The equine intestinal microbiome

Aleurone supplementation enhances the metabolic benefits of training in Standardbred mares: impacts on glucose-insulin dynamics and gut microbiome composition

Introduction

Aleurone, derived from the bran layer of grains like wheat and barley, has demonstrated positive effects on energy metabolism in pigs, mice, and untrained horses, influencing glucose-insulin dynamics and gut microbiome composition. Training itself enhances insulin sensitivity in horses, similar to the improvements in performance capacity observed in human athletes. This study aimed to investigate whether aleurone supplementation provides additional benefits to training by modulating insulin metabolism and gut microbiota in Standardbred mares.

Methods

Sixteen Standardbred mares (aged 3-5 years) participated in a cross-over study with two 8-week training periods separated by 8 weeks of detraining. Each horse received either 200 g/day aleurone supplementation or a control diet. Insulin metabolism was evaluated using oral (OGTT) and intravenous (FSIGTT) glucose tolerance tests, measuring parameters such as Maximumglucose, AUCglucose, Maximuminsulin, AUCinsulin, Time to peakinsulin (OGTT), Acute Insulin Response to Glucose (AIRg), glucose effectiveness (Sg), and disposition index (DI) (FSIGTT). Fecal samples underwent metagenomic analysis to assess alpha and beta diversity and microbial composition.

Results

Training alone: Training significantly improved OGTT parameters by decreasing Maximuminsulin (P = 0.005) and AUCinsulin (P = 0.001), while increasing Time to peakinsulin (P = 0.03), indicating enhanced insulin sensitivity. FSIGTT results also showed a decrease in logAIRg (P = 0.044). Training with Aleurone: Aleurone supplementation further reduced FSIGTT AIRg (P = 0.030), logAIRg (P = 0.021) while increasing glucose effectiveness (Sg; P = 0.031). These findings suggest aleurone improves insulin sensitivity, glucose disposal, and fasting glucose regulation beyond training. Microbiome analysis revealed training decreased Pseudomonas, associated with dysbiosis, while aleurone reduced inflammation-associated Desulfovibrio. Beta diversity metrics showed no significant changes.

Conclusion

Aleurone supplementation enhances training-induced improvements in glucose metabolism and fecal microbiota composition, which could offer potential benefits for equine athletes by optimizing metabolic flexibility. It also supports improvements in glucose and insulin dynamics, particularly by further enhancing insulin sensitivity and glucose-mediated disposal. Future studies should investigate the mechanisms of aleurone at the muscle and gut level and explore its potential applications for metabolic disorders such as Equine Metabolic Syndrome.

Changes in bacterial viability after preparation and storage of fecal microbiota transplantation solution using equine feces

Background

Fecal microbiota transplantation (FMT) has been used as a treatment option for horses (Equus caballus) with gastrointestinal diseases. Several preparation and conservation protocols to improve bacterial survival have been studied in other species.

Methods

This study aimed to evaluate the impact of oxygen exposure and different protectant solutions on bacterial viability before and after freezing using horse feces. Fecal samples from 10 healthy horses were aliquoted and diluted in cryoprotectant solutions containing antioxidants (n = 40) or 10% glycerol (n = 40). Half of the aliquots from each dilution condition were prepared inside an anaerobic chamber, while the other half were prepared under ambient air conditions. Each sample was also analyzed fresh and after freezing at -20 °C for 90 days. Bacterial viability was assessed using flow cytometry. A mixed linear model and the Friedman and Wilcoxon tests were used depending on data distribution.

Results

Freeze-thawing decreased bacterial viability by 47% (mean ± SD: 51 ± 27% before, 27 ± 8% after; p < 0.001). Glycerol was superior to the cryoprotectant after freezing (32 ± 8% glycerol, 24 ± 8% cryoprotectant; p < 0.001). Oxygen exposure did not affect viability (p = 0.13). There was no statistical difference between protectant solutions in fresh samples (p = 0.16).

Conclusions

Fresh FMT solutions may be better for treating horses with dysbiosis, but if freezing cannot be avoided, glycerol should be used to dilute feces.

Unravelling Faecal Microbiota Variations in Equine Atypical Myopathy: Correlation with Blood Markers and Contribution of Microbiome

Hypoglycin A and methylenecyclopropylglycine are protoxins responsible for atypical myopathy in equids. These protoxins are converted into toxins that inhibit fatty acid β-oxidation, leading to blood accumulation of acylcarnitines and toxin conjugates, such as methylenecyclopropylacetyl-carnitine. The enzymes involved in this activation are also present in some prokaryotic cells, raising questions about the potential role of intestinal microbiota in the development of intoxication. Differences have been noted between the faecal microbiota of cograzers and atypical myopathy-affected horses. However, recent blood acylcarnitines profiling revealed subclinical cases among cograzers, challenging their status as a control group. This study investigates the faecal microbiota of horses clinically affected by atypical myopathy, their cograzers, and a control group of toxin-free horses while analysing correlations between microbiota composition and blood parameters. Faecal samples were analysed using 16S amplicon sequencing, revealing significant differences in α-diversity, evenness, and β-diversity. Notable differences were found between several genera, especially Clostridia_ge, Bacteria_ge, Firmicutes_ge, Fibrobacter, and NK4A214_group. Blood levels of methylenecyclopropylacetyl-carnitine and C14:1 correlated with variations in faecal microbial composition. The theoretical presence of enzymes in bacterial populations was also investigated. These results underscore the critical need to investigate the potential role of intestinal microbiota in this poisoning and may provide insights for developing prevention and treatment strategies.

Stability of Gastric Fluid and Fecal Microbial Populations in Healthy Horses under Pasture and Stable Conditions

Equine gastrointestinal microbial communities vary across the gastrointestinal tract and in response to diet or disease. Understanding the composition and stability of gastric fluid microbiota in healthy horses is a prerequisite to understanding changes associated with the development of disease. The objective of this study was to describe microbial communities in the gastric fluid and feces of healthy horses longitudinally. Horses were maintained on pasture (6 weeks), stabled (5 weeks), then returned to pasture. A consistent forage diet was provided throughout. Native gastric fluid and feces were collected weekly for full-length 16S ribosomal DNA sequencing and microbial profiling analysis. Fewer taxa were identified in the gastric fluid (770) than in the feces (5284). Species richness and diversity were significantly different between sample types (p < 0.001), but not between housing locations (p = 0.3). There was a significant effect of housing and horse on the Bray-Curtis compositional diversity of gastric (p = 0.005; p = 0.009) and fecal (p = 0.001; p = 0.001) microbiota. When horses moved from pasture to stable, the relative proportions of gastric fluid Lactobacillaceae increased and Streptococcaceae decreased, while fecal Firmicutes increased and Bacteriodota decreased. Within each housing condition, there was no significant week-to-week variation in gastric (p = 0.9) or fecal (p = 0.09) microbiota. Overall, these findings support the maintenance of stable gastric and fecal microbial populations under each management condition, providing a basis for further investigation of gastric fluid microbiota in diseases of the foregut.

A Review of Epithelial Ion Transporters and Their Roles in Equine Infectious Colitis

Equine colitis is a devastating disease with a high mortality rate. Infectious pathogens associated with colitis in the adult horse include Clostridioides difficile, Clostridium perfringens, Salmonella spp., Neorickettsia risticii/findlaynesis, and equine coronavirus. Antimicrobial-associated colitis can be associated with the presence of infectious pathogens. Colitis can also be due to non-infectious causes, including non-steroidal anti-inflammatory drug administration, sand ingestion, and infiltrative bowel disease. Current treatments focus on symptomatic treatment (restoring fluid and electrolyte balance, preventing laminitis and sepsis). Intestinal epithelial ion channels are key regulators of electrolyte (especially sodium and chloride) and water movement into the lumen. Dysfunctional ion channels play a key role in the development of diarrhea. Infectious pathogens, including Salmonella spp. and C. difficile, have been shown to regulate ion channels in a variety of ways. In other species, there has been an increased interest in ion channel manipulation as an anti-diarrheal treatment. While targeting ion channels also represents a promising way to manage diarrhea associated with equine colitis, ion channels have not been well studied in the equine colon. This review provides an overview of what is known about colonic ion channels and their known or putative role in specific types of equine colitis due to various pathogens.

Oral probiotic administration attenuates postexercise inflammation in horses

Probiotics are commonly incorporated into equine diets to impart health and performance benefits; however, peer-reviewed evidence supporting their efficacy in horses is limited. Interestingly, bacteria from the Bacillus genus are gaining interest for their unique ability to impact metabolic, immune, and inflammatory pathways. The objective of this trial was to evaluate a selection of Bacilli for their role in altering the inflammatory response in horses to exercise. Eighteen horses were utilized in a randomized cross-over trial. Horses were randomly assigned to one of 6 starting treatments including a negative and positive control, and groups that received one of 4 probiotics (Bacillus coagulans GBI-30, 6086, Bacillus subtilis-1, Bacillus subtilis-2, or Bacillus amyloliquefaciens) top dressed to their daily ration at a rate of 8 billion CFU/d mixed into dried whey powder. All horses received a similar base diet of grass hay offered at 2.0% of bodyweight daily along with 4.54 kg of a commercially available textured horse feed. Each 3-wk phase of the trial consisted of a 2-wk dietary acclimation followed by a 1-wk exercise challenge and sample collection. Between phases, horses were offered only their base diet. On the day of exercise, horses were offered their 0700 ration and then subjected to a 2-h standardized exercise test. Blood samples were obtained prior to starting exercise and then again at 0, 2, 4, 6, 8, 24, 48, and 72-h postexercise. Horses in the positive control group were administered 0.23 mg/kg BW flunixin meglumine immediately following the 0-h sampling. Samples were analyzed for serum amyloid A (SAA), interleukin-6 (IL-6), and prostaglandin E2 (PGE2) concentrations. Data were evaluated via ANOVA using the MIXED procedure in SAS 9.4. Exercise-induced inflammation as evidenced by SAA, IL-6, and PGE2 increases postexercise. Horses consuming B. coagulans GBI-30, 6086 had reduced production of SAA, IL-6, and PGE2 compared to all other probiotic-fed groups and the negative control (P < 0.001). The positive control successfully ameliorated the postexercise inflammatory response. These data highlight the potential for B. coagulans GBI-30, 6086 to be incorporated into equine rations as a method to support optimal response to exercise or other inflammation-inducing challenges. Additional research is ongoing to elucidate the methodology by which these results occur.

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi)

The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analysed faecal DNA for both the trnL-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (E. quagga) and Grevy's zebra (E. grevyi). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.

Effects of astaxanthin on gut microbiota of polo ponies during deconditioning and reconditioning periods

To determine the effects of astaxanthin (ASTX) supplementation on the equine gut microbiota during a deconditioning-reconditioning cycle, 12 polo ponies were assigned to a control (CON; n = 6) or supplemented (ASTX; 75 mg ASTX daily orally; n = 6) group. All horses underwent a 16-week deconditioning period, with no forced exercise, followed by a 16-week reconditioning program where physical activity gradually increased. Fecal samples were obtained at the beginning of the study (Baseline), after deconditioning (PostDecon), after reconditioning (PostRecon), and 16 weeks after the cessation of ASTX supplementation (Washout). Following DNA extraction from fecal samples, v4 of 16S was amplified and sequenced to determine operational taxonomic unit tables and α-diversity and β-diversity indices. The total number of observed species was greater at Baseline than PostDecon, PostRecon, and Washout (p ≤ 0.02). A main effect of ASTX (p = 0.01) and timepoint (p = 0.01) was observed on β-diversity, yet the variability of timepoint was greater (13%) than ASTX (6%), indicating a greater effect of timepoint than ASTX. Deconditioning and reconditioning periods affected the abundance of the Bacteroidetes and Fibrobacteres phyla. Physical activity and ASTX supplementation affect the equine gut microbiome, yet conditioning status may have a greater impact.

Microbiota characterization throughout the digestive tract of horses fed a high-fiber vs. a high-starch diet

Introduction

Diet is one of the main factors influencing the intestinal microbiota in horses, yet a systematic characterization of the microbiota along the length of the digestive tract in clinically healthy horses, homogenous for age and breed and receiving a specific diet is lacking.

Methods

The study used 16S rRNA amplicon sequencing to characterize the microbiota of the intestinal tracts of 19 healthy Bardigiano horses of 14.3  ±  0.7  months of age fed one of two diets. Nine horses received a high-starch diet (HS), and ten horses received a high-fiber diet (HF). After 129  days, the horses were slaughtered, and samples were collected from the different intestinal tract compartments.

Results and discussion

The microbiota alpha diversity indices were lower in the caecum, pelvic flexure and right dorsal colon of the horses fed the HS diet (False Discovery Rate, FDR  <  0.05). The values of beta diversity indicated significant compositional differences between the studied intestinal tract compartments according to the diet received (FDR  <  0.05). At the lower taxonomic level (genus or family), the HS diet was associated with a higher relative frequency of Enterobacteriaceae within the small intestine (jejunum and duodenum) (FDR  <  0.05). Within the hindgut (caecum and sternal flexure), the HS diet was associated with lower relative frequencies (i.e., a smaller core community) of bacteria belonging to Fibrobacteraceae and Prevotellaceae (FDR  <  0.05). Moreover, horses fed the HS diet displayed a higher relative abundance of Streptococcus in the caecum (FDR  <  0.05) and Fusobacterium in the sternal flexure (FDR  <  0.05), both of which are pathogenic bacteria responsible for inflammation diseases. Samples collected from the pelvic flexure and rectum of horses fed the HS diet showed significantly higher relative frequencies of Succinivibrionaceae (FDR  <  0.05) - amylolytic bacteria associated with acidosis. The relative frequencies of the Lachnospiraceae and Ruminococcaceae were lower in the feces collected from the rectum of horses receiving the HS diet vs. HF diet, indicating smaller core communities of these bacteria (FDR  <  0.05). Fibrous diets should be promoted to prevent dysbiosis of the microbiota associated with high-starch diet.

Comparison of the fecal microbiota with high- and low performance race horses

Exercise plays an important role in regulating energy homeostasis, which affects the diversity of the intestinal microbial community in humans and animals. To the best of the authors' knowledge, few studies have reported the associations between horse gut microbiota along with their predicted metabolic activities and the athletic ability of Jeju horses and Thoroughbreds living in Korea. This study was conducted to investigate the association between the gut microbiota and athletic performance in horses. This study sequenced the V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from racehorse fecal samples and compared the fecal microbiota between high- and low-performance Jeju horses and Thoroughbreds. Forty-nine fecal samples were divided into four groups: high-performance Jeju horses (HJ, n = 13), low-performance Jeju horses (LJ, n = 17), high-performance Thoroughbreds (HT, n = 9), and low-performance Thoroughbreds (LT, n = 10). The high-performance horse groups had a higher diversity of the bacterial community than the low-performance horse groups. Two common functional metabolic activities of the hindgut microbiota (i.e., tryptophan and succinate syntheses) were observed between the low-performance horse groups, indicating dysbiosis of gut microbiota and fatigue from exercise. On the other hand, high-performance horse groups showed enriched production of polyamines, butyrate, and vitamin K. The racing performance may be associated with the composition of the intestinal microbiota of Jeju horses and Thoroughbreds in Korea.

Current Understanding of Equine Gut Dysbiosis and Microbiota Manipulation Techniques: Comparison with Current Knowledge in Other Species

Understanding the importance of intestinal microbiota in horses and the factors influencing its composition have been the focus of many studies over the past few years. Factors such as age, diet, antibiotic administration, and geographic location can affect the gut microbiota. The intra- and inter-individual variability of fecal microbiota in horses complicates its interpretation and has hindered the establishment of a clear definition for dysbiosis. Although a definitive causal relationship between gut dysbiosis in horses and diseases has not been clearly identified, recent research suggests that dysbiosis may play a role in the pathogenesis of various conditions, such as colitis and asthma. Prebiotics, probiotics, and fecal microbiota transplantation to modulate the horse's gastrointestinal tract may eventually be considered a valuable tool for preventing or treating diseases, such as antibiotic-induced colitis. This article aims to summarize the current knowledge on the importance of intestinal microbiota in horses and factors influencing its composition, and also to review the published literature on methods for detecting dysbiosis while discussing the efficacy of gut microbiota manipulation in horses.

The Microbiota and Equine Asthma: An Integrative View of the Gut-Lung Axis

Both microbe-microbe and host-microbe interactions can have effects beyond the local environment and influence immunological responses in remote organs such as the lungs. The crosstalk between the gut and the lungs, which is supported by complex connections and intricate pathways, is defined as the gut-lung axis. This review aimed to report on the potential role of the gut-lung gut-lung axis in the development and persistence of equine asthma. We summarized significant determinants in the development of asthma in horses and humans. The article discusses the gut-lung axis and proposes an integrative view of the relationship between gut microbiota and asthma. It also explores therapies for modulating the gut microbiota in horses with asthma. Improving our understanding of the horse gut-lung axis could lead to the development of techniques such as fecal microbiota transplants, probiotics, or prebiotics to manipulate the gut microbiota specifically for improving the management of asthma in horses.

Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis

Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros' fecal bacterial microbiota composition. fecal samples were collected from rhinoceroses at capture (n = 16) and after a >30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros' fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.

Species interactions, stability, and resilience of the gut microbiota - Helminth assemblage in horses

The nature and strength of interactions entertained among helminths and their host gut microbiota remain largely unexplored. Using 40 naturally infected Welsh ponies, we tracked the gut microbiota-cyathostomin temporal dynamics and stability before and following anthelmintic treatment and the associated host blood transcriptomic response. High shedders harbored 14 species of cyathostomins, dominated by Cylicocyclus nassatus. They exhibited a highly diverse and temporal dynamic gut microbiota, with butyrate-producing Clostridia likely driving the ecosystem steadiness and host tolerance toward cyathostomins infection. However, anthelmintic administration sharply bent the microbial community. It disrupted the ecosystem stability and the time-dependent network of interactions, affecting longer term microbial resilience. These observations highlight how anthelmintic treatments alter the triangular relationship of parasite, host, and gut microbiota and open new perspectives for adding nutritional intervention to current parasite management strategies.

Direct and culture-enriched 16S rRNA sequencing of cecal content of healthy horses and horses with typhlocolitis

Next generation sequencing has demonstrated that alpha diversity of the fecal microbiota is significantly altered in horses with typhlocolitis. The objective of this study was to evaluate the bacterial composition of the cecum content of horses with and without typhlocolitis through direct and culture-enriched 16S gene sequencing of six healthy horses and six horses with acute typhlocolitis; a case-control study design. Cecal content was collected after euthanasia. An aliquot was used for direct 16S gene sequencing. Another was serially diluted with brain heart infusion (BHI) and plated onto five different agar media. All culture medias, except for MacConkey, were incubated anaerobically. Bacterial colonies were harvested in bulk and used for DNA extraction, 16S PCR amplification, and sequenced using the Illumina MiSeq platform. Predominant phyla in healthy and diseased horses were Firmicutes, followed by Bacteroidetes in all cultured medias, except for MacConkey agar, in which Proteobacteria was the dominant phylum. Greater bacterial richness was identified in sequenced cecal contents as compared to cultured plates (P < 0.05). Culture-enriched molecular profiling combined with 16S rRNA gene sequencing offer an alternative method for the study of the gut microbiota of horses. For direct cecum content 16S gene amplification, the alpha diversity indices were lower in diarrheic horses compared to healthy horses (P < 0.05). A higher relative abundance of Fusobacteriota was found in 2/6 samples from diarrheic horses. The role of Fusobacteriota in equine colitis deserves investigation.

The Role of Yeast Saccharomyces cerevisiae in Supporting Gut Health in Horses: An Updated Review on Its Effects on Digestibility and Intestinal and Fecal Microbiota

To support the overall health of horses, it is essential to maintain an optimal gut health (GH) status, which encompasses several physiological and functional aspects, including the balance and functionality of intestinal microbial populations and, accordingly, the effective digestion and absorption of nutrients. Numerous biotic and abiotic stressors can lead to an imbalance of GH, such as the quality of forages and the composition of diet, e.g., the inclusion of high energy-dense feeds to meet the energy requirements of performance horses. To support the digestive function and the intestinal microbial populations, the diet can be supplemented with feed additives, such as probiotic yeasts, that promote the ability of cellulolytic bacteria in the hindgut to digest the available fiber fractions, finally increasing feed efficiency. Among the different yeasts available, S. cerevisiae is the most used in horses' nutrition; however, results of digestibility trials, as well as data on intestinal and fecal microbial populations, are sometimes contradictory. Therefore, the purpose of this review is to summarize the effects of S. cerevisiae on in vivo and in vitro digestibility, providing an updated overview of its effects on the intestinal and fecal microbial population.

Effects of different grains on bacterial diversity and enzyme activity associated with digestion of starch in the foal stomach

Background

Compared with the stomach of ruminant cattle, the stomach of horse is small and mainly for chemical digestion, but the microorganisms in the stomach play an important role in maintaining the homeostasis of the internal environment. Due to the complexity of the microbes in the stomach, little is known about the diversity and structure of bacteria in the equine stomach. Grains are the main energy source for plant-eating livestock and energy is derived through enzymatic hydrolysis of grains into glucose or their microbial fermentation into Volatile fatty acids (VFA). However, the mechanism through which these ingested grains are chemically digested as well as the effect of these grains on the stomach remains elusive. This study explored the effects of feeding different grains (corn, oats, and barley) on bacterial diversity, structure, and composition in the foal’s stomach content. Furthermore, the effects of different grains on the vitality of starch digestion-related stomach enzymes were investigated.

Results

No significant differences were observed (P > 0.05) in the bacterial rarefaction curves of Operational Taxonomic Units (OTUs) and diversity of the stomach microbiota in all foals. This study also revealed the statistical differences for Firmicutes, Cyanobacteria, Actinobacteria, Fibrobacteres, Lactobacillaceae, Streptococcaceae, Unidentified_Clostridiales, Prevotellaceae, Lactobacillus, Streptococcus, Unidentified_Cyanobacteria, Unidentified_Clostridiales, Lactococcus, Sphingomonas, Lactobacillus_hayakitensis, Lactobacillus_equigenerosi, and Clostridium_perfringens. The linear discriminant analysis effect size analysis revealed 9 bacteria at each classification level. The functional analysis of species information by using FAPROTAX software was able to predict 35 functions, and the top 5 functions were chemoheterotrophy, fermentation, animal_parasites_or_symbionts, nitrate_reduction, and aerobic_chemoheterotrophy. The study also revealed statistical differences for pH, glucose concentration, β-amylase, maltase, and amylase.

Conclusions

The different grains had no significant effect on the microbial diversity of the stomach content of the foal. However, the relative bacterial abundances differed significantly in response to different diets. Particularly, oats fed to the foals significantly increased the relative abundance of Firmicutes, Lactobacillaceae, Lactobacillus, and Lactobacillus_hayakitensis. The grain had no significant effect on the pH of the stomach content, glucose concentration, and enzyme viability in the foal.

Fecal Microbiota Comparison between Healthy Teaching Horses and Client-Owned Horses

The objective of this study was to compare the fecal microbiota of 2 healthy teaching horse herds with that of client-owned horses from the same geographic areas. The fecal microbiota of client-owned horses from Ontario Canada (n = 15) and Florida, USA (n = 11) was compared with that teaching horses from the University of Guelph, Ontario, Canada (n = 10) and the University of Florida, Florida, USA (n = 15). The fecal microbiota was characterized by sequencing of bacterial DNA using the V4 hypervariable region of the 16S rRNA gene. The diversity (inverse Simpson index) of the fecal microbiota was significantly higher in teaching than client owned horses from the same geographical area (P < 0.05). The community membership (Jaccard Index) and structure (Yue and Clayton index) of teaching horses was also significantly different from that of client owned horses from the same geographical area (AMOVA P < 0.001). The bacterial membership and structure of the fecal microbiota of Ontario and Florida teaching horses were significantly different, while the bacterial membership, but not the structure of Ontario and Florida client owned horses was significantly different (AMOVA P < 0.001). In all 4 groups of healthy horses, Lachnospiraceae, Ruminococcaceae, Bacteroidales, Clostridiales, and Treponema were detected in high relative abundance. The fecal microbiota of healthy horses from teaching herds kept in the same environment with identical management practices differs significantly from that of horses housed in different facilities with dissimilar management practices. Our results suggest an effect of the environment and management practices on the gastrointestinal microbiota. Researchers should attempt to include healthy horses from the same farm with similar management as control groups when comparing with diseased horses.

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems

BACKGROUND

Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C-W) and WSG to CSG (W-C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing.

RESULTS

Regardless of IRS or transition (C-W vs. W-C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting β-diversity was the individual horse (R² ≥ 0.24; P = 0.0001). Random forest modeling was unable to accurately predict days within C-W and W-C, but could predict the individual horse based on microbial composition (accuracy: 0.92 ± 0.05). Only three differentially abundant bacterial co-abundance groups (BCG) were identified across days within all C-W and W-C for both IRS (W ≥ 126). The BCG differing by day for all transitions included amplicon sequence variants (ASV) assigned to bacterial groups with known fibrolytic and butyrate-producing functions including members of Lachnospiraceae, Clostridium sensu stricto 1, Anaerovorax the NK4A214 group of Oscillospiraceae, and Sarcina maxima. In comparison, 38 BCG were identified as differentially abundant by horse (W ≥ 704). The ASV in these groups were most commonly assigned to genera associated with degradation of structural carbohydrates included Rikenellaceae RC9 gut group, Treponema, Christensenellaceae R-7 group, and the NK4A214 group of Oscillospiraceae. Fecal pH also did not differ by day.

CONCLUSIONS

Overall, these results demonstrated a strong influence of individual horse on the fecal microbial community, particularly on the specific composition of fiber-degraders. The equine fecal microbiota were largely stable across transitions between forages within IRS suggesting that the equine gut microbiota adjusted at the individual level to the subtle dietary changes imposed by these transitions. This adaptive capacity indicates that horses can be managed in IRS without inducing gastrointestinal dysfunction.

A study comparing the healthy and diseased equine glandular gastric microbiota sampled with sheathed transendoscopic cytology brushes

BACKGROUND

The role of the equine gastrointestinal microbiota in the pathogenesis of equine glandular gastric disease (EGGD) is poorly understood.

OBJECTIVES

To investigate whether the glandular gastric microbiota is altered in horses with EGGD.

STUDY DESIGN

Prospective longitudinal study METHODS: Five Thoroughbred racehorses from one training centre underwent gastroscopy as part of poor performance investigation. Samples were taken from EGGD lesions and adjacent normal mucosa using sheathed transendoscopic cytology brushes and frozen at -80 °C. DNA was extracted for 16S rRNA sequencing, and sequences compared against a database to generate taxonomic classification of the microbiota. The same horses were sampled six months later.

RESULTS

Normal glandular mucosal samples were characterised by a higher proportion of Proteobacteria (46.3 %) than EGGD lesions (18.9 %). Relative abundance of Firmicutes was lower in samples from normal mucosa (20.0 %) than EGGD lesions (41.2 %). Linear discriminant analysis effect size (LEfSe) confirmed a greater proportion of Firmicutes species was characteristic of samples collected from EGGD lesions due to a very high relative abundance of Sarcina (up to 92.4 %) in two horses with EGGD. We were unable to comment on the stability of the glandular gastric microbiota over time.

MAIN LIMITATIONS

Small sample population. None of the horses examined had grossly normal gastric mucosa.

CONCLUSIONS

The gastric microbiota appears altered in EGGD, although we are unable to demonstrate a causative effect. Sarcina was particularly increased in abundance in EGGD and may be a useful biomarker of disease. Sheathed cytology brushes were an effective method for sampling the gastric mucosa.

Fecal extract from obese horses induces an inflammatory response by murine macrophages in vitro

OBJECTIVE

To compare the inflammatory response of murine macrophages exposed to the enteric microbiome of obese horses versus nonobese horses.

SAMPLE

Fecal samples from 12 obese horses (body condition score ≥ 7/9) and 12 nonobese horses (body condition score 4 to 5/9) with similar dietary management.

PROCEDURES

Fecal supernatant was prepared from frozen fecal samples. RAW 264.7 macrophage cells were exposed to the fecal extract. Inflammatory cytokine (interleukin-1β, tumor necrosis factor-α, and interleukin-6) gene expression was quantified via real-time quantitative reverse transcription PCR assay, and cytokine concentration was quantified via ELISA. Lipopolysaccharide was evaluated in fecal extract via chromo-limulus amoebocyte lysate assay.

RESULTS

Compared with fecal extracts from nonobese horses, fecal extracts from obese horses presented higher concentrations of lipopolysaccharide and induced a heightened expression of the proinflammatory cytokines interleukin-1β, tumor necrosis factor-α, and interleukin-6 from macrophages.

CLINICAL RELEVANCE

The increased levels of inflammatory markers induced in murine macrophages by the microbiome of obese horses in vitro suggested important differences in the enteric microbial composition of these horses, compared with nonobese horses. Overall, this study showed that the microbiome may play a role in mediating an inflammatory response within the gastrointestinal tract of obese horses. Mechanisms of obesity in the horse have not been fully elucidated. Improved understanding of the pathophysiology of disease will guide future research into potential diagnostic and therapeutic interventions for equine obesity.

Nasopharyngeal bacterial and fungal microbiota in normal horses and horses with nasopharyngeal cicatrix syndrome

Background

The nasopharyngeal bacterial and fungal microbiota of normal horses and those with nasopharyngeal cicatrix syndrome (NCS) are unknown.

Hypotheses/Objectives

To describe the microbiota from nasopharyngeal washes of healthy horses and of horses acutely affected with NCS.

Animals

Twenty‐six horses acutely affected with NCS horses and 14 unaffected horses.

Methods

Prospective, observational cohort study. Horses were recruited by investigators through personal communications in central Texas. Bacterial (16s RNA) and fungal (internal transcribed spacer) microbiota from nasopharyngeal washes were evaluated. Polymerase chain reaction for detection of Pythium insidiosum was performed.

Results

Results indicated that 6 fungal genera (Alternaria, Bipolaris, Microascus, Spegazzinia, Paraconiothyrium, Claviceps) and 1 bacterial genera (Staphylococcus) were significantly different between affected and unaffected horses. The fungal genus Bipolaris had increased abundance in NCS affected horses and on NCS affected farms. Pythium insidiosum was absent in the nasopharyngeal wash of all horses, irrespective of health status.

Conclusion and Clinical Importance

Significant differences were identified in the fungal microbiota in horses affected with NCS and farms affected with NCS compared to those unaffected. Therefore, Bipolaris warrants further investigation.

Impact of Dietary Zinc Chloride Hydroxide and Zinc Methionine on the Faecal Microbiota of Healthy Adult Horses and Ponies

Zinc supplements are often used in equine nutrition to support skin and hoof quality or the immune function. However, no data on the effects of dietary zinc on the intestinal microbiota of horses and ponies are available so far. In the present study, varying dietary zinc concentrations (maintenance (4 mg/kg BW^0.75/day), 120 mg/kg dry matter (DM)/day and 240 mg/kg DM/day) were achieved by the supplementation of either zinc chloride hydroxide or zinc methionine (six treatment periods of 4 weeks each). Eight healthy adult ponies and two healthy adult horses were included, and faecal samples were collected at the end of each treatment period to analyse the microbiota (16S rDNA sequencing) and microbial metabolites. With increasing dietary zinc concentrations, the richness of the faecal microbiota decreased, independently of the zinc compound used. In addition, a decrease of the relative abundance of Bacteroidetes and Fibrobacteres as well as of acetate and total short-chain fatty acids in the faeces of the animals was observed at high zinc intakes. Effects on the bacterial order, family and genus level were also detected, which were partly more pronounced for zinc chloride hydroxide. It can be concluded that high dietary zinc levels decrease the richness and fermentative activity of the faecal microbiota of horses and ponies. Although all animals were healthy throughout the study, the effects could be critical for gut health, and deserve more research. The detected differences between the zinc compounds used indicate differences in the bioavailability of organic and inorganic zinc sources in equines.

Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses

BACKGROUND

Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep sequencing methods.

RESULTS

After sequencing and analysis, a total of 68 and 86 phyla were detected in the material originating from 49 equine abortion samples and 8 samples from normal deliveries, respectively. Most phyla were present in both groups, with the exception of Chlamydiae that were only present in abortion samples. Around 2886 genera were present in the abortion samples and samples from normal deliveries at a cut off value of 0.001% of relative abundance. Significant differences in species diversity between aborted and normal tissues was observed. Several potential abortigenic pathogens were identified at a high level of relative abundance in a number of the abortion cases, including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus and Chlamydia psittaci.

CONCLUSIONS

This work revealed the presence of several potentially abortigenic pathogens in aborted specimens. No novel potential abortigenic agents were detected. The ability to screen samples for multiple pathogens that may not have been specifically targeted broadens the frontiers of diagnostic potential. The future use of metagenomic approaches for diagnostic purposes is likely to be facilitated by further improvements in deep sequencing technologies.

Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity

Simple Summary

Free faecal water (FFW) in equines causes soiling of the hindquarters and tail and may also include additional symptoms. The cause of FFW is unknown. In this study it was investigated whether the microbes present in the last part of the gut (i.e., the hindgut microbiota) may be involved. From the analysis of faecal samples, it was found that horses suffering from FFW had no differences in their hindgut microbiota compared to healthy horses stabled at the same location. However, subsequent treatment of the FFW horses with a faecal microbiota transplantation (FMT) from a healthy donor animal resulted in a decrease in FFW symptom severity. Nevertheless, animals did not respond uniformly to this treatment, with some only having temporary decreases in FFW symptom severity. No lasting changes in the hindgut microbiota of the FFW horses occurred as a result of the faecal transplant. The practical implication of these findings is that FMT can potentially be used to temporarily alleviate FFW symptom severity in horses, although future studies using controls are needed to confirm the effectiveness of FMT to treat FFW.

Abstract

Free faecal water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. Though the cause of FFW is unknown, it was hypothesized that it may involve the gut microbiota. This hypothesis was addressed as follows. First, the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n = 10) was compared. Second, FFW horses were treated with a standardised faecal microbiota transplantation (FMT) protocol (n = 10), followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (p > 0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (p = 0.02) and remained decreased for the remainder of the study (p < 0.02). However, individual animal responses to FMT varied. FMT had no effect on FFW horse faecal prokaryotic community composition in terms of alpha or beta diversity. Alpha diversity of the donor inocula used in the FMT was always lower than that of the faecal microbiota of the FFW treated horses (p < 0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, some horses that received FMT had a temporary alleviation of FFW symptom severity without causing changes in the faecal microbiota. Future studies using controls are now needed to confirm the effectiveness of FMT to treat FFW.

Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets

The management of competition horses in New Zealand often involves rotations of short periods of stall confinement and concentrate feeding, with periods of time at pasture. Under these systems, horses may undergo abrupt dietary changes, with the incorporation of grains or concentrate feeds to the diet to meet performance needs, or sudden changes in the type of forage fed in response to a lack of fresh or conserved forage. Abrupt changes in dietary management are a risk factor for gastrointestinal (GI) disturbances, potentially due to the negative effects observed on the population of GI microbiota. In the present study, the faecal microbiota of horses was investigated to determine how quickly the bacterial communities; (1) responded to dietary change, and (2) stabilised following abrupt dietary transition. Six Thoroughbred mares were stabled for six weeks, consuming freshly cut pasture (weeks 1, 3 and 5), before being abruptly transitioned to conserved forage-based diets, both offered ad libitum. Intestinal markers were administered to measure digesta transit time immediately before each diet change. The conserved forage-based diets were fed according to a 3 × 3 Latin square design (weeks 2, 4 and 6), and comprised a chopped ensiled forage fed exclusively (Diet FE) or with whole oats (Diet FE + O), and perennial ryegrass hay fed with whole oats (Diet H + O). Faecal samples were collected at regular intervals from each horse following the diet changes. High throughput 16S rRNA gene sequencing was used to evaluate the faecal microbiota. There were significant differences in alpha diversity across diets (p < 0.001), and a significant effect of diet on the beta diversity (ANOSIM, p = 0.001), with clustering of samples observed by diet group. There were differences in the bacterial phyla across diets (p < 0.003), with the highest relative abundances observed for Firmicutes (62-64%) in the two diets containing chopped ensiled forage, Bacteroidetes (32-38%) in the pasture diets, and Spirochaetes (17%) in the diet containing hay. Major changes in relative abundances of faecal bacteria appeared to correspond with the cumulative percentage of intestinal markers retrieved in the faeces as the increasing amounts of digesta from each new diet transited the animals. A stable faecal microbiota profile was observed in the samples from 96 h after abrupt transition to the treatment diets containing ensiled chopped forage. The present study confirmed that the diversity and community structure of the faecal bacteria in horses is diet-specific and resilient following dietary transition and emphasised the need to have modern horse feeding management that reflects the ecological niche, particularly by incorporating large proportions of forage into equine diets.

Characterization of the seminal bacterial microbiome of healthy, fertile stallions using next-generation sequencing

High-throughput sequencing studies have shown the important role microbial communities play in the male reproductive tract, indicating differences in the semen microbial composition between fertile and infertile males. Most of these studies were made on human beings but little is known regarding domestic animals. Seminal bacteria studies made in stallions mostly focus on pathogenic bacteria and on their impact on reproductive technology. However, little is known about stallion commensal seminal microflora. That ultimately hinders our capacity to associate specific bacteria to conditions or seminal quality. Therefore, the aim of this study was to characterize the seminal microbial composition of 12 healthy, fertile stallion using next-generation sequencing. Hypervariable region V3 was chosen for bacterial identification. A total of nine phyla was detected. The most abundant ones were Bacteroidetes (46.50%), Firmicutes (29.92%) and Actinobacteria (13.58%). At family level, we found 69 bacterial families, but only nine are common in all samples. Porphyromonadaceae (33.18%), Peptoniphilaceae (14.09%), Corynebacteriaceae (11.32%) and Prevotellaceae (9.05%) were the most representative ones, while the Firmicutes phylum displayed the highest number of families (23, a third of the total). Samples showed high inter-subject variability. Findings previously described in other species notably differ from our findings. Families found in human such as Lactobacillaceae, Staphylococcaceae and Streptococcaceae only represented a 0.00%, 0.17% and 0.22% abundance in our samples, respectively. In conclusion, Porphyromonadaceae, Prevotellaceae, Peptoniphilaceae and Corynebacteriaceae families are highly represented in the seminal microbiome of healthy, fertile stallions. A high variation among individuals is also observed.

Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand

Simple Summary

Ten horses were kept on pasture for one year, with hay provided from June to October. Each month we measured how much pasture was present and collected pasture and hay samples to assess their nutrient content, and faecal samples from all horses to investigate the diversity of the bacterial species present using next-generation sequencing technology. The population of faecal bacteria was more diverse during the months when the horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. The diet offered, and the season and the month we sampled the paddock all had a major influence on the diversity of the species of bacteria in the faeces. While there were some differences between the horses, generally the bacterial populations could be grouped together in samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought). More specifically we were able to show an association between specific bacterial species, nutrients (dry matter, protein, and structural carbohydrates), and climatic conditions (rainfall and temperature). Our study showed that the diversity and composition of the bacterial population of horses kept on pasture changes over a 12-month period, and this reflects changes in the nutrient composition of the pasture, which in turn is influenced by climate. The findings of this study may have implications for managing horses on pasture and the use of forages for horses susceptible to digestive problems.

Abstract

Seasonal variation in the faecal microbiota of forage-fed horses was investigated over a 12-month period to determine whether the bacterial diversity fluctuated over time. Horses (n = 10) were maintained on pasture for one year, with hay supplemented from June to October. At monthly intervals, data were recorded on pasture availability and climate (collected continuously and averaged on monthly basis), pasture and hay samples were collected for nutrient analysis, and faecal samples were collected from all horses to investigate the diversity of faecal microbiota using next-generation sequencing on the Illumina MiSeq platform. The alpha diversity of bacterial genera was high in all samples (n = 118), with significantly higher Simpson’s (p < 0.001) and Shannon-Wiener (p < 0.001) diversity indices observed during the months when horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. There were significant effects of diet, season, and month (ANOSIM, p < 0.01 for each comparison) on the beta diversity of bacterial genera identified in the faeces. While there was some inter-horse variation, hierarchical clustering of beta diversity indices showed separate clades originating for samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought), with a strong association between bacterial taxa and specific nutrients (dry matter, protein, and structural carbohydrates) and climate variables (rainfall and temperature). Our study supports the hypothesis that the diversity and community structure of the faecal microbiota of horses kept on pasture varied over a 12-month period, and this variation reflects changes in the nutrient composition of the pasture, which in turn is influenced by climatic conditions. The findings of this study may have implications for grazing management and the preparation of conserved forages for those horses susceptible to perturbations of the hindgut microbiota.

Probiotics-Live Biotherapeutics: a Story of Success, Limitations, and Future Prospects-Not Only for Humans

In livestock production, lactic acid bacteria (LAB) represent the most widespread microorganisms used as probiotics. For such critical use, these bacteria must be correctly identified and characterized to ensure their safety and efficiency. Recently, probiotics have become highly recognized as supplements for humans and in particular for animals because of their beneficial outcome on health improvement and well-being maintenance. Various factors, encompassing dietary and management constraints, have been demonstrated to tremendously influence the structure, composition, and activities of gut microbial communities in farm animals. Previous investigations reported the potential of probiotics in animal diets and nutrition. But a high rate of inconsistency in the efficiency of probiotics has been reported. This may be due, in a major part, to the dynamics of the gastrointestinal microbial communities. Under stressing surroundings, the direct-fed microbials may play a key role as the salient limiting factor of the severity of the dysbiosis caused by disruption of the normal intestinal balance. Probiotics are live microorganisms, which confer health benefits on the host by positively modifying the intestinal microflora. Thus, the aim of this review is to summarize and to highlight the positive influence of probiotics and potential probiotic microbe supplementation in animal feed with mention of several limitations.

Comparison of the Fecal Microbiota of Horses with Intestinal Disease and Their Healthy Counterparts

(1) Background: The intestinal microbiota plays an essential role in maintaining the host's health. Dysbiosis of the equine hindgut microbiota can alter the fermentation patterns and cause metabolic disorders. (2) Methods: This study compared the fecal microbiota composition of horses with intestinal disease and their healthy counterparts living in Korea using 16S rRNA sequencing from fecal samples. A total of 52 fecal samples were collected and divided into three groups: horses with large intestinal disease (n = 20), horses with small intestinal disease (n = 8), and healthy horses (n = 24). (3) Results: Horses with intestinal diseases had fewer species and a less diverse bacterial population than healthy horses. Lactic acid bacteria, Lachnospiraceae, and Lactobacillaceae were overgrown in horses with large intestinal colic. The Firmicutes to Bacteroidetes ratio (F/B), which is a relevant marker of gut dysbiosis, was 1.94, 2.37, and 1.74 for horses with large intestinal colic, small intestinal colic, and healthy horses, respectively. (4) Conclusions: The overgrowth of two lactic acid bacteria families, Lachnospiraceae and Lactobacillaceae, led to a decrease in hindgut pH that interfered with normal fermentation, which might cause large intestinal colic. The overgrowth of Streptococcus also led to a decrease in pH in the hindgut, which suppressed the proliferation of the methanogen and reduced methanogenesis in horses with small intestinal colic.

Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea

(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.

Effects of hypersensitivity disorders and environmental factors on the equine intestinal microbiota

Background

Recent evidence suggests that an altered intestinal microbiota, specifically a reduction of bacterial diversity or a shift in microbial composition, is associated with the development of hypersensitivity disorders in humans, but this is unknown for horses.

Objectives

In this study we hypothesized that horses affected by either Culicoides hypersensitivity or severe equine asthma or both show a decreased diversity of their intestinal microbiota. We also investigated environmental effects.

Methods

Rectal swab samples of a total of 140 horses were collected and the owners completed a detailed questionnaire about their horse. For each allergic horse, a healthy peer from the same stable was equally sampled as an environmentally matched control. Microbiota in the swabs was determined by assessing the V4 region of the bacterial 16S rRNA gene. Structures of bacterial communities were investigated by means of alpha and beta diversity indices.

Results

Group wise comparisons between healthy and allergic horses showed no significant differences regarding alpha (p = 0.9) and beta diversity (p = 0.5). However, the microbial structure was associated with environmental factors such as the type of stable (p = 0.001), access to pasture (p = 0.001) or the type of feeding (p = 0.003). There was also a strong location effect meaning that the microbiota was more similar within the same as compared between farms within this study.

Conclusion

Our observations suggest that hypersensitivity disorders in adult horses are not associated with an alteration of the intestinal microbiota, but environmental and/or location factors strongly influence these bacteria.

Impact of Ambient Temperature Sample Storage on the Equine Fecal Microbiota

Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at -80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae (Fibrobacter) and Ruminococcaceae (Ruminococcus) were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at -80 °C.

Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea

BACKGROUND AND AIMS

Fecal microbial transplantation (FMT) is empirically implemented in horses with colitis to facilitate resolution of diarrhea. The purpose of this study was to assess FMT as a clinical treatment and modulator of fecal microbiota in hospitalized horses with colitis.

METHODS

A total of 22 horses with moderate to severe diarrhea, consistent with a diagnosis of colitis, were enrolled at two referral hospitals (L1: n = 12; L2: n = 10). FMT was performed in all 12 patients on 3 consecutive days at L1, while treatment at L2 consisted of standard care without FMT. Manure was collected once daily for 4 days from the rectum in all colitis horses, prior to FMT for horses at L1, and from each manure sample used for FMT. Fecal samples from 10 clinically healthy control horses housed at L2, and 30 healthy horses located at 5 barns in regional proximity to L1 were also obtained to characterize the regional healthy equine microbiome. All fecal microbiota were analyzed using 16S amplicon sequencing.

RESULTS AND CONCLUSIONS

As expected, healthy horses at both locations showed a greater α-diversity and lower β-diversity compared to horses with colitis. The fecal microbiome of healthy horses clustered by location, with L1 horses showing a higher prevalence of Kiritimatiellaeota. Improved manure consistency (lower diarrhea score) was associated with a greater α-diversity in horses with colitis at both locations (L1: r = -0.385, P = 0.006; L2: r = -0.479, P = 0.002). Fecal transplant recipients demonstrated a greater overall reduction in diarrhea score (median: 4±3 grades), compared to untreated horses (median: 1.5±3 grades, P = 0.021), with a higher incidence in day-over-day improvement in diarrhea (22/36 (61%) vs. 10/28 (36%) instances, P = 0.011). When comparing microbiota of diseased horses at study conclusion to that of healthy controls, FMT-treated horses showed a lower mean UniFrac distance (0.53±0.27) than untreated horses (0.62±0.26, P<0.001), indicating greater normalization of the microbiome in FMT-treated patients.

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.

Abrupt dietary changes between grass and hay alter faecal microbiota of ponies

Abrupt dietary changes, as can be common when managing horses, may lead to compositional changes in gut microbiota, which may result in digestive or metabolic disturbances. The aim of this study was to describe and compare the faecal microbiota of ponies abruptly changed from pasture grazing ad libitum to a restricted hay-only diet and vice versa. The experiment consisted of two, 14-day periods. Faecal samples were collected on day 0 and days 1–3,7,14 after abrupt dietary change from grass to hay and from hay to grass. Microbial populations were characterised by sequencing the V3-V4 region of the 16S rRNA gene using the Illumina MiSeq platform, 4,777,315 sequences were obtained from 6 ponies. Further analyses were performed to characterise the microbiome as well as the relative abundance of microbiota present. The results of this study suggest that the faecal microbiota of mature ponies is highly diverse, and the relative abundances of individual taxa change in response to abrupt changes in diet. The faecal microbiota of ponies maintained on a restricted amount of hay-only was similar to that of the ponies fed solely grass ad libitum in terms of richness and phylogenetic diversity; however, it differed significantly in terms of the relative abundances at distinct taxonomic levels. Class Bacilli, order Lactobacillales, family Lactobacillaceae, and genus Lactobacillus were presented in increased relative abundance on day 2 after an abrupt dietary change from hay to grass compared to all other experimental days (P <0.05). Abrupt changes from grass to hay and vice versa affect the faecal microbial community structure; moreover, the order of dietary change appears to have a profound effect in the first few days following the transition. An abrupt dietary change from hay to grass may represent a higher risk for gut disturbances compared to abrupt change from grass to hay.

Luminal and Mucosal Microbiota of the Cecum and Large Colon of Healthy and Diarrheic Horses

Simple Summary

Acute diarrhea (colitis) is a major problem in adult horses and the role of the intestinal bacteria (microbiota) is still poorly understood in this species. The aim of this study was to compare the mucosal and luminal content microbiota of the cecum and colon of healthy and diarrheic horses. We concluded that microbial dysbiosis (changes in the normal microbiota composition) occurs in horses with colitis at different levels of the intestinal tract and microbiota composition is different between the mucosa and luminal content of diarrheic horses. Changes in species associated with dysbiosis could be used in the future for disease diagnosis, prognosis and treatment of equine colitis.

Abstract

The aim of this study was to compare the mucosal and luminal content microbiota of the cecum and colon of healthy and diarrheic horses. Marked differences in the richness and in the community composition between the mucosal and luminal microbiota of the cecum and large colon of horses with colitis were observed. Microbial dysbiosis occurs in horses with colitis at different levels of the intestinal tract, and microbiota composition is different between the mucosa and luminal content of diarrheic horses. The changes in some key taxa associated with dysbiosis in the equine intestinal microbiota, such as Escherichia, Fusobacterium and Lactobacillus, deserve further inquiry in order to determine their utility for disease diagnosis and treatment.

Dysbiosis is not present in horses with fecal water syndrome when compared to controls in spring and autumn

BACKGROUND

Fecal water syndrome (FWS) is long-standing and common in horses, particularly in central Europe. No large epidemiological data sets exist, and the cause remains elusive. Dysbiosis could play a role in pathogenesis.

OBJECTIVES

To evaluate whether dysbiosis is present in horses with FWS when compared to stable-matched control horses in spring and autumn.

ANIMALS

Fecal samples were collected from horses with FWS (n = 16; 9 mares, 7 geldings) and controls (n = 15; 8 mares, 7 geldings).

METHODS

The bacterial microbiome of samples collected in spring and autumn of 2016 was analyzed using high-throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity, and beta diversity indices were assessed between horses with FWS and controls based on season.

RESULTS

Differences in microbial community composition based on time point and health status were not observed on any taxonomic level. Limited differences were seen on linear discriminant analysis effect size analysis. No difference in alpha diversity indices was observed including richness, diversity based on health status, or time point. No effect of health status on microbial community membership structure was observed.

CONCLUSIONS AND CLINICAL IMPORTANCE

Limited differences were found in the bacterial microbiota of horses with and without FWS, regardless of season. Further research is needed to elucidate the role of microbiota in the development of FWS.

Impact of Dietary Cellobiose on the Fecal Microbiota of Horses

Cellobiose is a disaccharide with potential prebiotic effects, as demonstrated in different animal species, but not yet in horses. It was, therefore, the aim of the present study to evaluate the impact of dietary cellobiose on the fecal microbiota of horses. Eight healthy adult horses and two ponies were included in this study. The animals received a diet without or with 10 g and 20 g cellobiose per day for 14 days each. At the end of the feeding periods, fresh fecal samples were collected to measure bacterial metabolites and the microbial composition. For the microbiota analysis, 16S rRNA gene sequencing was used. Cellobiose was well accepted and tolerated by the animals. The lowest fecal concentrations of D-lactate, propionic acid, i-valeric acid, and total short-chain fatty acids were measured at the dose 10 g cellobiose per horse per day (quadratic effect: P < .05). A dose-dependent increase of the relative abundance of Firmicutes (P = .049), Coriobacteriales (P < .001), and Clostridium (P = .031) could be detected. In addition, a dose-dependent decrease of the relative abundance of Bacteroidetes (P = .035) was observed. In conclusion, the increase of Coriobacteriales and Clostridium indicates a bacterial fermentation of cellobiose in the equine intestine, as members of both groups exert saccharolytic activity. As clostridia have previously been assumed to be a key component of the intestinal microbiota in horses, the observed increase of Clostridium in the feces might indicate beneficial and potentially prebiotic effects of cellobiose in horses. However, this finding requires further investigation, particularly with regard to the Clostridium species that have been promoted by dietary cellobiose.

Prenatal establishment of the foal gut microbiota: a critique of the in utero colonisation hypothesis

Bacteria colonisation of the foal’s gastrointestinal tract (GIT) is a critical developmental stage, effecting subsequent immunological and health outcomes. It has long been thought that the equine fetus develops in a sterile intrauterine environment and GIT colonisation commences at birth. Research now suggests that bacteria isolated from amniotic fluid are the initial colonisers of the fetal GIT, and exposure to the dam’s microbiota and the external environment during birth provide supplementary colonisation. This in utero colonisation hypothesis has only recently been examined in the horse and microbiota were detected in the amniotic fluid and meconium of healthy equine pregnancies. This review highlights the possible colonisation routes of these bacteria into the fetal compartments and examines their likely origins from the existing maternal microbiome. However, the current data describing the amniotic microbiota of the horse are limited and there is a need for research to fill this gap. Understanding the significance of intrauterine microbes for foal GIT colonisation may provide strategies to improve neonatal health.

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.

Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum

Billions of bacteria inhabit the gastrointestinal tract. Immune-microbial cross talk is responsible for immunological homeostasis, and symbiotic microbial species induce regulatory immunity, which helps to control the inflammation levels. In this study we aimed to identify species within the equine intestinal microbiota with the potential to induce regulatory immunity. These could be future targets for preventing or treating low-grade chronic inflammation occurring as a result of intestinal microbial changes and disruption of the homeostasis. 16S rRNA gene amplicon sequencing was performed on samples of intestinal microbial content from ileum, cecum, and colon of 24 healthy horses obtained from an abattoir. Expression of genes coding for IL-6, IL-10, IL-12, IL-17, 18 s, TNFα, TGFβ, and Foxp3 in the ileum and mesenteric lymph nodes was measured by qPCR. Intestinal microbiota composition was significantly different in the cecum and colon compared to the ileum, which contains large abundances of Proteobacteria. Especially members of the Clostridiales order correlated positively with the regulatory T-cell transcription factor Foxp3 and so did the phylum Verrucomicrobia. We conclude that Clostridiales and Verrucomicrobia have the potential to induce regulatory immunity and are possible targets for intestinal microbial interventions aiming at regulatory immunity improvement.

Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation

The objective of this study was to investigate the impact of natural prebiotic active compounds on the microbial composition in different regions of the equine gastrointestinal tract. Twelve adult horses (body weight [bwt] 534 ± 64.5 kg; age 14 ± 7.5 years) were randomly divided into two feeding groups. Six horses received a basal diet consisting of 1.5 kg hay/100 kg bwt x d^-1 and oat grains equal to 1.19 g starch/kg bwt x d^-1, supplemented with Jerusalem artichoke meal providing prebiotic fructooligosaccharides + inulin in a quantity of 0.15 g/kg bwt x d^-1. The remaining horses received a placebo added to the basal diet. The horses were fed for 21 d and euthanized at the end of the feeding period. Digesta samples from different parts of the gastrointestinal tract were taken, DNA extracted and the V1-V2 region of the 16S rRNA gene amplified. Supplementation with the prebiotic increased the relative abundance of Lactobacillus (P < 0.05), with a concurrent reduction of the relative abundance of Streptococcus mainly in the stomach (P < 0.05). In the hindgut, the supplemental prebiotic also increased the relative abundance of Lactobacillus but further reduced the relative abundance of fibrolytic bacteria, specifically the unclassified members of the families Lachnospiraceae (P < 0.05) and Ruminococcaceae. The relative abundance of the genus Ruminococcus increased solely in the caecum and colon transversum. Overall, the addition of the prebiotic significantly increased the diversity in nearly all parts of the gastrointestinal tract (P < 0.05). The feeding of this natural prebiotic compound to horses had an impact on the microbial community in the entire gastrointestinal tract. Furthermore, the effect on the bacterial community in the foregut (especially the stomach) was more pronounced in comparison to the effect in the hindgut. Therefore, the impact on stomach health should be carefully considered.

Community Composition and Diversity of Intestinal Microbiota in Captive and Reintroduced Przewalski's Horse (Equus ferus przewalskii)

Large and complex intestinal microbiota communities in hosts have profound effects on digestion and metabolism. To better understand the community structure of intestinal microbiota in Przewalski’s horse (Equus ferus przewalskii) under different feeding regimes, we compared bacterial diversity and composition between captive and reintroduced Przewalski’s horses, using high-throughput 16S-rRNA gene sequencing for identification. Reintroduced Przewalski’s horses were sampled in two Chinese nature reserves, i.e., Dunhuang Xihu Nature Reserve (DXNR; n = 8) in Gansu Province and Kalamaili Nature Reserve (KNR; n = 12) in Xinjiang Province, and compared to a captive population at the Przewalski’s Horse Breeding Center in Xinjiang (PHBC; n = 11). The composition of intestinal microbiota in Przewalski’s horses was significantly different at the three study sites. Observed species was lowest in DXNR, but highest in KNR. Lowest Shannon diversity was observed in DXNR, while in KNR and PHBC had a moderately high diversity; Simpson diversity showed an opposite trend compared with the Shannon index. Linear Discriminant Analysis effect size was used to determine differentially distributed bacterial taxa at each study site. The most dominant phyla of intestinal microbiota were similar in all feeding regimes, including mainly Firmicutes, Bacteroidetes, Verrucomicrobia, and Spirochaetes. Differing abundances of intestinal microbiota in Przewalski’s horses may be related to different food types at each study site, differences in diversity may be attributed to low quality food in DXNR. Results indicated that diet is one of the important factors that can influence the structure of intestinal microbiota communities in Przewalski’s horse. These findings combined with a detailed knowledge of the available and consumed food plant species could provide guidelines for the selection of potential future reintroduction sites.

Dysbiosis associated with acute helminth infections in herbivorous youngstock - observations and implications

A plethora of data points towards a role of the gastrointestinal (GI) microbiota of neonatal and young vertebrates in supporting the development and regulation of the host immune system. However, knowledge of the impact that infections by GI helminths exert on the developing microbiota of juvenile hosts is, thus far, limited. This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin). We observed that high versus low parasite burdens (measured via parasite egg counts in faecal samples) were associated with specific compositional alterations of the developing microbiome; in particular, the faecal microbiota of animals with heavy worm infection burdens was characterised by lower microbial richness, and alterations to the relative abundances of bacterial taxa with immune-modulatory functions. Amino acids and glucose were increased in faecal samples from the same cohort, which indicated the likely occurrence of intestinal malabsorption. These data support the hypothesis that GI helminth infections in young livestock are associated with significant alterations to the GI microbiota, which may impact on both metabolism and development of acquired immunity. This knowledge will direct future studies aimed to identify the long-term impact of infection-induced alterations of the GI microbiota in young livestock.

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning

A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.

Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses

Metabolic diseases such as obesity and type 2 diabetes in humans have been linked to alterations in the gastrointestinal microbiota and metabolome. Knowledge of these associations has improved our understanding of the pathophysiology of these diseases and guided development of diagnostic biomarkers and therapeutic interventions. The cellular and molecular pathophysiology of equine metabolic syndrome (EMS) and obesity in horses, however, remain ill-defined. Thus, the objectives of this study were to characterize the fecal microbiome, fecal metabolome, and circulating lipidome in obese and non-obese horses. The fecal microbiota, fecal metabolome, and serum lipidome were evaluated in obese (case) horses (n = 20) and non-obese (control) horses (n = 20) matched by farm of origin (n = 7). Significant differences in metabolites of the mitochondrial tricarboxylic acid cycle and circulating free fatty acids were identified in the obese horses compared to the non-obese horses. These results indicate that the host and bacterial metabolism should be considered important in obese horses. Further studies to determine whether these associations are causal and the mechanistic basis of the association are warranted because they might reveal diagnostic biomarkers and therapeutic interventions to mitigate obesity, EMS, and sequelae including laminitis.

Effect of oral supplementation of probiotic strains of Lactobacillus rhamnosus and Enterococcus faecium on the composition of the faecal microbiota of foals

Effects of probiotics on the intestinal microbiota of foals are yet insufficiently studied. The aim of this study was to investigate whether supplementation of Lactobacillus rhamnosus (DSM 7133) and Enterococcus faecium (DSM 7134) influences the bacterial composition of the faecal microbiota of foals. A total of 34 newborn foals were randomly assigned to the placebo group (PG, n = 16) and the treatment group (TG, n = 18). From day 1 to day 14 of life, foals orally received 3 ml of either a probiotic preparation (1.05 × 10⁹ CFU E. faecium and 4.50 × 10⁸ CFU L. rhamnosus) or placebo (carrier) once a day. Faeces were collected directly from the rectum immediately after birth (meconium) and at day 14 and day 56 of life. Samples of 12 foals per group were selected for microbiological analysis. DNA was extracted and used for polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR. No DNA or amplicons were obtained from meconium. There were no differences in richness of bands and Shannon index of diversity regarding the Clostridium cluster XIVa between groups. Cluster analysis and principal coordinate analysis of DGGE data showed a clear effect of age. Band-based similarity of bacterial clusters (Dice coefficient) decreased from day 14 to day 56 of life (p < 0.001) in PG foals only resulting in lower similarity in PG versus TG foals when 2 month old (p < 0.01). Five of thirty re-amplified bands were identified on species level. Others were assigned either to family (mainly Lachnospiraceae) or genus level (Akkermansia). The bands related to Akkermansia muciniphila or Akkermansia spp. appeared almost in all DGGE profiles. Two-week supplementation of the probiotic preparation to foals had no significant impact on the composition of the faecal microbiota but it appears to have prevented the reduction of bacterial similarity between 2 and 8 weeks of age observed in not treated foals.