawbacks include hot weather and heat stress, the lack of availability of adequate feeds, poor infrastructure, and cold chain and the competition with cheap imports from temperate countries. This position paper reviews the major drawbacks in dairy production for the five major dairy species: cattle, water buffalo, sheep, goat, and camel, as well as the future trends in research and development. It also concerns the major trends in reproduction and production systems and health issues as well as environmental concerns, particularly those related to greenhouse gas emissions. Tropical Animal Health and Production now launches a topical collection on Tropical Dairy Science. We aim to publish interesting and significant papers in tropical dairy science. On behalf of the editorial board of the Tropical Animal Health and Production, we would like to invite all authors working in this field to submit their works on this topic to this topical collection in our journal.

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.

Assessing mineral status in edible tissues of domestic and game animals: a review with a special emphasis in tropical regions

Mineral status in edible tissues has been extensively studied since the beginning of the twentieth century. Most research focus on nutrition, as the earliest reports were essentially related to nutrition, animal health and mineral deficiencies. Nutrition wise, minerals are of great importance for consumers worldwide, as meat (i.e. beef, pork, chicken) and fish are major sources of protein in human diets. Nutrition gains renewed importance in the tropical context, since tropical forages are poor in minerals. This fact contributes to mineral deficiencies and impaired production performance in extensive production systems, with greater emphasis in ruminant species. In addition to nutrition, several other factors have an important impact in mineral metabolism such as geographic location, gender and species. In this article, we aim to infer on both the role in the organism and the amount present in various edible tissues of different species, either game or production animals, presenting an overall perspective in the context of tropical animal production.

Tools for Enhanced NMR-Based Metabolomics Analysis

Metabolomics is the study of profiles of small molecules in biological fluids, cells, or organs. These profiles can be thought of as the "fingerprints" left behind from chemical processes occurring in biological systems. Because of its potential for groundbreaking applications in disease diagnostics, biomarker discovery, and systems biology, metabolomics has emerged as a rapidly growing area of research. Metabolomics investigations often, but not always, involve the identification and quantification of endogenous and exogenous metabolites in biological samples. Software tools and databases play a crucial role in advancing the rigor, robustness, reproducibility, and validation of these studies. Specifically, the establishment of a robust library of spectral signatures with unique compound descriptors and atom identities plays a key role in profiling studies based on data from nuclear magnetic resonance (NMR) spectroscopy. Here, we discuss developments leading to a rigorous basis for unique identification of compounds, reproducible numbering of atoms, the compact representation of NMR spectra of metabolites and small molecules, tools for improved compound identification, quantification and visualization, and approaches toward the goal of rigorous analysis of metabolomics data.

Mammary gland and milk fatty acid composition of two dairy goat breeds under feed-restriction

Goat dairy products are an important source of animal protein in the tropics. During the dry season, pasture scarcity leads animals to lose up to 40% of their body weight, a condition known as Seasonal Weight Loss (SWL) that is one of the major constraints in ruminant production. Breeds with high tolerance to SWL are relevant to understand the physiological responses to pasture scarcity so they could be used in programs for animal breeding. In the Canary Islands there are two dairy goat breeds with different levels of tolerance to SWL: the Palmera, susceptible to SWL; and the Majorera, tolerant to SWL. Fat is one of the milk components most affected by environmental and physiological conditions. This study hypothesises that feed-restriction affects Majorera and Palmera breeds differently, leading to different fatty acid profiles in the mammary gland and milk. An interaction between breed and feed-restriction was observed in the mammary gland. Feed-restriction was associated with an increase in oleic acid and a decrease in palmitic acid percentage in the Palmera breed whereas no differences were observed in the Majorera breed. Palmitic and oleic acids together constituted around 60% of the total fatty acids identified, which suggests that Palmera breed is more susceptible to SWL. In milk, feed-restriction affected both breeds similarly. Regarding the interaction of the breed with the treatment, we also observed similar responses in both breeds, but this influence affects only around 2% of the total fatty acids. In general, Majorera breed is more tolerant to feed-restriction.

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

Background

Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns during lactation using the overall biofluid metabolomics and the metabolic differences from non-lactation periods, as determined using partial tissue-metabolomics. We analyzed the metabolomic profiles of four biofluids (rumen fluid, serum, milk and urine) and their relationships in six mid-lactation Holstein cows and compared their mammary gland (MG) metabolomic profiles with those of six non-lactating cows by using gas chromatography-time of flight/mass spectrometry.

Results

In total, 33 metabolites were shared among the four biofluids, and 274 metabolites were identified in the MG tissues. The sub-clusters of the hierarchical clustering analysis revealed that the rumen fluid and serum metabolomics profiles were grouped together and highly correlated but were separate from those for milk. Urine had the most different profile compared to the other three biofluids. Creatine was identified as the most different metabolite among the four biofluids (VIP = 1.537). Five metabolic pathways, including gluconeogenesis, pyruvate metabolism, the tricarboxylic acid cycle (TCA cycle), glycerolipid metabolism, and aspartate metabolism, showed the most functional enrichment among the four biofluids (false discovery rate < 0.05, fold enrichment >2). Clear discriminations were observed in the MG metabolomics profiles between the lactating and non-lactating cows, with 54 metabolites having a significantly higher abundance (P < 0.05, VIP > 1) in the lactation group. Lactobionic acid, citric acid, orotic acid and oxamide were extracted by the S-plot as potential biomarkers of the metabolic difference between lactation and non-lactation. The TCA cycle, glyoxylate and dicarboxylate metabolism, glutamate metabolism and glycine metabolism were determined to be pathways that were significantly impacted (P < 0.01, impact value >0.1) in the lactation group. Among them, the TCA cycle was the most up-regulated pathway (P < 0.0001), with 7 of the 10 related metabolites increased in the MG tissues of the lactating cows.

Conclusions

The overall biofluid and MG tissue metabolic mechanisms in the lactating cows were interpreted in this study. Our findings are the first to provide an integrated insight and a better understanding of the metabolic mechanism of lactation, which is beneficial for developing regulated strategies to improve the metabolic status of lactating dairy cows.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4314-1) contains supplementary material, which is available to authorized users.

Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening

The exceptionally rich information content of nuclear magnetic resonance (NMR) spectra is routinely used to identify and characterize molecules and molecular interactions in a wide range of applications, including clinical biomarker discovery, drug discovery, environmental chemistry, and metabolomics. The set of peak positions and intensities from a reference NMR spectrum generally serves as the identifying signature for a compound. Reference spectra normally are collected under specific conditions of pH, temperature, and magnetic field strength, because changes in conditions can distort the identifying signatures of compounds. A spin system matrix that parametrizes chemical shifts and coupling constants among spins provides a much richer feature set for a compound than a spectral signature based on peak positions and intensities. Spin system matrices expand the applicability of NMR spectral libraries beyond the specific conditions under which data were collected. In addition to being able to simulate spectra at any field strength, spin parameters can be adjusted to systematically explore alterations in chemical shift patterns due to variations in other experimental conditions, such as compound concentration, pH, or temperature. We present methodology and software for efficient interactive optimization of spin parameters against experimental 1D-¹H NMR spectra of small molecules. We have used the software to generate spin system matrices for a set of key mammalian metabolites and are also using the software to parametrize spectra of small molecules used in NMR-based ligand screening. The software, along with optimized spin system matrix data for a growing number of compounds, is available from http://gissmo.nmrfam.wisc.edu/ .

The hepatic and skeletal muscle ovine metabolomes as affected by weight loss: a study in three sheep breeds using NMR-metabolomics

Sheep are a valuable resource for meat and wool production. During the dry summer, pastures are scarce and animals face Seasonal Weight Loss (SWL), which decreases production yields. The study of breeds tolerant to SWL is important to understand the physiological mechanisms of tolerance to nutritional scarcity, and define breeding strategies. Merino, Damara and Dorper sheep breeds have been described as having different levels of tolerance to SWL. In this work, we assess their liver and muscle metabolomes, and compare the responses to feed restriction. Ram lambs from each breed were divided into growth and feed restricted groups, over 42 days. Tissue metabolomes were assessed by ¹H-NMR. The Dorper restricted group showed few changes in both tissues, suggesting higher tolerance to nutritional scarcity. The Merinos exhibited more differences between treatment groups. Major differences were related to fat and protein mobilization, and antioxidant activity. Between the Damara groups, the main differences were observed in amino acid composition in muscle and in energy-related pathways in the liver. Integration of present results and previous data on the same animals support the hypothesis that, Dorper and Damara breeds are more tolerant to SWL conditions and thus, more suitable breeds for harsh environmental conditions.