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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.
Complete Extruded Diet: How Does Equine Fecal Microbiota Change During Intake Adaptation? This study aimed to investigate the gradual adaptation of the fecal bacterial community and in vitro fermentative capacity of horses fed a complete extruded diet (CED). Twelve geldings weighing 370 kg were removed from a native pasture and fed coastcross hay (Cynodon spp) for 7 days. In the second week, horses were assigned to two groups: one group was fed exclusively with coastcross hay (HAY) for 28 days and the other group fed with weekly increases of CED (30%, 60%, and 100%) to replace HAY. Fecal samples were collected on Days 7, 14, 21, and 28 for microbiota and in vitro fermentati...
Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk. Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (M...
The horse gut microbiota genome represents a vast novel reservoir of CAZymes. Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilizat...
High-Altitude Extreme Environments Drive Convergent Evolution of Skin Microbiota in Humans and Horses. Unique skin microbial communities have been shaped by the harsh climatic conditions in high-altitude areas, such as intense ultraviolet radiation and low oxygen concentration. However, it is unknown whether high altitude contributes to shaping common microbiota inhabiting the skin across different mammals. The skin microbial communities of humans and horses living in high-altitude (Tibetan) and low-altitude areas were analyzed using full-length 16S rRNA sequencing technology. Alpha diversity differed between high- and low-altitude groups ( < 0.01). Skin microbial community composition also ...
Effects of Feeding Strategies on Gut Microbial Communities in Donkeys: A Comprehensive Narrative Review. Donkeys () remain nutritionally understudied despite their critical roles in agriculture across developing regions, with current feeding practices inappropriately extrapolating horse standards without accounting for species-specific digestive physiology. No comprehensive synthesis has integrated how dietary modifications systematically alter gut microbial communities to drive measurable health outcomes in donkeys, preventing development of evidence-based feeding strategies. This review critically synthesizes current evidence on donkey nutritional requirements and gut microbiota dynamics to est...
Effect of Supplemental Bamboo Leaf Extract on Milk Production, Composition, Biochemical Indices, and Fecal Microbiota Diversity in Grazing Yili Mares. : This study investigated the effects of dietary bamboo leaf extract (BLE) on milk parameters and intestinal microbiota in lactating mares. : Twenty-four mares of similar age (10 ± 2 years), weight (360.62 ± 15.23 kg) and body condition were selected for this study and randomly divided into four groups of six mares each: an untreated control group (CG) and three experimental groups (EG1, EG2, EG3) were fed a basal diet supplemented with 0, 10, 20, or 30 g/day of BLE, respectively, for 60 days. Then, horse milk composition, antioxidant activity, and immunoglobulin levels along with the rela...
Effect of surgical antimicrobial prophylaxis duration for colic surgery on complications and resistome. Based on human studies, surgical antimicrobial (AMD) prophylaxis (SAP) beyond 24 h is unnecessary and potentially detrimental. Objective: To compare clinical and microbiological outcomes in patients receiving 24- or 72-h of SAP for colic surgery. Methods: Prospective randomised clinical trial. Methods: Horses that recovered from colic surgery were considered. Exclusion criteria were (1) age <2 years; (2) Miniature Horses, pony, and draught breeds; (3) azotaemia; (4) recent hospitalisation, colic surgery, or AMDs; (5) local AMD administration. Eligible horses were randomly assigned to re...
Beneath the surface: gut microbes, cyathostomins and resident immune cells – Characterising the baseline. Cyathostomins are the most prevalent and currently considered the most pathogenic gastrointestinal nematodes in horses. Their life cycle includes an encystment phase within the large intestinal mucosa, where up to 90 % of the total worm burden resides. Clinical disease ranges from chronic protein-losing enteropathy to acute, sometimes fatal, typhlocolitis. Despite their significance, the ecological interplay between cyathostomins, the host immune response, and the gut microbiota remains poorly understood. To our knowledge, this is the first study to investigate these interactions at the mucos...
Eco-friendly biodegradation processes for affordable wastewater treatment in agricultural and horse stable environments. The pursuit of sustainable livestock farming and environmentally responsible agricultural practices has spurred the development of innovative and affordable wastewater treatment technologies. This study investigates new biological treatment approaches that integrate the complementary processes of filtration, biosorption, and biodegradation to enhance eco-friendly wastewater management. A novel treatment concept was developed, representing a modern modification of the biosorption method that combines the oxidation of organic pollutants with ammonium reduction by an immobilized biocenosis, achie...
A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease. Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria. Results: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with advers...
The Role of Short-Chain Fatty Acids (SCFAs) in Colic and Anti-Inflammatory Pathways in Horses. Equine colic remains a prevalent and potentially life-threatening condition with multifactorial origins, including dietary imbalances, stress, and microbial dysbiosis. Central to equine gut health is the production of short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate, generated through microbial fermentation of dietary fibers in the hindgut. These metabolites not only serve as vital energy sources but also play crucial roles in maintaining intestinal barrier integrity, modulating motility, and suppressing inflammation. This review explores the role of SCFAs in equine...
Gut microbial signatures and cardiac-microbiota axis in Yili horses with divergent exercise-induced cardiac remodeling. This study aimed to investigate how different training outcomes affect the gut microbiota composition in racehorses. Twenty-six Yili horses underwent a 9-month conditioning training regimen under uniform husbandry and management conditions. Post-training, the horses were divided into an excellence group (D. Y group) and a general group (D. P group) based on their athletic performance, with the top 10 performers constituting the D. Y group and the bottom 10 the D. P group. Cardiac morphology and function were quantitatively assessed via echocardiography, and metagenomic sequencing was performed...
An in vitro investigation into the effects of postbiotic supplementation on stabilising equine hindgut pH. Dysbiosis of the intestinal microbiome is a precursor to hindgut acidosis. As microbial diversity and fermentation are influenced by diet, including a postbiotic could help maintain healthy gastrointestinal microbes and reduce acidosis risk. Objective: It was hypothesised that including a postbiotic in batch culture would reduce the degree of pH decline and lactate accumulation during fermentation. Methods: In vitro batch cultures with faecal inoculant were prepared with either low starch (LS) or high glucose (G) substrate to represent normal and acidic fermentation. Saccharomyces cerevisiae d...
Using culture ‘omics to explore the microbial structure and function in an equid in vitro digestion model. The in vitro gas production system (GPS), developed to estimate degradation of ruminant feedstuffs, has been adapted for equine use. This study aimed to characterise the bacterial community profile and metabolome of donor faeces and faecal inoculum within the GPS when fermenting the same diet as faecal donors. Six Welsh ponies on identical diets were faecal donors with samples collected for microbiome profiling and system inoculation. Gas production (manual pressure transducer technique) was performed for 156 h with 2 replicate bottles from each donor harvested at 8,20,28 and 36 h. Faecal an...
Bile acids segregate metabolic syndrome in a cohort of 100 deeply phenotyped horses. Metabolic syndrome (MetS)-encompassing obesity, insulin resistance, dyslipidemia, and hypertension-is prevalent in both humans and horses, offering a unique opportunity to explore shared pathophysiological mechanisms across species in a controlled model organism. In this first report from the Pioneer 100 Horse Health Project (P100HHP), we conducted a longitudinal, multi-omic analysis of 108 deeply phenotyped horses to interrogate individual health trajectories for precision insights into MetS. We identified two primary metabotypes: one characterized by elevated unsaturated triglycerides (TGs) ...
In Vitro Investigation of Equine Gut Microbiota Alterations During Hypoglycin A Exposure. Hypoglycin A is a plant-derived protoxin that causes atypical myopathy in equids. In atypical myopathy-affected horses, metabolomic and microbiome studies have reported alterations in metabolic markers and faecal microbiota composition, pointing to a potential disruption of microbial homeostasis. However, in vivo observations are strongly confounded by host-related factors, underscoring the need for controlled in vitro approaches. To address this, we used an in vitro static batch fermentation model simulating the equine colon to investigate the direct effects of hypoglycin A on microbiota comp...
Beyond nocardioform: Transcriptionally active microbes and host responses in equine mucoid placentitis. Nocardioform placentitis (NP) is an understudied form of equine placentitis historically attributed to nocardioform bacteria, yet it remains uncertain whether these organisms are the sole pathogens involved. Objective: To elucidate the pathophysiology of NP and the host-pathogen interaction. Methods: In vivo clinical multi-omics study. Methods: Dual RNA sequencing was performed to profile transcriptionally active microbial communities and concurrent placental transcriptome responses in samples from 31 placentas with and without NP. Untargeted metabolomics was performed to study the associated ...
Characterization of surface properties and antimicrobial activity of autochthonous lactic acid bacteria isolated from the reproductive tract of healthy mares. Equine endometritis, a major cause of subfertility in mares, has a significant economic impact on horse breeding. In the face of rising antimicrobial resistance, the use of beneficial bacteria to prevent this disease is a non-antibiotic alternative which aligns with "One Health" principles. This study characterised vaginal autochthonous lactic acid bacteria (LAB) from healthy mares. Out of the 25 presumptive LAB isolates obtained from 15 clinically healthy thoroughbred mares, 24 were confirmed. Surface properties were assessed (autoaggregation, hydrophobicity, biofilm formation, exopolysacchar...
Dietary Proline Supplementation Promotes Growth and Development in Weaned Foals by Modulating Gut Microbial Amino Acid Metabolism. This study investigated the effects of varying proline supplementation doses in weaned foals. Twenty-eight weaned foals (approximately 5 months of age; body weight: 54.45 ± 11.33 kg; with an equal number of males and females) were randomly assigned to one of four groups-a control group, a low-dose group (20 mg/kg·d), a medium-dose group (40 mg/kg·d), and a high-dose group (60 mg/kg·d)- receiving continuous supplementation for 60 days. Blood samples were collected periodically for the analysis of hormones, antioxidants, immune parameters, and plasma amino acids. Concurrently, fecal 16S rRNA...
From wheat bran to equine gut: the in vitro fermentation dynamics of aleurone. Aleurone, a bioactive wheat bran component, has been shown to modulate host metabolism and gut microbiota, but its effects across different compartments of the equine gastrointestinal (GI) tract remain unclear. In this study, we aimed to characterize aleurone-derived metabolite profiles using an fermentation model with digesta from three equine GI compartments (jejunum, cecum, and colon). Unassigned: Three substrates (control feed, aleurone-containing feed, and pure aleurone) were fermented over 72 h, and targeted metabolomics was performed on 38 metabolites. Unassigned: Significant substrate...
Analysis of Staphylococcal Diversity in the Skin Microbiota of Healthy Riding Horses. In animals, staphylococci constitute a significant part of the normal skin microbiota and mucous membranes. There is limited information available on staphylococci isolated from healthy horses. These skin-associated bacteria can be easily transferred between animals and horse riders via direct contact. Patients undergoing hippotherapy (i.e., medical or therapeutic sessions with horses) are especially at risk of being colonized by horse skin-associated bacteria. However, it remains unclear whether equine skin is colonized by antimicrobial-resistant (AMR) opportunistic pathogens, which may be o...
Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions. Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host-microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants...
Newly isolated bacteriophages show efficacy and phage-antibiotic synergy in vitro against the equine genital pathogens Klebsiella pneumoniae and Pseudomonas aeruginosa. Bacterial infections of the genital tract are a severe problem in equine reproduction. Biofilms produced by Klebsiella (K.) pneumoniae and Pseudomonas (P.) aeruginosa present further concerns in such cases as they can limit the success of antibiotic treatments. Alternative treatment approaches are urgently needed for treating bacterial equine genital tract infections and thus, reduce antibiotic use. The present study reports on the bactericidal efficacy of both, novel K. pneumoniae- and P. aeruginosa-specific phages, in a biofilm model and in conjunction with antibiotic drugs as tested in vitr...
Correlation of hindgut microbiome and fermentation properties with a history of gas and/or impaction colic in Japanese draft horses. Colic, a major gastrointestinal disease in horses, has a high recurrence rate and can lead to surgery or fatal outcomes, highlighting the need for effective prevention measures. Disruption of the microbiome is a multifaceted problem and can occur from a variety of factors, such as high-concentrate diets, which can then potentially cause colic. However, individual variation in the incidence of colic can occur when under identical management practices. The aim of this study was to characterize the fecal bacterial composition of Japanese draft horses with and without a history of colic in the pas...
Sensory Assessment of Hay Samples: Abnormal Odor Predicts Increased Dust Levels and Impurities Suggest Microbiological Contamination. Hay quality is a key factor in equine respiratory health, with microbiological contaminants in inhaled organic dust posing significant risks. Sensory assessment has been used to evaluate hay hygiene, but its value to identify deficiencies remains unclear. This study aimed to explore the potential of sensory assessment to predict both particulate matter (PM) dust concentrations and microbiological contamination. Fifty hay samples were collected from horse owners and evaluated using a structured sensory examination, microbiological analyses, and dust concentration measurements obtained with the ...
Postbiotics and Parabiotics in Veterinary Medicine: A Market Overview. Postbiotics and parabiotics (PP) are innovative concepts in veterinary medicine that have garnered substantial interest owing to their unique properties and potential benefits. PP offers a promising alternative to live bacteria, demonstrating properties such as prebiotic, immunomodulatory, antimicrobial, anti-inflammatory, antioxidant, and anticancer effects, while potentially mitigating some of the common challenges associated with live bacterial applications. PP products are manufactured and commercially employed in livestock, poultry, and pets. Moreover, postbiotic-based commercial products...
Microbiome and Dental Changes in Horses Fed a High Soluble Carbohydrate Diet. This study investigated the oral microbiome of horses maintained on a high soluble carbohydrate diet based on sugarcane, in comparison to those fed a pasture-based diet composed of spp., aiming to identify associations between dietary intake, the composition of oral microbial communities, and the occurrence of dental caries and diastemata. A total of 20 healthy horses, both male and female, with an average age of 9 ± 3 years and weight of 400 ± 100 kg, without a defined breed, were selected. They were divided into two groups: the High Soluble Carbohydrate Group (HSCCG), consisting of 10 hor...
Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk. This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in se...
The horse gut bacteriome and anaerobic mycobiome are influenced by seasonal forages and small intestinal starch digestibility. The equine gut microbiome is a complex and dynamic ecosystem, housing a diverse consortium of bacteria and anaerobic fungi (AF) capable of breaking down complex plant matter and converting it into vital energy sources for their host. The aim of this study was to broaden our current understanding of bacterial and AF diversity in the equine hindgut and how it differs between cohorts and responds to dietary shifts. Results: Faecal samples were collected from 48 horses and the bacteriome and anaerobic mycobiome analysed using long-read amplicon sequencing. Samples were collected from racehorses (R...
The effect of topical antibiotic or antibiotic-corticosteroid treatment on the ocular surface microbiota of healthy horses. Information regarding the impact of topical antibiotics with or without corticosteroids on the microbiota of the horses' eyes is limited. This study aimed to describe the bacterial ocular surface microbiota in healthy horses and evaluate the effect of topical antibiotics or antibiotic-corticosteroid medication on the ocular surface microbiota. Unassigned: This was a prospective, randomized, longitudinal, blinded study in which one eye of 12 horses was treated 3 times daily for 7 days with neomycin, polymyxin B and bacitracin ophthalmic ointment ( = 6) or neomycin, polymyxin B and dexametha...
