Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNomics in horses

Immunology of Physical Exercise: Is Equus caballus an Appropriate Animal Model for Human Athletes?

Domestic horses routinely participate in vigorous and various athletic activities. This enables the horse to serve as a model for studying athletic physiology and immunology in other species, including humans. For instance, as a model of physical efforts, such as endurance rides (long-distance running/aerobic exercise) and races (anaerobic exercise), the horse can be useful in evaluating post-exercise response. Currently, there has been significant interest in finding biomarkers, which characterize the advancement of training and adaptation to physical exercise in the horse. The parallels in cellular responses to physical exercises, such as changes in receptor expression and blood cell activity, improve our understanding of the mechanisms involved in the body's response to intense physical activity. This study focuses on the changes in levels of the pro- and anti-inflammatory cytokines and cellular response in the context of post-exercise immune response. Both the direction of changes in cytokine levels and cellular responses of the body, such as proliferation and expression of surface markers on lymphocytes, monocytes and neutrophils, show cross-functional similarities. This review reveals that horses are robust research models for studying the immune response to physical exercise in human athletes.

Nuclear Magnetic Resonance (NMR) Metabolomics: Current Applications in Equine Health Assessment

Metabolomics can allow for the comprehensive identification of metabolites within biological systems, at given time points, in physiological and pathological conditions. In the last few years, metabolomic analysis has gained popularity both in human and in veterinary medicine, showing great potential for novel applications in clinical activity. The aim of applying metabolomics in clinical practice is understanding the mechanisms underlying pathological conditions and the influence of certain stimuli (i.e., drugs, nutrition, exercise) on body systems, in the attempt of identifying biomarkers that can help in the diagnosis of diseases. Proton Nuclear Magnetic Resonance spectroscopy (1H-NMR) is well tailored to be used as an analytical platform for metabolites' detection at the base of metabolomics studies, due to minimal sample preparation and high reproducibility. In this mini-review article, the scientific production of NMR metabolomic applications to equine medicine is examined. The research works are very different in methodology and difficult to compare. Studies are mainly focused on exercise, reproduction, and nutrition, other than respiratory and musculoskeletal diseases. The available information on this topic is still scant, but a greater collection of data could allow researchers to define new reliable markers to be used in clinical practice for diagnostic and therapeutical purposes.

Untargeted Metabolomics Profiling Reveals Exercise Intensity-Dependent Alterations in Thoroughbred Racehorses' Plasma after Routine Conditioning Sessions

Thoroughbred (TB) racehorses undergo rigorous conditioning programs to optimize their physical and mental capabilities through varied exercise sessions. While conventional investigations focus on limited hematological and biochemical parameters, this field study employed untargeted metabolomics to comprehensively assess metabolic responses triggered by exercise sessions routinely used in TB conditioning. Blood samples were collected pre- and post-exercise from ten racehorses, divided into two groups based on exercise intensity: high intensity (n = 6, gallop at ± 13.38 m/s, 1400 m) and moderate intensity (n = 4, soft canter at ± 7.63 m/s, 2500 m). Intensity was evaluated through monitoring of the speed, heart rate, and lactatemia. Resting and 30 min post-exercise plasma samples were analyzed using ultraperformance liquid chromatography coupled with high-resolution mass spectrometry. Unsupervised principal component analysis revealed exercise-induced metabolome changes, with high-intensity exercise inducing greater alterations. Following high-intensity exercise, 54 metabolites related to amino acid, fatty acid, nucleic acid, and vitamin metabolism were altered versus 23 metabolites, primarily linked to fatty acid and amino acid metabolism, following moderate-intensity exercise. Metabolomics confirmed energy metabolism changes reported by traditional biochemistry studies and highlighted the involvement of lipid and amino acid metabolism during routine exercise and recovery, aspects that had previously been overlooked in TB racehorses.

Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability

RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses (Equus caballus) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1, CCL5, CD40LG, FOS, IL1R2, IL20RA, and IL22RA2, on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2, GYG1, HIF1A, MOGAT1, PFKFB3, PLIN5, SIK1, and STBD1.

Comparison of muscle metabolomics between two Chinese horse breeds

With their enormous muscle mass and athletic ability, horses are well-positioned as model organisms for understanding muscle metabolism. There are two different types of horse breeds-Guanzhong (GZ) horses, an athletic breed with a larger body height (~148.7 cm), and the Ningqiang pony (NQ) horses, a lower height breed generally used for ornamental purposes-both inhabited in the same region of China with obvious differences in muscle content. The main objective of this study was to evaluate the breed-specific mechanisms controlling muscle metabolism. In this study, we observed muscle glycogen, enzyme activities, and LC-MS/MS untargeted metabolomics in the gluteus medius muscle of six, each of GZ and NQ horses, to explore differentiated metabolites that are related to the development of two muscles. As expected, the glycogen content, citrate synthase, and hexokinase activity of muscle were significantly higher in GZ horses. To alleviate the false positive rate, we used both MS1 and MS2 ions for metabolite classification and differential analysis. As a result, a total of 51,535 MS1 and 541 MS2 metabolites were identified, and these metabolites can separate these two groups from each other. Notably, 40% of these metabolites were clustered into lipids and lipid-like molecules. Furthermore, 13 significant metabolites were differentially detected between GZ and NQ horses (fold change [FC] value ≥ 2, variable important in projection value ≥1, and Q value ≤ 0.05). They are primarily clustered into glutathione metabolism (GSH, p = 0.01), taurine, and hypotaurine metabolism (p < 0.05) pathways. Seven of the 13 metabolites were also found in thoroughbred racing horses, suggesting that metabolites related to antioxidants, amino acids, and lipids played a key role in the development of skeleton muscle in horses. Those metabolites related to muscle development shed a light on racing horses' routine maintenance and improvement of athletic performance.

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance. Still, the extent of its functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built an integrated horse gut gene catalog comprising ~25 million unique genes and 372 metagenome-assembled genomes. This catalog represents 4179 genera spanning 95 phyla and functional capacities primed to exploit energy from dietary, microbial, and host resources. The holo-omics approach shows that gut microbiomes enriched in Lachnospiraceae taxa are negatively associated with cardiovascular capacity. Conversely, more complex and functionally diverse microbiomes are associated with higher glucose concentrations and reduced accumulation of long-chain acylcarnitines and non-esterified fatty acids in plasma, suggesting increased ß-oxidation capacity in the mitochondria. In line with this hypothesis, more fit athletes show upregulation of mitochondrial-related genes involved in energy metabolism, biogenesis, and Ca²⁺ cytosolic transport, all of which are necessary to improve aerobic work power, spare glycogen usage, and enhance cardiovascular capacity. The results identify an associative link between endurance performance and gut microbiome composition and gene function, laying the basis for nutritional interventions that could benefit horse athletes.

An integrated gene catalog of the gut microbiome in elite endurance horses is build. The holo-omics analyses identify an associative link between endurance performance and gut microbiome composition and gene function.

Potential genetic robustness of Prnp and Sprn double knockout mouse embryos towards ShRNA-lentiviral inoculation

The Shadoo and PrP prion protein family members are thought to be functionally related, but previous knockdown/knockout experiments in early mouse embryogenesis have provided seemingly contradictory results. In particular, Shadoo was found to be indispensable in the absence of PrP in knockdown analyses, but a double-knockout of the two had little phenotypic impact. We investigated this apparent discrepancy by comparing transcriptomes of WT, Prnp^0/0 and Prnp^0/0Sprn^0/0 E6.5 mouse embryos following inoculation by Sprn- or Prnp-ShRNA lentiviral vectors. Our results suggest the possibility of genetic adaptation in Prnp^0/0Sprn^0/0 mice, thus providing a potential explanation for their previously observed resilience.

Metabolomics in clinical and forensic toxicology, sports anti-doping and veterinary residues

Metabolomics is a multidisciplinary field providing workflows for complementary approaches to conventional analytical determinations. It allows for the study of metabolically related groups of compounds or even the study of novel pathways within the biological system. The procedural stages of metabolomics; experimental design, sample preparation, analytical determinations, data processing and statistical analysis, compound identification and validation strategies are explored in this review. The selected approach will depend on the type of study being conducted. Experimental design influences the whole metabolomics workflow and thus needs to be properly assessed to ensure sufficient sample size, minimal introduced and biological variation and appropriate statistical power. Sample preparation needs to be simple, yet potentially global in order to detect as many compounds as possible. Analytical determinations need to be optimised either for the list of targeted compounds or a universal approach. Data processing and statistical analysis approaches vary widely and need to be better harmonised for review and interpretation. This includes validation strategies that are currently deficient in many presented workflows. Common compound identification approaches have been explored in this review. Metabolomics applications are discussed for clinical and forensic toxicology, human and equine sports anti-doping and veterinary residues.

Comparison of Shifts in Skeletal Muscle Plasticity Parameters in Horses in Three Different Muscles, in Answer to 8 Weeks of Harness Training

Training-induced follow-up of multiple muscle plasticity parameters in postural stability vs. locomotion muscles provides an integrative physiological view on shifts in the muscular metabolic machinery. It can be expected that not all muscle plasticity parameters show the same expression time profile across muscles. This knowledge is important to underpin results of metabolomic studies. Twelve non-competing Standardbred mares were subjected to standardized harness training. Muscle biopsies were taken on a non-training day before and after 8 weeks. Shifts in muscle fiber type composition and muscle fiber cross-sectional area (CSA) were compared in the m. pectoralis, the m. vastus lateralis, and the m. semitendinosus. In the m. vastus lateralis, which showed most pronounced training-induced plasticity, two additional muscle plasticity parameters (capillarization and mitochondrial density) were assessed. In the m. semitendinosus, additionally the mean minimum Feret's diameter was assessed. There was a significant difference in baseline profiles. The m. semitendinosus contained less type I and more type IIX fibers compatible with the most pronounced anaerobic profile. Though no baseline fiber type-specific and overall mean CSA differences could be detected, there was a clear post-training decrease in fiber type specific CSA, most pronounced for the m. vastus lateralis, and this was accompanied by a clear increase in capillary supply. No shifts in mitochondrial density were detected. The m. semitendinosus showed a decrease in fiber type specific CSA of type IIAX fibers and a decrease of type I fiber Feret's diameter as well as mean minimum Feret's diameter. The training-induced increased capillary supply in conjunction with a significant decrease in muscle fiber CSA suggests that the muscular machinery models itself toward an optimal smaller individual muscle fiber structure to receive and process fuels that can be swiftly delivered by the circulatory system. These results are interesting in view of the recently identified important fuel candidates such as branched-chain amino acids, aromatic amino acids, and gut microbiome-related xenobiotics, which need a rapid gut-muscle gateway to reach these fibers and are less challenging for the mitochondrial system. More research is needed with that respect. Results also show important differences between muscle groups with respect to baseline and training-specific modulation.

Flexibility of equine bioenergetics and muscle plasticity in response to different types of training: An integrative approach, questioning existing paradigms

Equine bioenergetics have predominantly been studied focusing on glycogen and fatty acids. Combining omics with conventional techniques allows for an integrative approach to broadly explore and identify important biomolecules. Friesian horses were aquatrained (n = 5) or dry treadmill trained (n = 7) (8 weeks) and monitored for: evolution of muscle diameter in response to aquatraining and dry treadmill training, fiber type composition and fiber cross-sectional area of the M. pectoralis, M. vastus lateralis and M. semitendinosus and untargeted metabolomics of the M. pectoralis and M. vastus lateralis in response to dry treadmill training. Aquatraining was superior to dry treadmill training to increase muscle diameter in the hindquarters, with maximum effect after 4 weeks. After dry treadmill training, the M. pectoralis showed increased muscle diameter, more type I fibers, decreased fiber mean cross sectional area, and an upregulated oxidative metabolic profile: increased β-oxidation (key metabolites: decreased long chain fatty acids and increased long chain acylcarnitines), TCA activity (intermediates including succinyl-carnitine and 2-methylcitrate), amino acid metabolism (glutamine, aromatic amino acids, serine, urea cycle metabolites such as proline, arginine and ornithine) and xenobiotic metabolism (especially p-cresol glucuronide). The M. vastus lateralis expanded its fast twitch profile, with decreased muscle diameter, type I fibers and an upregulation of glycolytic and pentose phosphate pathway activity, and increased branched-chain and aromatic amino acid metabolism (cis-urocanate, carnosine, homocarnosine, tyrosine, tryptophan, p-cresol-glucuronide, serine, methionine, cysteine, proline and ornithine). Trained Friesians showed increased collagen and elastin turn-over. Results show that branched-chain amino acids, aromatic amino acids and microbiome-derived xenobiotics need further study in horses. They feed the TCA cycle at steps further downstream from acetyl CoA and most likely, they are oxidized in type IIA fibers, the predominant fiber type of the horse. These study results underline the importance of reviewing existing paradigms on equine bioenergetics.

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse

Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPARγ, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.

Use of Omics Data in Fracture Prediction; a Scoping and Systematic Review in Horses and Humans

Simple Summary

Despite many recent advances in imaging and epidemiological data analysis, musculoskeletal injuries continue to be a welfare issue in racehorses. Omics studies describe the study of protein, genetic material (both DNA and RNA, including microRNAs—small non-coding ribonucleic acids) and metabolites that may provide insights into the pathophysiology of disease or opportunities to monitor response to treatment when measured in bodily fluids. As these fields of study are scientifically complex and highly specialised, it is timely to perform a review of the current literature to allow for the design of robust studies that allow for repeatable work. Systematic reviews have been introduced into the medical literature and are a methodological way of searching for relevant papers followed by critical review of the content and a detection of biases. The objectives of the current systematic review were to identify and critically appraise the literature pertaining to microRNA (miRNA) and their target genes that are correlated with stress fractures in racehorses and humans. The object was to define a panel of miRNAs and their target genes as potential biomarkers in either horses or human subjects. The online scientific databases were searched and a reviewed was performed according to preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. MicroRNA profiling studies in horses continue to emerge, but as of yet, no miRNA profile can reliably predict the occurrence of fractures. It is very important that future studies are well designed to mitigate the effects of variation in sample size, exercise and normalisation methods.

Abstract

Despite many recent advances in imaging and epidemiological data analysis, musculoskeletal injuries continue to be a welfare issue in racehorses. Peptide biomarker studies have failed to consistently predict bone injury. Molecular profiling studies provide an opportunity to study equine musculoskeletal disease. A systematic review of the literature was performed using preferred reporting items for systematic reviews and meta-analyses protocols (PRISMA-P) guidelines to assess the use of miRNA profiling studies in equine and human musculoskeletal injuries. Data were extracted from 40 papers between 2008 and 2020. Three miRNA studies profiling equine musculoskeletal disease were identified, none of which related to equine stress fractures. Eleven papers studied miRNA profiles in osteoporotic human patients with fractures, but differentially expressed miRNAs were not consistent between studies. MicroRNA target prediction programmes also produced conflicting results between studies. Exercise affected miRNA profiles in both horse and human studies (e.g., miR-21 was upregulated by endurance exercise and miR-125b was downregulated by exercise). MicroRNA profiling studies in horses continue to emerge, but as yet, no miRNA profile can reliably predict the occurrence of fractures. It is very important that future studies are well designed to mitigate the effects of variation in sample size, exercise and normalisation methods.

Metabolomics and Lipidomics: Expanding the Molecular Landscape of Exercise Biology

Dynamic changes in circulating and tissue metabolites and lipids occur in response to exercise-induced cellular and whole-body energy demands to maintain metabolic homeostasis. The metabolome and lipidome in a given biological system provides a molecular snapshot of these rapid and complex metabolic perturbations. The application of metabolomics and lipidomics to map the metabolic responses to an acute bout of aerobic/endurance or resistance exercise has dramatically expanded over the past decade thanks to major analytical advancements, with most exercise-related studies to date focused on analyzing human biofluids and tissues. Experimental and analytical considerations, as well as complementary studies using animal model systems, are warranted to help overcome challenges associated with large human interindividual variability and decipher the breadth of molecular mechanisms underlying the metabolic health-promoting effects of exercise. In this review, we provide a guide for exercise researchers regarding analytical techniques and experimental workflows commonly used in metabolomics and lipidomics. Furthermore, we discuss advancements in human and mammalian exercise research utilizing metabolomic and lipidomic approaches in the last decade, as well as highlight key technical considerations and remaining knowledge gaps to continue expanding the molecular landscape of exercise biology.

Metabolic Predictors of Equine Performance in Endurance Racing

Equine performance in endurance racing depends on the interplay between physiological and metabolic processes. However, there is currently no parameter for estimating the readiness of animals for competition. Our objectives were to provide an in-depth characterization of metabolic consequences of endurance racing and to establish a metabolic performance profile for those animals. We monitored metabolite composition, using a broad non-targeted metabolomics approach, in blood plasma samples from 47 Arabian horses participating in endurance races. The samples were collected before and after the competition and a total of 792 metabolites were measured. We found significant alterations between before and after the race in 417 molecules involved in lipids and amino acid metabolism. Further, even before the race starts, we found metabolic differences between animals who completed the race and those who did not. We identified a set of six metabolite predictors (imidazole propionate, pipecolate, ethylmalonate, 2R-3R-dihydroxybutyrate, β-hydroxy-isovalerate and X-25455) of animal performance in endurance competition; the resulting model had an area under a receiver operating characteristic (AUC) of 0.92 (95% CI: 0.85-0.98). This study provides an in-depth characterization of metabolic alterations driven by endurance races in equines. Furthermore, we showed the feasibility of identifying potential metabolic signatures as predictors of animal performance in endurance competition.

Epigenetic control of exercise adaptations in the equine athlete: Current evidence and future directions

Horses (Equus ferus caballus) have evolved over the past 300 years in response to man-made selection for particular athletic traits. Some of the selected traits were selected based on the size and horses' muscular power (eg Clydesdales), whereas other breeds were bred for peak running performance (eg Thoroughbred and Arabian). Although the physiological changes and some of the cellular adaptations responsible for athletic potential of horses have been identified, the molecular mechanisms are only just beginning to be comprehensively investigated. The purpose of this review was to outline and discuss the current understanding of the molecular mechanisms underpinning the athletic performance and cardiorespiratory fitness in athletic breeds of horses. A brief review of the biology of epigenetics is provided, including discussion on DNA methylation, histone modifications and small RNAs, followed by a summary and critical review of the current work on the exercise-induced epigenetic and transcriptional changes in horses. Important unanswered questions and currently unexplored areas that deserve attention are highlighted. Finally, a rationale for the analysis of epigenetic modifications in the context with exercise-related traits and ailments associated with athletic breeds of horses is outlined in order to help guide future research.

Affecting Lipid Metabolism Salivary MicroRNAs Expressions in Arabian Racehorses Before and After the Race

The active roles of microribonucleic acids (miRNAs) in gene regulation have made miRNAs a key point for the scientific world in the study of physiological processes. Although saliva includes the largest number of miRNAs, there is no miRNA study in saliva on horses has been found. Our study is the first study on miRNAs isolation from saliva in horses. In the present study, saliva was studied in Arabian racehorses to better understand the molecular mechanisms of expression levels that are effective in lipid metabolism of miRNAs and their target genes during the race. Identification of lipid metabolism of miRNAs and their target genes is an opportunity to provide information about biomarkers in Arabian racehorses on energy supply for race performance. Arabian racehorses have low glycogen content and high triglyceride storage capability, thanks to the high amount of oxidative type I fiber in their muscle tissue. Therefore, Arabian racehorses can provide higher levels of energy using more fat. The aim of this study is to determine the prerace and postrace expression levels of eight miRNAs in saliva that are known to affect lipid metabolism in Arabian racehorses. The expression level of eca-miR-33a was found to be statistically significant (P < .05). Target genes of eca-miR-33a have been copredicted as ABCA1, CROT, ABHD2, and SATB2, with three validated databases and other analysis tools. In conclusion, these findings revealed that both eca-miR-33a and its target genes could be potential core genes that play important roles in lipid metabolism in Arabian racehorses to provide energy during the race.

Exercise Induced Changes in Salivary and Serum Metabolome in Trained Standardbred, Assessed by 1H-NMR

In the present study, data related to the metabolomics of saliva and serum in trained standardbred horses are provided for the first time. Metabolomic analysis allows to analyze all the metabolites within selected biofluids, providing a better understanding of biochemistry modifications related to exercise. On the basis of the current advances observed in metabolomic research on human athletes, we aimed to investigate the metabolites’ profile of serum and saliva samples collected from healthy standardbred horses and the relationship with physical exercise. Twelve trained standardbred horses were sampled for blood and saliva before (T₀) and immediately after (T₁) standardized exercise. Metabolomic analysis of both samples was performed by ¹H-NMR spectroscopy. Forty-six metabolites in serum and 62 metabolites in saliva were detected, including alcohols, amino acids, organic acids, carbohydrates and purine derivatives. Twenty-six and 14 metabolites resulted to be significantly changed between T₀ and T₁ in serum and saliva, respectively. The findings of 2-hydroxyisobutyrate and 3-hydroxybutyrate in serum and GABA in equine saliva, as well as their modifications following exercise, provide new insights about the physiology of exercise in athletic horses. Glycerol might represent a novel biomarker for fitness evaluation in sport horses.

Metabolomics in equine sport and exercise

metabolomics is the high-throughput, multiparametric identification and classification of hundreds of low molecular weight metabolites in a biological sample. Ultimately, metabolites are the downstream readouts of cellular signalling, transcriptomic and proteomic changes that can provide a comprehensive view of tissue and organismal phenotype. The popularity of metabolomics in human sport and exercise has been gaining over the past decade and has provided important insights into the energetic demands and mechanistic underpinnings of exercise and training. To the contrary, metabolomics in the field of equine exercise physiology is lagging despite the horse's superior aerobic and muscular capabilities, as well as its prominence in competitive sport. As such, this narrative review aims to describe metabolomics, its routine implementation, the various analytical methods applied and the state of its use in the equine athlete. Sufficient attention will be paid to methodological considerations, as well as gaps in the equine literature, particularly with regard to the skeletal muscle metabolome. Finally, there will be a brief discussion of the future directions and barriers to metabolomics use in the athletic horse. A thorough understanding of the metabolomics changes that occur in the equine athlete with exercise will undoubtedly help to improve horse management and health across the lifespan.

Priming for welfare: gut microbiota is associated with equitation conditions and behavior in horse athletes

We simultaneously measured the fecal microbiota and multiple environmental and host-related variables in a cohort of 185 healthy horses reared in similar conditions during a period of eight months. The pattern of rare bacteria varied from host to host and was largely different between two time points. Among a suite of variables examined, equitation factors were highly associated with the gut microbiota variability, evoking a relationship between gut microbiota and high levels of physical and mental stressors. Behavioral indicators that pointed toward a compromised welfare state (e.g. stereotypies, hypervigilance and aggressiveness) were also associated with the gut microbiota, reinforcing the notion for the existence of the microbiota-gut-brain axis. These observations were consistent with the microbiability of behaviour traits (> 15%), illustrating the importance of gut microbial composition to animal behaviour. As more elite athletes suffer from stress, targeting the microbiota offers a new opportunity to investigate the bidirectional interactions within the brain gut microbiota axis.

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data

The Cancer Genome Atlas (TCGA) is a publicly funded project that aims to catalog and discover major cancer-causing genomic alterations with the goal of creating a comprehensive ‘atlas’ of cancer genomic profiles. The availability of this genome-wide information provides an unprecedented opportunity to expand our knowledge of tumourigenesis. Computational analytics and mining are frequently used as effective tools for exploring this byzantine series of biological and biomedical data. However, some of the more advanced computational tools are often difficult to understand or use, thereby limiting their application by scientists who do not have a strong computational background. Hence, it is of great importance to build user-friendly interfaces that allow both computational scientists and life scientists without a computational background to gain greater biological and medical insights. To that end, this survey was designed to systematically present available Web-based tools and facilitate the use TCGA data for cancer research.

Network-Based Approaches for Multi-omics Integration

Network-based approach is rapidly emerging as a promising strategy to integrate and interpret different -omics datasets, including metabolomics. The first section of this chapter introduces the current progresses and main concepts in multi-omics integration. The second section provides an overview of the public resources available for creation of biological networks. The third section describes three common application scenarios including subnetwork identification, network-based enrichment analysis, and systems metabolomics. The section four introduces the concept of hierarchical community network analysis. The section five discusses different tools for network visualization. The chapter ends with a future perspective on multi-omics integration.

Inter-breed diversity and temporal dynamics of the faecal microbiota in healthy horses

Understanding gut microbiota similarities and differences across breeds in horses has the potential to advance approaches aimed at personalized microbial modifications, particularly those involved in improving sport athletic performance. Here, we explore whether faecal microbiota composition based on faecal 16S ribosomal RNA gene sequencing varies across six different sport breeds at two time points 8 months apart within a cohort of 189 healthy horses cared for under similar conditions. Lusitano horses presented the smallest and Hanoverians the greatest bacterial diversity. We found subtle but significant differences in β-diversity between Lusitano, Anglo Arabian and the central European breeds, and we reproduced these results across the two time points. Repeat sampling of subjects showed community to be temporally more stable in Lusitano and Anglo Arabian breeds. Additionally, we found that 27 genera significantly varied in abundance across breeds. Overall, 33% of these taxa overlapped with previously identified taxa that were associated with genetic variation in humans or other species. However, a non-significant correlation was observed between microbial composition and the host pedigree-based kinship. Despite a notable variation in the diversity and composition of the faecal microbiota, breed exerted limited effects on the equine faecal microbiota.

The Genetics of Racing Performance in Arabian Horses

Arabian horses are commonly believed to be one of the oldest and most influential horse breeds in the world. The high financial benefits obtained from races tend to search for genetic markers strongly correlated with the results achieved. To date, the modern approaches such as transcriptome, miRNAome, and metabolome analyses have been used to investigate the genetic background of racing performance as well as endurance capacity in Arabians. The analysis of polymorphisms at the genome level has also been applied to the detection of genetic variants associated with exercise phenotype in the Arabian breed. The presented review summarizes these findings, with a focus on the genetics underlying flat racing and endurance performance traits in different Arabian horse populations.

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology

An integrated analysis of gut microbiota, blood biochemical and metabolome in 52 endurance horses was performed. Clustering by gut microbiota revealed the existence of two communities mainly driven by diet as host properties showed little effect. Community 1 presented lower richness and diversity, but higher dominance and rarity of species, including some pathobionts. Moreover, its microbiota composition was tightly linked to host blood metabolites related to lipid metabolism and glycolysis at basal time. Despite the lower fiber intake, community type 1 appeared more specialized to produce acetate as a mean of maintaining the energy supply as glucose concentrations fell during the race. On the other hand, community type 2 showed an enrichment of fibrolytic and cellulolytic bacteria as well as anaerobic fungi, coupled to a higher production of propionate and butyrate. The higher butyrate proportion in community 2 was not associated with protective effects on telomere lengths but could have ameliorated mucosal inflammation and oxidative status. The gut microbiota was neither associated with the blood biochemical markers nor metabolome during the endurance race, and did not provide a biomarker for race ranking or risk of failure to finish the race.

An Improved Version of the Classical Banister Model to Predict Changes in Physical Condition

In this paper, we formulate and provide the solutions to two new models to predict changes in physical condition by using the information of the training load of an individual. The first model is based on a functional differential equation, and the second one on an integral differential equation. Both models are an extension to the classical Banister model and allow to overcome its main drawback: the variations in physical condition are influenced by the training loads of the previous days and not only of the same day. Finally, it is illustrated how the first model works with a real example of the training process of a cyclist.

The lipidome of Thoroughbred racehorses before and after supramaximal exercise

BACKGROUND

A comprehensive study of the effect of supramaximal exercise in lipid homeostasis of Thoroughbreds provides the basis for future research on the role of lipids on energy metabolism in racehorses.

OBJECTIVE

To compare the plasma lipidome of Thoroughbreds before and after supramaximal exercise using an untargeted lipidomics approach.

STUDY DESIGN

Pilot experimental study.

METHODS

Four Thoroughbred horses were used. The maximal oxygen consumption (VO_{2 max} ) was calculated for each horse. Horses then underwent treadmill exercise at the speed for which the oxygen requirements had been calculated to be 115% VO_{2 max} . Plasma samples were obtained before (T0) and immediately (T1), 15 (T2) and 30 (T3) minutes post-exercise, and evaluated using liquid chromatography/mass spectrometry. Data analysis consisted of principal component analysis and one-way repeated measures analysis of variance.

RESULTS

A total of 933 plasma lipids were detected. Supramaximal exercise-induced significant changes in the signal intensity of 13 lipids; all ubiquitous in the organism as major components of biological membranes or energy substrates.

MAIN LIMITATIONS

A treadmill was used to replicate track conditions. Also, sample size involved only four horses and the statistical analyses failed to achieve the desired power of 80%.

CONCLUSIONS

The findings in this pilot study suggest that supramaximal exercise induces changes in specific plasma lipids in Thoroughbred racehorses. While the biological significance of these findings remains to be determined, these results provide baseline information for future studies in lipidomics applied to equine exercise physiology. Further research is warranted to better understand the role of lipids on energy metabolism in Thoroughbred racehorses.

MicroRNAs in equine veterinary science

MicroRNAs are small noncoding RNAs that play a pivotal role in diverse cellular processes through post-transcriptional regulation of gene expression. The dysregulation of specific microRNAs is associated with disease development and progression. In this review, we summarise how microRNAs modulate gene expression, and explain microRNA nomenclature. We discuss the potential applications of microRNAs in equine disease diagnosis and treatment, in the context of the sum of current knowledge about microRNA expression in normal and diseased equine tissues.

Circulating miRNAs as Putative Biomarkers of Exercise Adaptation in Endurance Horses

Endurance exercise induces metabolic adaptations and has recently been reported associated with the modulation of a particular class of small noncoding RNAs, microRNAs, that act as post-transcriptional regulators of gene expression. Released into body fluids, they termed circulating miRNAs, and they have been recognized as more effective and accurate biomarkers than classical serum markers. This study examined serum profile of miRNAs through massive parallel sequencing in response to prolonged endurance exercise in samples obtained from four competitive Arabian horses before and 2 h after the end of competition. MicroRNA identification, differential gene expression (DGE) analysis and a protein-protein interaction (PPI) network showing significantly enriched pathways of target gene clusters, were assessed and explored. Our results show modulation of more than 100 miRNAs probably arising from tissues involved in exercise responses and indicating the modulation of correlated processes as muscle remodeling, immune and inflammatory responses. Circulating miRNA high-throughput sequencing is a promising approach for sports medicine for the discovery of putative biomarkers for predicting risks related to prolonged activity and monitoring metabolic adaptations.

The Crosstalk between the Gut Microbiota and Mitochondria during Exercise

Many physiological changes occur in response to endurance exercise in order to adapt to the increasing energy needs, mitochondria biogenesis, increased reactive oxygen species (ROS) production and acute inflammatory responses. Mitochondria are organelles within each cell that are crucial for ATP production and are also a major producer of ROS and reactive nitrogen species during intense exercise. Recent evidence shows there is a bidirectional interaction between mitochondria and microbiota. The gut microbiota have been shown to regulate key transcriptional co-activators, transcription factors and enzymes involved in mitochondrial biogenesis such as PGC-1α, SIRT1, and AMPK genes. Furthermore, the gut microbiota and its metabolites, such as short chain fatty acids and secondary bile acids, also contribute to host energy production, ROS modulation and inflammation in the gut by attenuating TNFα- mediated immune responses and inflammasomes such as NLRP3. On the other hand, mitochondria, particularly mitochondrial ROS production, have a crucial role in regulating the gut microbiota via modulating intestinal barrier function and mucosal immune responses. Recently, it has also been shown that genetic variants within the mitochondrial genome, could affect mitochondrial function and therefore the intestinal microbiota composition and activity. Diet is also known to dramatically modulate the composition of the gut microbiota. Therefore, studies targeting the gut microbiota can be useful for managing mitochondrial related ROS production, pro-inflammatory signals and metabolic limits in endurance athletes.

Acute and Chronic Exercise in Animal Models

Numerous animal cardiac exercise models using animal subjects have been established to uncover the cardiovascular physiological mechanism of exercise or to determine the effects of exercise on cardiovascular health and disease. In most cases, animal-based cardiovascular exercise modalities include treadmill running, swimming, and voluntary wheel running with a series of intensities, times, and durations. Those used animals include small rodents (e.g., mice and rats) and large animals (e.g., rabbits, dogs, goats, sheep, pigs, and horses). Depending on the research goal, each experimental protocol should also describe whether its respective exercise treatment can produce the anticipated acute or chronic cardiovascular adaptive response. In this chapter, we will briefly describe the most common kinds of animal models of acute and chronic cardiovascular exercises that are currently being conducted and are likely to be chosen in the near future. Strengths and weakness of animal-based cardiac exercise modalities are also discussed.