Effect of transportation on fecal bacterial communities and fermentative activities in horses: impact of Saccharomyces cerevisiae CNCM I-1077 supplementation

Dysbiosis not observed in Canadian horse with free fecal liquid (FFL) using 16S rRNA sequencing

Free Fecal Liquid (FFL), also termed Fecal Water Syndrome (FWS), is an ailment in horses characterized by variable solid and liquid (water) phases at defecation. The liquid phase can be excreted before, during, or after the solid defecation phase. While the underlying causes of FFL are unknown, hindgut dysbiosis is suggested to be associated with FFL. Three European studies investigated dysbiosis in horses with FFL using 16S rRNA sequencing and reported results that conflicted between each other. In the present study, we also used 16S rRNA sequencing to study the fecal microbial composition in 14 Canadian horses with FFL, and 11 healthy stable mate controls. We found no significant difference in fecal microbial composition between FFL and healthy horses, which further supports that dysbiosis is not associated with FFL.

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.

What Is the Microbiota and What Is Its Role in Colic?

The fecal microbiome of the horse is reflective of the large colon and plays an important role in the health of the horse. The microbes of the gastrointestinal tract digest fiber and produce energy for the host. Healthy horses have Firmicutes, Bacteroidetes, and Verrucromicrobia as the most common phyla. During gastrointestinal disease such as colic or colitis, the microbiome shows less diversity and changes in bacterial community composition.

Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome

BACKGROUND

Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids.

METHODS

In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples.

RESULTS

Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later.

CONCLUSIONS

Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.

Multidose misoprostol pharmacokinetics and its effect on the fecal microbiome in healthy, adult horses

OBJECTIVE

To compare the pharmacokinetics between repeated doses and to characterize changes in the fecal microbiome after oral and rectal multidose misoprostol administration.

ANIMALS

6 healthy university-owned geldings.

PROCEDURES

In a randomized, crossover study, misoprostol (5 μg/kg) was administered orally or rectally every 8 hours for 10 doses, or not administered (control), with a 21-day washout between treatments. Concentration-versus-time data for dose 1 and dose 10 were subject to noncompartmental analysis. For microbiota analysis using 16S rRNA amplicon sequencing, manure was collected 7 days before study onset, immediately before dose 1, and 6 hours, 7 days, and 14 days after dose 10, with time-matched points in controls.

RESULTS

Repeated dosing-related differences in pharmacokinetic parameters were not detected for either administration route. The area under the concentration-versus-time curve was greater (P < .04) after oral versus rectal administration. The relative bioavailability of rectal administration was 4 to 86% of that of oral administration. Microbial composition, richness, and β-diversity differed among subjects (P < .001 all) while only composition differed between treatments (P ≤ .01). Richness was decreased 6 hours after dose 10 and at the control-matched time point (P = .0109) in all subjects. No other differences for time points, treatments, or their interactions were observed.

CLINICAL RELEVANCE

Differences in systemic exposure were associated with the route of administration but were not detected after repeated administration of misoprostol. Differences in microbiota parameters were primarily associated with interindividual variation and management rather than misoprostol administration.

Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens

Horses are large non-ruminant herbivores and rely on microbial fermentation for energy, with more than half of their maintenance energy requirement coming from microbial fermentation occurring in their enlarged caecum and colon. To achieve that, the gastro-intestinal tract (GIT) of horses harbors a broad range of various microorganisms, differing in each GIT segment, which are essential for efficient utilization of feed, especially to use nutrients that are not or little degraded by endogenous enzymes. In addition, like in other animal species, the GIT microbiota is in permanent interplay with the host's cells and is involved in a lot of functions among which inflammation, immune homeostasis, and energy metabolism. As for other animals and humans, the horse gut microbiome is sensitive to diet, especially consumption of starch, fiber, and fat. Age, breeds, stress during competitions, transportation, and exercise may also impact the microbiome. Because of its size and its complexity, the equine GIT microbiota is prone to perturbations caused by external or internal stressors that may result in digestive diseases like gastric ulcer, diarrhea, colic, or colitis, and that are thought to be linked with systemic diseases like laminitis, equine metabolic syndrome or obesity. Thus, in this review we aim at understanding the common core microbiome -in terms of structure and function- in each segment of the GIT, as well as identifying potential microbial biomarkers of health or disease which are crucial to anticipate putative perturbations, optimize global practices and develop adapted nutritional strategies and personalized nutrition.

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.

Utilizing the Gastrointestinal Microbiota to Modulate Cattle Health through the Microbiome-Gut-Organ Axes

The microorganisms inhabiting the gastrointestinal tract (GIT) of ruminants have a mutualistic relationship with the host that influences the efficiency and health of the ruminants. The GIT microbiota interacts with the host immune system to influence not only the GIT, but other organs in the body as well. The objective of this review is to highlight the importance of the role the gastrointestinal microbiota plays in modulating the health of a host through communication with different organs in the body through the microbiome-gut-organ axes. Among other things, the GIT microbiota produces metabolites for the host and prevents the colonization of pathogens. In order to prevent dysbiosis of the GIT microbiota, gut microbial therapies can be utilized to re-introduce beneficial bacteria and regain homeostasis within the rumen environment and promote gastrointestinal health. Additionally, controlling GIT dysbiosis can aid the immune system in preventing disfunction in other organ systems in the body through the microbiome-gut-brain axis, the microbiome-gut-lung axis, the microbiome-gut-mammary axis, and the microbiome-gut-reproductive axis.

Degradation of Monosaccharides, Disaccharides, and Fructans in the Stomach of Horses Adapted to a Prebiotic Dose of Fructooligosaccharides and Inulin

For a period of 20 days, 12 horses either received a prebiotic supplementation with fructooligosaccharides and inulin via Jerusalem artichoke meal (JAM) or corncob meal without grains (CMG) as placebo. The horses were euthanized 1 hour postprandial, gastric digesta was sampled from pars nonglandularis (PNG) and pars glandularis (PG), and concentrations of starch, mono- and disaccharides, fructans, d- and l-lactic acid, and short chain fatty acids were analyzed. Concentrations of starch and simple sugars were widely the same in JAM supplemented and not supplemented meals. However, fructans were less than half as much without supplementation as with supplementation of JAM. Glucose, fructose, sucrose, and fructans disappeared to a larger extent with prebiotic supplementation than without (106.6% vs. 86.7% glucose, 73.1% vs. 66.8% fructose, 91.5% vs. 14.7% sucrose, and 68.3% vs. 35.4% fructans remained in PNG; 81.9% vs. 38.3% glucose, 52.2% vs. 53.4% fructose, 47.1% vs. 0% sucrose, and 48.5% vs. 31.7% fructans remained in PG with CMG vs. JAM feeding). Disappearance of simple sugars and fructans was primarily associated with appearance of n-butyric acid (r = -0.21 - r = -0.33).

Responses to an intra-articular lipopolysaccharide challenge following dietary supplementation of Saccharomyces cerevisiae fermentation product in young horses

Dietary intervention may be a valuable strategy to optimize the intra-articular environment in young horses to prolong their performance career. To test the hypothesis that dietary supplementation of a Saccharomyces cerevisiae fermentation product would reduce markers of joint inflammation and increase markers of cartilage metabolism following a single inflammatory insult, Quarter Horse yearlings (mean ± SD; 9 ± 1.0 mo) were balanced by age, sex, body weight (BW), and farm of origin and randomly assigned to the following treatment groups: 1.25% BW/d (dry matter basis) custom-formulated concentrate only (CON; n = 9) or concentrate top-dressed with 21 g/d S. cerevisiae fermentation product (SCFP; n = 10) for 98 d. Horses had ad libitum access to Coastal bermudagrass hay. On day 84, one randomly selected radial carpal joint from each horse was injected with 0.5 ng lipopolysaccharide (LPS) solution. The remaining carpal joint was injected with sterile lactated Ringer’s solution as a contralateral control. Synovial fluid obtained before supplementation (day 0) and on day 84 at preinjection hour 0 and 6, 12, 24, 168, and 336 h postinjection was analyzed for prostaglandin E₂ (PGE₂), carboxypropeptide of type II collagen (CPII), and collagenase cleavage neopeptide (C2C) by commercial assays. Rectal temperature, heart rate, respiration rate, carpal surface temperature, and carpal circumference were recorded prior to each sample collection and for 24 h postinjection. Data were analyzed using linear models with repeated measures. From day 0 to 84, synovial C2C declined (P ≤ 0.01) and the CPII:C2C ratio increased (P ≤ 0.01) in all horses with no effect of diet. In response to intra-articular LPS, synovial PGE₂ increased by hour 6 (P ≤ 0.01) and returned to baseline by hour 336; CPII increased by hour 12, remained elevated through hour 168 (P ≤ 0.01), and returned to baseline by hour 336; and C2C increased by hour 6 (P ≤ 0.01) but did not return to baseline through hour 336 (P ≤ 0.01). Post-intra-articular injection, PGE₂ levels were lower in SCFP than CON horses (P = 0.01) regardless of injection type. Synovial CPII and the CPII:C2C ratio demonstrated stability during the LPS challenge in SCFP compared with CON horses (P ≤ 0.01). Clinical parameters were not influenced by diet but increased in response to repeated arthrocentesis (P ≤ 0.01). Dietary SCFP may favorably modulate intra-articular inflammation following an acute stressor and influence cartilage turnover in young horses.

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.

Transport stress affects the fecal microbiota in healthy donkeys

Background

With the development of large‐scale donkey farming in China, long‐distance transportation has become common practice, and the incidence of intestinal diseases after transportation has increased. The intestinal microbiota is important in health and disease, and whether or not transportation disturbs the intestinal microbiota in donkeys has not been investigated.

Objectives

To determine the effects of transportation on the fecal microbiota of healthy donkeys using 16S rRNA sequencing.

Animals

Fecal and blood samples were collected from 12 Dezhou donkeys before and after transportation.

Methods

Prospective controlled study. Cortisol, ACTH, and heat‐shock protein 90 (HSP90) concentrations were measured. Sequencing of 16S rRNA was used to assess the microbial composition. Alpha diversity and beta diversity were assessed.

Results

Results showed significant (P < .05) increases in cortisol (58.1 ± 14.6 to 71.1 ± 9.60 ng/mL), ACTH (163.8 ± 31.9 to 315.8 ± 27.9 pg/mL), and HSP90 (10.8 ± 1.67 to 14.6 ± 1.75 ng/mL) on the day of arrival. A significantly lower (P = .04) level of bacterial richness was found in fecal samples after transportation, compared with that before transportation without distinct changes in diversity. Most notably, donkeys had significant decreases in Atopostipes, Eubacterium, Streptococcus, and Coriobacteriaceae.

Conclusions and Clinical Importance

Transportation can induce stress in healthy donkeys and have some effect on the composition of the in fecal microbiota. Additional studies are required to understand the potential effect of these microbiota changes, especially significantly decreased bacteria, on the development intestinal diseases in donkeys during recovery from transportation.

The effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or Salmonella infection on the fecal microbiome of horses

BACKGROUND

The fecal microbiome of healthy horses may be influenced by signalment, diet, environmental factors, and disease.

OBJECTIVES

To assess the effects of age, breed, sex, geographic location, season, diet, and colitis caused by antibiotic use (antimicrobial-associated diarrhea [AAD]) and Salmonella infection on fecal microbiota.

ANIMALS

Healthy horses (n = 80) were sampled from nonhospital environments across multiple geographical locations in the United States. Horses with AAD (n = 14) were defined as those that developed diarrhea secondary to antimicrobial use. Horses with Salmonella infection (n = 12) were presented with spontaneous onset of colitis and subsequently tested positive on Salmonella quantitative polymerase chain reaction. All horses were >1 year of age and stratified by a dietary scale that included forages (pasture and hay) and concentrates grouped by percentage of fiber and amount.

METHODS

Illumina sequencing of 16S rRNA genes was performed on fecal DNA.

RESULTS

Healthy horses fed higher amounts of grain clustered separately from those fed lower amounts of grain (analysis of similarities [ANOSIM], R = 0.356-0.385, Q = 0.002). Horses with AAD and Salmonella had decreased richness and evenness compared to healthy horses (P < .05). Univariable analysis of the 3 groups identified increases in Bacteroidetes (Q = 0.002) and Protebacteria (Q = 0.001) and decreases in Verrucomicrobia (Q = 0.001) in AAD horses whereas Salmonella horses had less Firmicutes (Q = 0.001) when compared to healthy horses.

CONCLUSIONS AND CLINICAL IMPORTANCE

Although the amount of grain in the diet had some impact on the fecal microbiome, colitis had a significantly larger influence. Horses with ADD have a more severe dysbiosis than do horses with Salmonella.

The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors

Simple Summary

Several studies have described the bacterial composition in the intestines of horses, and several factors of influence have been detected. Variation in the results between studies, however, is substantial. Therefore, the current study aimed to study the bacterial composition in the faeces of healthy horses and ponies kept under standard housing and management condition in The Netherlands. Seventy-nine horses and ponies originating from two farms were included. Several factors, such as location, age, the season of sampling, horse type (horses vs. ponies) and pasture access significantly affected the bacterial composition. The current study provides important baseline information on variation in the bacterial composition in healthy horses and ponies under standard housing and management conditions. The aforementioned factors identified in this study to affect the bacterial population of the gut should be considered in future studies regarding the bacterial population of the equine gut.

Abstract

Several studies have described the faecal microbiota of horses and the factors that influence its composition, but the variation in results is substantial. This study aimed to investigate the microbiota composition in healthy equids in The Netherlands under standard housing and management conditions and to evaluate the effect of age, gender, horse type, diet, pasture access, the season of sampling and location on it. Spontaneously produced faecal samples were collected from the stall floor of 79 healthy horses and ponies at two farms. The validity of this sampling technique was evaluated in a small pilot study including five ponies showing that the microbiota composition of faecal samples collected up to 6 h after spontaneous defaecation was similar to that of the samples collected rectally. After DNA extraction, Illumina Miseq 16S rRNA sequencing was performed to determine microbiota composition. The effect of host and environmental factors on microbiota composition were determined using several techniques (NMDS, PERMANOVA, DESeq2). Bacteroidetes was the largest phylum found in the faecal microbiota (50.1%), followed by Firmicutes (28.4%). Alpha-diversity and richness decreased significantly with increasing age. Location, age, season, horse type and pasture access had a significant effect on beta-diversity. The current study provides important baseline information on variation in faecal microbiota in healthy horses and ponies under standard housing and management conditions. These results indicate that faecal microbiota composition is affected by several horse-related and environment-related factors, and these factors should be considered in future studies of the equine faecal microbiota.

In Vitro Gas Production from Batch Cultures of Stomach and Hindgut Digesta of Horses Adapted to a Prebiotic Dose of Fructooligosaccharides and Inulin

Fructooligosaccharides (FOS) and inulin may modulate hindgut fermentation. It was tested if digesta batch cultures taken from horses adapted to FOS and inulin show different fermentation compared with such taken from nonsupplemented horses. Six horses received 0.15 g FOS and inulin/kg body weight/d via Jerusalem artichoke meal (JAM) upon a hay-based diet; six horses received corncob meal without grains (CMG) as placebo. The horses were euthanized after 20 days. Digesta samples were taken from stomach, cecum, ventral colon ascendens (VCA), and colon transversum (CT). Digesta batch cultures were incubated 48 hours to measure in vitro gas production as well as pre- and post-incubation pH and oxidation-reduction potential (ORP). A distinct fermentation of the surplus of fructans present in the inoculum was found with JAM-adapted batch cultures. Gas production was accelerated in inoculated gastric contents of horses adapted to JAM compared with CMG adapted ones (7.8 vs. 16.4 hours to achieve half of the 48 hours gas quantity, respectively; P > .05). Although buffered, pH decreased during fermentation. Postincubation pH was lower with JAM than CMG-adapted batch cultures (P > .05). Preinoculation ORP was lower with stomach batch cultures adapted to CMG than with such adapted to JAM. The ORP increased twofold from pre- to post-incubation with the latter. Asymptotic maximal gas production decreased gradually using cecum, VCA, or CT digesta. Parts of FOS and inulin of digesta are fermented in the stomach, which reduce possible effects on hindgut fermentation. Elevated fermentation may considerably impact stomach health.

Transporting and Exercising Unconditioned Horses: Effects on Microflora Populations

The objective of this study was to determine if transportation and exercise stress in horses affect the microflora populations in the equine hindgut. Four horses were subjected to three transport periods (0, 3, and 6 hours) with a 7-d rest period between each transport. Horses were fed 0.91 kg/day of Purina Impact All Stages 12% and had ad libitum access to Cynodon dactylon (Coastal Bermudagrass) hay. Fecal samples were collected before (0 hours) and after (48 hours) transport. In addition, three horses underwent a different standardized exercise test with a 7-d rest period between each exercise. Standardized exercise test intensity was determined by heart rate to validate if the horse was in aerobic or anaerobic work. The protocol for fecal sample collection after exercise was the same as for transport. Prokaryotic community profiling was conducted by 16S metagenomic analysis. After DNA evaluation, differences were found in the microbiome at transport 0 hours and grouped transport 3 hours time 48 and transport 6 hours time 48 (PERMANOVA P = .037) where Bacteroidetes increased 48 hours after transport and Firmicutes decreased 48 hours after transport. Exercise microbial communities showed no difference in either alpha or beta diversity when compared with controls (0 hours). In the present study, difference in microflora may have resulted from stress duration of transport rather than stress duration of exercise.

Effects of transportation on gastric pH and gastric ulceration in mares

Background

Transportation has been suggested as a risk factor for gastric ulceration in horses, but limited evidence supports this assumption.

Animals

Twenty‐six Standardbred, Thoroughbred, and Warmblood mares from a university teaching herd.

Methods

Twelve mares were confined for 12 hours, overnight, in reproductive stocks with indwelling nasogastric tubes (NGTs) to assess pH of gastric fluid (GF). Gastric ulceration was assessed endoscopically before and after confinement. Subsequently, 26 horses were transported for 12 hours, overnight, in 2 consignments. During transportation, GF was aspirated from indwelling NGT placed in the same 12 mares used in the confinement study, and gastric ulceration was assessed endoscopically before and after transportation in all horses.

Results

The median pH of GF in confined horses was 1.70‐2.49 at each sampling point, and there was no apparent effect on gastric squamous ulcer scores. The median pH of GF from the same 12 horses at corresponding sampling times during transportation was 6.82‐7.22. Transportation was associated with increased gastric squamous ulcer scores, particularly in horses fasted for gastroscopy and NGT placement immediately before departure. Gastric emptying appeared delayed after transportation in horses fed before departure.

Conclusions and Clinical Importance

Transportation is associated with increased gastric squamous ulceration and with increased pH of GF. These findings may be a consequence of impaired gastric emptying and reflux of alkaline small intestinal content, with factors such as duodenal bile salts and short‐chain fatty acids mediating mucosal injury.

Factors Influencing Equine Gut Microbiota: Current Knowledge

Gastrointestinal microbiota play a crucial role in nutrient digestion, maintaining animal health and welfare. Various factors may affect microbial balance often leading to disturbances that may result in debilitating conditions such as colic and laminitis. The invention of next-generation sequencing technologies and bioinformatics has provided valuable information on the effects of factors influencing equine gut microbiota. Among those factors are nutrition and management (e.g., diet, supplements, exercise), medical substances (e.g., antimicrobials, anthelmintics, anesthetics), animal-related factors (breed and age), various pathological conditions (colitis, diarrhea, colic, laminitis, equine gastric ulcer syndrome), as well as stress-related factors (transportation and weaning). The aim of this review is to assimilate current knowledge on equine microbiome studies, focusing on the effect of factors influencing equine gastrointestinal microbiota. Decrease in microbial diversity and richness leading to decrease in stability; decrease in Lachnospiraceae and Ruminococcaceae family members, which contribute to gut homeostasis; increase in Lactobacillus and Streptococcus; decrease in lactic acid utilizing bacteria; decrease in butyrate-producing bacteria that have anti-inflammatory properties may all be considered as a negative change in equine gut microbiota. Shifts in Firmicutes and Bacteroidetes have often been observed in the literature in response to certain treatments or when describing healthy and unhealthy animals; however, these shifts are inconsistent. It is time to move forward and use the knowledge now acquired to start manipulating the microbiota of horses.

Dietary composition and yeast/microalgae combination supplementation modulate the microbial ecosystem in the caecum, colon and faeces of horses

Starchy diets can induce hindgut dysbiosis in horses. The present study evaluated the impact of a yeast (Saccharomyces cerevisiae) and microalgae (Aurantiochytrium limacinum) supplementation on caecal, colonic and faecal microbial ecosystem and on blood inflammatory parameters of horses fed high-fibre or high-starch diets. Six fistulated geldings in a 2 × 2 Latin-square design were alternatively supplemented and received during each period 100 % hay (4 weeks) followed by a 56/44 hay/barley diet (3 weeks). Caecal, colonic and faecal samples were collected 4 h after the morning meal three times per diet, at 5-d intervals, to measure bacterial composition and microbial end products. Blood was simultaneously collected for measuring inflammatory markers. The starchy diet clearly modified the microbial ecosystem in the three digestive segments, with an increase of the amylolytic function and a decrease of the fibrolytic one. However, no effect of the diet was observed on the blood parameters. When horses were supplemented, no significant change was found in lipopolysaccharides, PG-E2, serum amyloid A concentrations and complete blood count neither in cellulose-utilising, starch-utilising and lactate-utilising bacteria concentrations nor in the volatile fatty acids and lactate concentrations and pH. Under supplementation, relative abundance of Family XIII Clostridiales increased in caecum and faeces irrespective of diet and relative abundance of Veillonellaceae was higher during the hay/barley diet in colon and faeces. Most variations of faecal bacterial taxa under supplementation were not observed in the hindgut. However, all variations suggested that supplementation could increase fibrolytic function whatever the diet and limit dysbiosis when the horses' diet changed from high fibre to high starch.

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review

There is increasing evidence of a pivotal role of the gut microbiota (GUT-M) in key physiological functions in vertebrates. Many studies discuss functional implications of the GUT-M not only on immunity, growth, metabolism, but also on brain development and behavior. However, while the influence of the microbiota-gut-brain axis (MGBA) on behavior is documented in rodents and humans, data on farm animals are scarce. This review will first report the well-known influence of the MGBA on behavior in rodent and human and then describe its influence on emotion, memory, social and feeding behaviors in farm animals. This corpus of experiments suggests that a better understanding of the effects of the MGBA on behavior could have large implications in various fields of animal production. Specifically, animal welfare and health could be improved by selection, nutrition and management processes that take into account the role of the GUT-M in behavior.

Removal of adult cyathostomins alters faecal microbiota and promotes an inflammatory phenotype in horses

The interactions between parasitic helminths and gut microbiota are considered to be an important, although as yet incompletely understood, factor in the regulation of immunity, inflammation and a range of diseases. Infection with intestinal helminths is ubiquitous in grazing horses, with cyathostomins (about 50 species of which are recorded) predominating. Consequences of infection include both chronic effects, and an acute inflammatory syndrome, acute larval cyathostominosis, which sometimes follows removal of adult helminths by administration of anthelmintic drugs. The presence of cyathostomins as a resident helminth population of the equine gut (the "helminthome") provides an opportunity to investigate the effect helminth infection, and its perturbation, has on both the immune system and bacterial microbiome of the gut, as well as to determine the specific mechanisms of pathophysiology involved in equine acute larval cyathostominosis. We studied changes in the faecal microbiota of two groups of horses following treatment with anthelmintics (fenbendazole or moxidectin). We found decreases in both alpha diversity and beta diversity of the faecal microbiota at Day 7 post-treatment, which were reversed by Day 14. These changes were accompanied by increases in inflammatory biomarkers. The general pattern of faecal microbiota detected was similar to that seen in the relatively few equine gut microbiome studies reported to date. We conclude that interplay between resident cyathostomin populations and the bacterial microbiota of the equine large intestine is important in maintaining homeostasis and that disturbance of this ecology can lead to gut dysbiosis and play a role in the aetiology of inflammatory conditions in the horse, including acute larval cyathostominosis.

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period

Colic (abdominal pain) is a common cause of mortality in horses. Change in management of horses is associated with increased colic risk and seasonal patterns of increased risk have been identified. Shifts in gut microbiota composition in response to management change have been proposed as one potential underlying mechanism for colic. However, the intestinal microbiota in normal horses and how this varies over different seasons has not previously been investigated. In this study the faecal microbiota composition was studied over 12 months in a population of horses managed at pasture with minimal changes in management. We hypothesised that gut microbiota would be stable in this population over time. Faecal samples were collected every 14 days from 7 horses for 52 weeks and the faecal microbiota was characterised by next-generation sequencing of 16S rRNA genes. The faecal microbiota was dominated by members of the phylum Firmicutes and Bacteroidetes throughout. Season, supplementary forage and ambient weather conditions were significantly associated with change in the faecal microbiota composition. These results provide important baseline information demonstrating physiologic variation in the faecal microbiota of normal horses over a 12-month period without development of colic.

Understanding the Intestinal Microbiome in Health and Disease

This article provides readers with the basic concepts necessary to understand studies using recent molecular methods performed in intestinal microbiome assessment, with special emphasis on the high throughput sequencing. This review also summarizes the current knowledge on this topic and discusses future insights on the interaction between the intestinal microbiome and equine health.

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change

Faeces could be used for evaluating the balance of the equine hindgut microbial ecosystem, which would offer a practical method for assessing gut health and how this relates to disease. However, previous studies concluded that faeces microbial ecosystem was not representative of the proximal hindgut (caecum and ventral colon). This study aimed to evaluate if variations of the faecal microbial ecosystem were similar to those observed in the proximal hindgut. Six horses, fistulated in the caecum and right ventral (RV) colon, were subjected to a gradual change of diet, from a 100% hay (high fibre) diet (2.2 DM kg/day per 100 kg BW) to a 57% hay+43% barley (high starch) diet (0.8 DM kg/day per 100 kg BW hay and 0.6 DM kg/day per 100 kg BW barley). The two diets were iso-energetic and fed over a 3-week trial period. Samples of digesta from the caecum, RV colon and faeces were collected two times on the 10th and 20th day of the trial, for each diet to assess the microbial ecosystem parameters by both classical culture technics and biochemical methods. The variations observed in the caecal and colonic bacterial composition (increase in total anaerobic, amylolytic and lactate-utilizing and decrease in cellulolytic bacteria concentrations) and microbial activity (changes in volatile fatty acids concentrations and increase in lactate concentrations) demonstrated that the hay+barley diet caused changes in the hindgut microbial ecosystem. Similar variations were observed in the faecal microbial ecosystem. Feeding the hay+barley diet resulted in higher concentrations of faecal lipopolysaccharides. The functional bacterial group concentrations (cellulolytics, amylolytics and lactate utilizers) were significantly correlated between caecum and faeces and between colon and faeces. From analyses of the metabolites produced from microbial activity, only valerate concentration in the caecum and the proportion of propionate were significantly correlated with the same parameters in the faeces. Results of the principal component analysis performed between all the caecal/faecal and colonic/faecal parameters revealed that the total anaerobic and cellulolytic bacteria concentrations, as well as valerate, l-lactate and lipopolysaccharide concentrations were strongly correlated with several microbial parameters in the caecum (P|0.45|) and in the colon (P|0.50|). This demonstrated that faecal samples and their bacterial analyses could be used to represent caecum and RV colon hindgut microbial ecosystem in terms of variations during a change from a high-fibre to a high-starch diet, and thus could be markers of particular interest to diagnostic proximal hindgut microbial disturbances.

Effect of Dietary Starch Source and Concentration on Equine Fecal Microbiota

Starch from corn is less susceptible to equine small intestinal digestion than starch from oats, and starch that reaches the hindgut can be utilized by the microbiota. The objective of the current study was to examine the effects of starch source on equine fecal microbiota. Thirty horses were assigned to treatments: control (hay only), HC (high corn), HO (high oats), LC (low corn), LO (low oats), and LW (low pelleted wheat middlings). Horses received an all-forage diet (2 wk; d -14 to d -1) before the treatment diets (2 wk; d 1 to 14). Starch was introduced gradually so that horses received 50% of the assigned starch amount (high = 2 g starch/kg BW; low = 1 g starch/kg BW) by d 4 and 100% by d 11. Fecal samples were obtained at the end of the forage-only period (S0; d -2), and on d 6 (S1) and d 13 (S2) of the treatment period. Cellulolytics, lactobacilli, Group D Gram-positive cocci (GPC), lactate-utilizers and amylolytics were enumerated. Enumeration data were log transformed and analyzed by repeated measures ANOVA. There were sample day × treatment interactions (P < 0.0001) for all bacteria enumerated. Enumerations from control horses did not change during the sampling period (P > 0.05). All treatments except LO resulted in increased amylolytics and decreased cellulolytics, but the changes were larger in horses fed corn and wheat middlings (P < 0.05). Feeding oats resulted in increased lactobacilli and decreased GPC (P < 0.05), while corn had the opposite effects. LW had increased lactobacilli and GPC (P < 0.05). The predominant amylolytic isolates from HC, LC and LW on S2 were identified by 16S RNA gene sequencing as Enterococcus faecalis, but other species were found in oat fed horses. These results demonstrate that starch source can have a differential effect on the equine fecal microbiota.

Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs

BACKGROUND

The intestinal tract is a rich and complex environment and its microbiota has been shown to have an important role in health and disease in the host. Several factors can cause disruption of the normal intestinal microbiota, including antimicrobial therapy, which is an important cause of diarrhea in horses. This study aimed to characterize changes in the fecal bacterial populations of healthy horses associated with the administration of frequently used antimicrobial drugs.

RESULTS

Twenty-four adult mares were assigned to receive procaine penicillin intramuscularly (IM), ceftiofur sodium IM, trimethoprim sulfadiazine (TMS) orally or to a control group. Treatment was given for 5 consecutive days and fecal samples were collected before drug administration (Day 1), at the end of treatment (Days 5), and on Days 14 and 30 of the trial. High throughput sequencing of the V4 region of the 16S rRNA gene was performed using an Illumina MiSeq sequencer. Significant changes of population structure and community membership were observed after the use of all drugs. TMS caused the most marked changes on fecal microbiota even at higher taxonomic levels including a significant decrease of richness and diversity. Those changes were mainly due to a drastic decrease of Verrucomicrobia, specifically the "5 genus incertae sedis". Changes in structure and membership caused by antimicrobial administration were specific for each drug and may be predictable. Twenty-five days after the end of treatment, bacterial profiles were more similar to pre-treatment patterns indicating a recovery from changes caused by antimicrobial administration, but differences were still evident, especially regarding community membership.

CONCLUSIONS

The use of systemic antimicrobials leads to changes in the intestinal microbiota, with different and specific responses to different antimicrobials. All antimicrobials tested here had some impact on the microbiota, but TMS significantly reduced bacterial species richness and diversity and had the greatest apparent impact on population structure, specifically targeting members of the Verrucomicrobia phylum.