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Topic:Microbiome
The equine microbiome refers to the diverse community of microorganisms, including bacteria, fungi, and viruses, residing in various parts of a horse's body, such as the gastrointestinal tract, skin, and respiratory system. These microorganisms are involved in numerous physiological processes, including digestion, metabolism, and immune function. The composition and diversity of the microbiome can be influenced by factors such as diet, environment, and health status. Research in this area explores the characterization of the equine microbiome, its impact on health and disease, and potential applications in managing equine health. This page compiles peer-reviewed research studies and scholarly articles that investigate the composition, function, and implications of the microbiome in horses.
Thirteen years of environmental surveillance of ESKAPE organisms and Escherichia coli in an equine hospital: Informing infection control. Bacteria from the ESKAPE group (i.e., Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) and Escherichia coli are frequently multidrug-resistant and can be associated with healthcare-associated infections, an increasing concern for veterinary settings. Objective: To determine the environmental prevalence of ESKAPE and E. coli on surfaces which can act as reservoirs of infection in clinical areas in equine hospitals. Methods: Observational study. Methods: Routine environmental sampling was performed in on...
Fluorescent tagging for assessment of environmental cleaning in an equine hospital. Healthcare-associated infections increase morbidity, mortality, and treatment costs in both human and veterinary medicine, and environmental contamination can contribute to their occurrence. Monitoring of environmental cleaning is an important component of multimodal infection control strategies. Fluorescent tagging is a low-cost, practical approach that correlates with reduced environmental contamination in human and small animal hospitals. Its applicability in equine hospitals, where surface characteristics and contamination risks differ, has not yet been evaluated. Objective: To evaluate fl...
Quantitative assessment of specific bacterial taxa of the intestinal microbiota of healthy and diarrheic horses. Alterations in intestinal microbiota composition, as determined by DNA sequencing, are reported in horses with acute colitis compared with healthy horses. Objective: Changes in specific bacterial populations can detect overall intestinal disruption of the normal intestinal microbiota. Identify bacterial taxa that indicate intestinal dysbiosis or health in horses using quantitative PCR (qPCR). Methods: Thirty horses with undifferentiated colitis, 13 with colitis associated with Salmonella spp., 14 with antibiotic-associated diarrhea (AAD), 52 healthy horses from Canada and 48 from the United St...
Alterations in the gut resistomes of endangered wild equids associated with anthropogenic activities: Insights for One Health surveillance. Antibiotic resistance genes (ARGs) are emerging environmental contaminants, but how human-associated management practices are associated with mobile resistomes in endangered wildlife remains poorly resolved. Here, we used fecal metagenomics to compare Przewalski's horses, Mongolian khulans, and domestic horses from Xinjiang, China, including Przewalski's horses from a protected area and a captive-breeding setting under human management. Across 47 fecal metagenomes, we identified 380 ARG subtypes, 23 metal resistance gene (MRG) types, and 26 mobile genetic element (MGE) subtypes. Przewalski's h...
Characterization of the Healthy Ocular Mycobiome of Purebred Lusitano Horses Using Oxford Nanopore Long-Read Sequencing. The ocular surface represents a unique microbial ecosystem continuously exposed to environmental microorganisms; however, the fungal component of the healthy equine ocular microbiome remains poorly characterized. This study aimed to characterize the ocular surface mycobiome of 12 clinically healthy Purebred Lusitano horses from three geographical regions in Portugal kept in two housing systems using Oxford Nanopore long-read sequencing and conventional fungal culture. Sequencing revealed a highly diverse fungal community with marked inter-individual variability. The most abundant genera were ,...
Effects of steaming and storage on microbial quality and nutrient losses of hay. Steaming reduces microbial content of hay but the effect of steaming on nutrient quality and the effects of storage after steaming on microbial content are incompletely known. Objective: It was hypothesized that steamed hay can be stored for up to 24 h without an increase in microbial content and that steaming of hay favors the increase in measurable Maillard reaction products. Methods: Spoiled hay was steamed and then stored in hay nets, buckets or the hay steamer itself under summer and winter climate conditions. Microbial content was assessed by bacterial and fungal culture before and after...
Gut Microbiota as a Molecular Regulator of Mineral Homeostasis in Horses: Mechanisms and Future Perspectives. Mineral homeostasis in horses is traditionally attributed to the coordinated regulation of the intestine, kidneys, skeleton, and endocrine system. Emerging evidence suggests the gut microbiota also shapes this process by modifying the intestinal environment where mineral absorption occurs. Despite the growing interest in host-microbiota interactions, the mechanisms linking the equine gut microbiota to mineral metabolism remain poorly understood and have not been comprehensively synthesized. This review integrates current knowledge of equine gastrointestinal physiology, gut microbial ecology, a...
Exhaled breath condensate in horses: a first microbiological insight. Exhaled breath condensate (EBC) is a non-invasive method for obtaining samples reflecting the airway lining fluid; however, its microbiological composition remains poorly characterized. Objective: To perform an exploratory microbiological comparison of EBC in clinically healthy horses maintained under different environmental conditions. Methods: An observational study included 30 mares equally distributed into two groups: horses housed in stalls (Racetrack group) and horses maintained under pasture conditions (Farm group). EBC samples were collected using a validated device developed by the re...
Multiple Probiotic Lactic Acid Bacteria with Marked Cholesterol-Lowering Effects Were Discovered in Equine Colostrum. Xinjiang ranks among the key domestication origins of horses. Local nomadic ethnic groups have a long-standing tradition of consuming equine dairy products, which endows mare-derived dairy matrices with abundant, distinctive and scarce probiotic resources. Equine colostrum is rich in immunoglobulins and growth factors; nevertheless, its pharmacological activities and micro-ecological composition remain poorly characterized. This study aimed to isolate and screen native strains with cholesterol-lowering potential from Xinjiang equine colostrum and conduct a preliminary investigation into their ...
Serum physiology, fecal microbiota, and metabolome signatures associated with perinatal stage transitions in Mongolian mares. Lactation is a critical reproductive trait that influences offspring survival and livestock productivity in equine production. Characterizing physiological transitions during the perinatal period can improve our understanding of how mares adapt to late gestation, parturition, and early lactation. However, in horses-a typical monogastric herbivore with unique digestive characteristics-the associations between gut microbiota and perinatal physiological adaptation, as well as related stage-associated microbial and metabolic features, remain largely uncharacterized. Unassigned: In this study, para...
Isolation of Moraxella spp. strains in horses. Two species of Moraxella were isolated from swabs obtained from two symptomatic horses suffering from conjunctivitis and rhinitis. The isolates were identified via MALDI-TOF as Moraxella osloensis and Moraxella equi respectively, with a good genus identification and a probable species identification score. The first one was also confirmed by BLAST sequence analysis with a high homology (99%). Antimicrobial susceptibility testing obtained by minimum inhibitory concentration method showed that the two isolates were sensitive to all the tested molecules. The therapeutic protocols applied had an e...
From Diet to Disease: The Role of the Gut Microbiome and Microbial Metabolites in Horses. The equine gastrointestinal microbiome plays an essential role in digestion, energy metabolism, immune regulation, and maintenance of intestinal homeostasis. Increasing evidence suggests that microbial-derived metabolites provide a functional link between diet, the microbiome, and host physiology. This narrative review summarizes current knowledge on how dietary factors, including structural carbohydrates, non-structural carbohydrates, protein, and lipids, influence microbial function and metabolite production in horses. Relevant publications available up to June 2026 were identified through s...
Horses with pituitary pars intermedia dysfunction have an altered fecal short-chain fatty acid profile. Pituitary pars intermedia dysfunction (PPID) is a prevalent endocrine disease in older horses sharing pathogenetic features with Parkinson disease, including dopaminergic neurodegeneration and α-synuclein aggregation. This study was conducted to determine whether horses with PPID exhibit changes in short-chain fatty acid (SCFA) profiles as described in Parkinson disease, providing further evidence for involvement of a microbiota-gut-brain axis in the pathogenesis of PPID. Unassigned: Prospective case-control study including 22 horses > 12 years of age. Diagnosis of PPID was based on clinical ...
Correlation between microbial communities, metabolites, and bioactivities in fermented mare’s milk revealed by metagenomics and metabolomics. Koumiss exhibits various functional properties, including antioxidant, hypoglycemic, and antihypertensive effects; however, natural fermentation is characterized by an uncontrollable microbial community structure, significant fluctuations in product quality, and a lack of specialized fermentation agents. The mechanisms underlying the links between microbial communities, functional metabolites, and bioactivity in natural and inoculated fermentation systems remain unclear. Therefore, this study employed bioactivity assays, metagenomics, and non-targeted metabolomics to systematically analyze dif...
Administration of the Postbiotic Substance 412 to Slovak Warm-Blooded Horses: A Pilot Experiment. Antimicrobial proteinaceous postbiotic substances (PS) and/or bacteriocins can beneficially influence animal health, as previously shown with enterocins from non-autochthonous enterococcal strains. Therefore, the effectiveness of PS 412, produced by our beneficial autochthonous strain EF 412, was assessed in horses. In the pilot experiment, PS 412 was administered to 12 horses of various ages and breeds for 21 days via a small feed ball. Sampling was performed on days 0/1, 21, and 42 (after a 3-week cessation of PS 412). The horses served as their own controls. Although the number of horses w...
Bacteremia in horses undergoing routine dental prophylaxis: Before, during, and after the procedure. Transient bacteremia after dental procedures is well-documented in the literature, but the prevalence and clinical significance in horses remains largely unexplored. Objective: To assess whether routine dental prophylaxis in clinically healthy horses is associated with detection of bacteria in blood, using culture and 16S rDNA sequencing. Our central hypothesis is that a percentage of horses would demonstrate detectable but transient bacteremia in the immediate post-procedural period following dental prophylaxis. Methods: Prospective, observational study. Methods: Venous blood samples from 20 ...
The Effects of Cysteamine Zinc Supplementation on Blood Hormones, Intestinal Flora, and Metabolites in Lactating Mares. This study aimed to investigate the effects of cysteamine zinc (CS-Zn) supplementation on blood biochemical indices, blood hormones, fecal fermentation, fecal microbial diversity, and blood metabolites in lactating mares. Blood samples were collected via jugular venipuncture, and fecal samples were collected via rectal sampling before morning tethering on days 30, 60, and 90 of the trial. Fecal samples were analyzed for volatile fatty acids (VFAs) and microbial diversity, while changes in blood biochemical indices, blood hormones, and blood non-targeted metabolomics were also analyzed. The res...
Differential shaping of equine gut microbiota structure and function by breed and feeding regimen. The gut microbiota plays an essential role in host energy metabolism and immune function. Horses are non-ruminant herbivores that rely heavily on hindgut microbial fermentation to meet their energy requirements. However, the relative contributions of host genetic background (breed) and environmental factors (feeding regimen and geographical location) to shaping the equine gut microbiota remain poorly understood. Unassigned: In this study, 16S rRNA gene sequencing and functional prediction analysis were performed on 139 equine fecal samples to systematically investigate the differential effects...
Clinical and microbiota alterations in performance horses undergoing long-distance transport. Transport-associated pneumonia contributes substantially to morbidity, impaired welfare, and economic loss in high-performance horses and may be associated with alterations in the respiratory microbiota. Objective: Examine the effect of long-distance transport on the respiratory microbiota and correlate changes in microbiota diversity and composition with systemic and airway inflammation. Methods: Seventeen client-owned performance horses transported from New England to Florida under optimized trailering conditions, and 12 non-traveling horses. Methods: Physical examination, blood testing, nas...
A Comprehensive Review of the Equine Gut Microbiome in Health and Disease. Molecular microbiology has revolutionized our understanding of the complex host-associated microbiomes required for normative development and physiology. Horses and other members of the family are particularly reliant on the early maturation and lifelong maintenance of an unusually rich hindgut microbiome for optimal digestion and overall health and performance. Research on the equine gut microbiome has accelerated in the past several years, necessitating a renewed appraisal of the field. The present work is a comprehensive and critical review of the literature regarding the bacterial gastroi...
Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing. The composition of the equine gut microbiome is associated with many aspects of gastrointestinal, respiratory and musculoskeletal health that have been reported in the horse. Scientific studies exploring the microbiome non-intestinal ecological niches in or on horses are lacking. The clinical use of bacterial community profiling in horses is currently limited by cost and by slow analytical workflows. Most equine microbiome studies have relied on 16S rRNA amplicon sequencing of bacterial DNA, using high-throughput short-read sequencing technologies. This is often provided by an external servic...
Inhaled Corticosteroids Influence Pulmonary Microbiota in Severe Equine Asthma. The use of inhaled corticosteroids (ICs) could influence the respiratory microbiota. In animals with asthma it is, however, difficult to separate the immunomodulatory effects of ICs from their indirect effects via improvement of ventilation. Our objective was to determine if ICs alter the pulmonary microbiota independently from their effects on lung function, using a blinded, controlled trial in an experimental model of asthma exacerbation in horses. We treated horses with severe asthma with either bronchodilators alone, or in combination with ICs. Twelve horses in exacerbation received long-a...
Short-term provision of moderate dietary starch alters fecal microbiota but does not exacerbate exercise-induced inflammation in yearling Quarter Horses. Energy-dense feeds commonly provided to equine athletes may be high in starch, which alter gastrointestinal microbiota and could promote systemic inflammation. Objective: To test the hypothesis that exercise-induced inflammation would be greater in horses receiving a starch- versus fiber-based concentrate. Methods: Quarter Horses (mean±SD 16±1mo; 337±30kg) received either a fiber-based control (CON; 7 fillies, 8 geldings) or an isocaloric, isonitrogenous starch concentrate (STARCH; 8 fillies, 7 geldings) for 24d. Fecal metagenomics were evaluated on d0 and 21. Blood inflammatory mediators w...
Fecal microbiota of weaned equine and mule foals grazing bermudagrass pastures. Weaning is a critical period in the lives of foals. After weaning, forage consumption represents a major challenge for both equine or mule foals. Objective: This study evaluated the fecal bacterial concentration, composition, diversity and differential abundance in weaned equine and mule foals under rotational grazing on Bermudagrass (Cynodon spp.) pasture. Methods: A randomized design was used with equine and mule foals grazing two rotations on three Bermudagrass cultivars (Coastcross, Florakirk, and Tifton-85). Pasture rotation occurred every 20 days. The first rotation was evaluated at 20, ...
In silico genome mining and characterization of putative horse feces-derived bacterial phytases as potential monogastric animal feed additive candidates. Phytic acid exerts a significant antinutritional effect in poultry, swine, and fish, which can be mitigated by supplementing monogastric feeds with efficient microbial phytases. Accordingly, mining bacterial genomes for novel phytases represents a strategic computational approach to identifying candidates for improving monogastric animal nutrition. In this study, 162 bacterial genomes associated with horse feces were systematically mined using an in silico pipeline to identify and characterize putative phytases.A total of 69 non-redundant sequences were identified and classified as histidine a...
Impact of collagen supplementation on the fecal microbiome of young horses in training. Intense training in athletic foals may alter fecal microbiota, highlighting the need for nutritional strategies such as hydrolyzed collagen supplementation. Objective: This study aimed to evaluate the effects of dietary hydrolyzed collagen on the fecal microbiome of weanlings in training. Methods: Twenty Mangalarga Marchador foals (206 ± 18 kg; 7 ± 1 mo age) were assigned to two groups: a supplemented group (50 g/day of hydrolyzed collagen for 180 days) and a control group. A completely randomized design with repeated measures over time was used. Foals were exercised five consecutive days pe...
Evaluation of autologous fecal microbiota transplantation for restoring equine gut microbiota after antibiotic-induced dysbiosis. Microbial resilience is important to maintain a healthy gut environment in horses, especially after antibiotic administration, but the efficacies of post-antibiotic recovery strategies remain poorly characterized. We used microbial amplicon sequencing to compare spontaneous recovery, autologous fecal microbiota transplantation (FMT), and probiotic administration in 18 horses following antibiotic-induced dysbiosis. Clinically healthy horses received a combination of cephalothin and minocycline for 5 consecutive days before intervention. Fecal microbial recovery was longitudinally evaluated by u...
Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses. The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses. Unassigned: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds. Unassigned: The results showed no significant differen...
Recent Advances in Natural Products for Colitis: Mechanisms and Translational Perspectives. Colitis is a chronic relapsing inflammatory disorder characterized by persistent mucosal inflammation, epithelial barrier disruption, oxidative stress, immune dysregulation, and gut microbiota imbalance. Although current therapies have improved disease management, their long-term use is still limited by incomplete response, relapse, adverse effects, and high cost. Natural products have attracted increasing attention as promising candidates for colitis intervention because of their structural diversity, broad bioactivity, and multitarget regulatory potential. In veterinary medicine, colitis and...
Effects of Dietary Zinc Cysteamine Supplementation on Growth Performance, Physiological Responses, and Fecal Microbiota in Weaned Foals. Zn-CS chelate has shown beneficial effects on gut health and growth in piglets, but its impact on weaned foals remains largely unknown. This study evaluated the effects of dietary Zn-CS supplementation on growth performance, nutrient digestibility, physiological status, and fecal microbiota in weaned Ili foals. Thirty-two six-month-old foals were randomly assigned to four treatment groups receiving 0, 2, 4, or 6 mg Zn-CS/kg body weight per day for 90 days. Growth performance, nutrient digestibility, plasma biochemical parameters, liver function enzymes, serum hormones, antioxidant indices, fec...
