The equine microbiome refers to the diverse community of microorganisms, including bacteria, fungi, and viruses, residing in various parts of a horse's body, such as the gastrointestinal tract, skin, and respiratory system. These microorganisms are involved in numerous physiological processes, including digestion, metabolism, and immune function. The composition and diversity of the microbiome can be influenced by factors such as diet, environment, and health status. Research in this area explores the characterization of the equine microbiome, its impact on health and disease, and potential applications in managing equine health. This page compiles peer-reviewed research studies and scholarly articles that investigate the composition, function, and implications of the microbiome in horses.
Kauter A, Brombach J, Lübke-Becker A, Kannapin D, Bang C, Franzenburg S, Stoeckle SD, Mellmann A, Scherff N, Köck R, Guenther S, Wieler LH....Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum β-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited. Unassigned: We collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-...
Ward AB, Harris PA, Argo CM, Watson C, Neacsu M, Russell WR, Ribeiro A, Collie-Duguid E, Heidari Z, Morrison PK.The equine faecal microbiota is often assessed as a proxy of the microbial community in the distal colon, where the microbiome has been linked to states of health and disease in the horse. However, the microbial community structure may change over time if samples are not adequately preserved. This study stored equine faecal samples from = 10 horses in four preservation treatments at room temperature for up to 150 h and assessed the resulting impact on microbial diversity and the differential abundance of taxa. Treatments included "COLD" (samples packaged with a cool pack), "CLX" (2% chlorhexi...
Gomez D, Toribio R, Caddey B, Costa M, Vijan S, Dembek K.Antimicrobial drug-associated diarrhea (AAD) is the most common adverse effect in horses receiving antimicrobials. Little information on how oral administration of antimicrobials alters intestinal microbiota in horses is available. Objective: Investigate changes of the fecal microbiota in response to oral administration of antimicrobials. Methods: Twenty healthy horses. Methods: Prospective, longitudinal study. Horses were randomly assigned to 4 groups comprising 4 horses each: group 1 (metronidazole); group 2 (erythromycin); group 3 (doxycycline); group 4 (sulfadiazine/trimethoprim, SMZ-TMP);...
Julien ME, Shih JB, Correa Lopes B, Vallone LV, Suchodolski JS, Pilla R, Scott EM.Next generation sequencing (NGS) studies in healthy equine eyes have shown a more diverse ocular surface microbiota compared to culture-based techniques. This study aimed to compare the bacterial ocular surface microbiota in both eyes of horses with unilateral ulcerative keratitis (UK) with controls free of ocular disease. Conjunctival swabs were obtained from both ulcerated eyes and unaffected eyes of 15 client-owned horses with unilateral UK following informed consent, as well as from one eye of 15 healthy horses. Genomic DNA was extracted from the swabs and sequenced on an Illumina platform...
Jin Y, Li W, Ba X, Li Y, Wang Y, Zhang H, Li Z, Zhou J.Zoonotic diseases pose a significant threat to public health. Chlamydia, as an intracellular pathogen, can colonize the intestinal tract of humans and animals, changing the gut microbiota. However, only a few studies have evaluated alterations in the gut microbiota of horses infected with Chlamydia. Therefore, this study aimed to investigate gut microbiota and serum biochemical indicators in horses with Chlamydial infection (IG) and healthy horses (HG). Fecal and blood samples were collected from 16 horses (IG: 10; HG: 6) before morning feeding for the determination of gut microbiota and serum...
Foury A, Mach N, Ruet A, Lansade L, Moisan MP.The improvement of horse welfare through housing conditions has become a real issue in recent years and have highlighted the detrimental effect of individual housing of horses on their health and behaviour. In this new study, we analysed the blood transcriptome of 45 sport horses housed individually that were previously examined for their behaviour and gut microbiota. We performed differential and regression analyses of gene expression, followed by downstream bioinformatic analyses, to unveil the molecular pathways related to the behavioural changes associated with welfare impairment in these ...
Zaitseva S, Dagurova O, Radnagurueva A, Kozlova A, Izotova A, Krylova A, Noskov S, Begmatov S, Patutina E, Barkhutova DD.The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistologic...
Lu H, Zhang W, Sun S, Mei Y, Zhao G, Yang K.Grazing is a common approach to rearing. We investigated the effects of supplementation during grazing on milk yield and composition, blood biochemistry, and fecal microflora in Yili horses. The control mares grazed normally, while those in groups I and II received 1 kg/d of concentrate and 1 kg/d of concentrate + 0.4 kg/d of coated FA, respectively. Milk volumes were significantly higher in groups I and II than in the control group, and among the previous two, milk volumes were significantly higher in group II than in group I. Milk fat, lactose, and protein levels were significantly higher in...
Lagounova M, MacNicol JL, Weese JS, Pearson W.Synbiotics are often provided to horses receiving antibiotics to protect against microbiome disturbances, despite a lack of evidence for efficacy. The purpose of this study was to evaluate the effect of a synbiotic product in horses receiving antibiotics. Sixteen actively racing Standardbred horses were randomly allocated (four-way crossover) to one of four groups: antibiotics (10 days; AB), synbiotics (28 days; PROBIOPlusTM; PBP), PBP + AB, or Control. The fecal microbiome was investigated using 16S rRNA sequencing, and fecal dry matter (DM; %), pH, and scores (FS; 0-9) were measured. Data we...
Li J, Huang X, He L, Li C, Jing H, Lin J, Ma C, Li X.This study aimed to investigate the effects of EA supplementation on body weight, nutrient digestibility, fecal microbiota, blood biochemical indices, and urolithin A metabolism in one-year-old Thoroughbred horses. A group of 18 one-year-old Thoroughbred horses, with an average weight of 339.00 ± 30.11 kg, were randomly allocated into three groups of six horses each (three males and three females). The control group (n=6) received only the basal diet, whereas test groups I (n=6) and II (n=6) were fed the basal diet supplemented with 15 mg/kg BW/d and 30 mg/kg BW/d of EA, respectively, for ...
Lee J, Kang YJ, Kim YK, Choi JY, Shin SM, Shin MC.The influences of diet and environmental factors on gut microbial profiles have been widely acknowledged; however, the specific roles of host genetics remain uncertain. To unravel host genetic effects, we raised 47 Jeju crossbred (Jeju × Thoroughbred) foals that exhibited higher genetic diversity. Foals were raised under identical environmental conditions and diets. Microbial composition revealed that Firmicutes, Bacteroidetes, and Spirochaetes were the predominant phyla. We identified 31 host-microbiome associations by utilizing 47,668 single nucleotide polymorphisms (SNPs) and 734 taxa with...
Hemberg E, Niazi A, Guo Y, Debnár VJ, Vincze B, Morrell JM, Kútvölgyi G.The presence of a microbiome/microbiota in the placenta is hotly debated. In previous studies, the presence of bacteria in equine amniotic fluid and umbilical blood was independent of foal health. The objective of the present study was to determine if the same bacteria are present in the equine placenta as in amniotic fluid and umbilical blood. Samples were obtained from 24 parturient mares and foals. Placental bacterial DNA was extracted, and the microbiome was identified using 16S rRNA sequencing. All amniotic fluid samples contained some polymorphonucleocytes; bacteria were isolated from fo...
Beckers KF, Gomes VCL, Crissman KR, Liu CC, Schulz CJ, Childers GW, Sones JL.Placentitis is the leading cause of infectious abortion in the horse. Additionally, it can result in weak and/or growth restricted offspring. While the etiology of ascending placentitis is well described in mares, less is known regarding the pathogenesis of other types, such as nocardioform placentitis. This study aims to identify the microbial communities in different body sites of the pregnant mare in early gestation to establish a core microbiome that may be perturbed in pathologic pregnancies such as placentitis. We hypothesize that the equine placenta harbors a distinct resident microbiom...
Bull K, Davies G, Jenkins TP, Peachey L.Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes. Objective: Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex. Methods: Cross-sectional descriptive. Methods: Faecal samples were collected from three populations of Exmo...
Vaziri GJ, Jones MM, Carr HA, Nuñez CMV.The disruption of animals' symbiotic bacterial communities (their microbiota) has been associated with myriad factors including changes to the diet, hormone levels, and various stressors. The maintenance of healthy bacterial communities may be especially challenging for social species as their microbiotas are also affected by group membership, social relationships, microbial transfer between individuals, and social stressors such as increased competition and rank maintenance. We investigated the effects of increased social instability, as determined by the number of group changes made by femal...
Holguin-Rocha AF, Calle-Tobon A, Vásquez GM, Astete H, Fisher ML, Tobon-Castano A, Velez-Tobon G, Maldonado-Ruiz LP, Silver K, Park Y....Ticks are obligatory hematophagous ectoparasites that transmit pathogens among various vertebrates, including humans. The composition of the microbial and viral communities in addition to the pathogenic microorganisms is highly diverse in ticks, but the factors driving the diversity are not well understood. The tropical horse tick, , is distributed throughout the Americas and it is recognized as a natural vector of and , the causal agents of equine piroplasmosis. We characterized the bacterial and viral communities associated with partially-fed females collected by a passive survey on hors...
van Heule M, Monteiro HF, Bazzazan A, Scoggin K, Rolston M, El-Sheikh Ali H, Weimer BC, Ball B, Daels P, Dini P.In spite of controversy, recent studies present evidence that a microbiome is present in the human placenta. However, there is limited information about a potential equine placental microbiome. In the present study, we characterized the microbial population in the equine placenta (chorioallantois) of healthy prepartum (280 days of gestation, n = 6) and postpartum (immediately after foaling, 351 days of gestation, n = 11) mares, using 16S rDNA sequencing (rDNA-seq). In both groups, the majority of bacteria belonged to the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota. T...
Arnold CE, Pilla R.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.
Ermers C, McGilchrist N, Fenner K, Wilson B, McGreevy P.Failure to meet the minimum forage requirement of 1.5% of the horse's bodyweight and the opportunity for foraging for a minimum of 8 h a day (not going without this opportunity longer than four to five consecutive hours) can have both physiological and behavioural consequences. To provide an energy source for horses, rations often include starch rather than fibre. This can result in health issues related to the gastrointestinal tract (GIT) in the horse. In the stomach, the main concern is equine gastric ulcer syndrome (EGUS) and, more specifically, equine squamous gastric disease (ESGD). Ulcer...
Tuniyazi M, Wang W, Zhang N.Fecal microbiota transplantation (FMT) is a technique involving transferring fecal matter from a healthy donor to a recipient, with the goal of reinstating a healthy microbiome in the recipient's gut. FMT has been used in horses to manage various gastrointestinal disorders, such as colitis and diarrhea. To evaluate the current literature on the use of FMT in horses, including its efficacy, safety, and potential applications, the authors conducted an extensive search of several databases, including PubMed, MEDLINE, Web of Science, and Google Scholar, published up to 11 January 2023. The authors...
Zakia LS, Gomez DE, Caddey BB, Boerlin P, Surette MG, Arroyo LG.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 f...
Di Pietro R, Arroyo LG, Leclere M, Costa M.Bacterial imbalances are observed in intestinal diseases and fecal microbiota transplantation (FMT) has been used to restore the intestinal microbiota of horses. However, there is evidence that the current methods proposed for FMT in horses have limited efficacy. The objective of this study was to concentrate the bacteria present in the donor stool by centrifugation, and to test the effect in horses with antibiotic-induced dysbiosis. One healthy 11-year-old horse was selected as a fecal donor and 9 horses were given trimethoprim sulfadiazine (TMS) for 5 days to induce dysbiosis. Horses receive...
Arantes JA, Borges AS, Zakia LS, Surette MG, Weese JS, Costa MC, Arroyo LG.Iron is an essential element for all living organisms, including bacteria, as several virulence factors and replication components are influenced by iron concentration. The objective of this study was to determine whether the composition and diversity of the fecal microbiota of adult horses are affected by supplemental dietary iron. Ten clinically healthy horses were randomly divided into a control and an iron-supplemented group ( = 5). The treated group was supplemented with oral ferrous sulphate monohydrate (720 ppm of iron), whereas the control group received 320 ppm of iron daily for 15 d....
Mo PM, Picard J, Gummow B.Fungi are ubiquitous in the environment and part of the commensal microflora on the conjunctiva of equine eyes. North Queensland, being tropical, presents an ideal environment for fungi growth. When the cornea is injured, fungi can invade the corneal stroma, resulting in keratomycosis. The objectives of this study were to determine the fungal species specific to the eyes of horses in the Townsville region; to investigate the potential risk factors associated with the presence of fungi; and to test their susceptibility to antifungals to create an empirical guide for treatment. The eyes of forty...
de Medeiros Ferreira JR, Mello Cerbaro AE, Bastos FL, Pereira RA, Duarte MA, Araújo Júnior ÂMC, da Silva AH, de Oliveira Gobesso AA.High amounts of grains in the equine diet led to high starch intake, causing gut alterations. Aimed at reducing harmful effects, extract (MCE) is a phytogenic additive that stands out for its antibiotic and anti-inflammatory effects proven in different species. However, there is no useful information for horses. The objective of this study was to evaluate the effects of different levels of the inclusion of commercial MCE on body weight (BW), body condition score (BCS), total apparent digestibility (AD) of nutrients, faecal pH and fermentative products, on ponies fed a high-starch diet. Eight ...
Mitchell SW, Moran RA, Elbourne LDH, Chapman B, Bull M, Muscatello G, Coleman NV.Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy farm horses, and horses undergoing veterinary treatment, and isolates (9,083 colonies) were screened by PCR for C1I; these were found at frequencies of 9.8% (vet horses), 0.31% (farm horses), and 0.05% (wild horses). A co...
Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Schaafstra FJWC, van Doorn DA, Zomer AL.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. In a longitudinal experimental study design, in which the ponies served as the...
Weinert-Nelson JR, Biddle AS, Sampath H, Williams CA.Integrating warm-season grasses into cool-season equine grazing systems can increase pasture availability during summer months. The objective of this study was to evaluate effects of this management strategy on the fecal microbiome and relationships between fecal microbiota, forage nutrients, and metabolic responses of grazing horses. Fecal samples were collected from 8 mares after grazing cool-season pasture in spring, warm-season pasture in summer, and cool-season pasture in fall as well as after adaptation to standardized hay diets prior to spring grazing and at the end of the grazing seaso...
MacNicol JL, Renwick S, Ganobis CM, Allen-Vercoe E, Weese JS, Pearson W.The microbes that reside within the equine hindgut create a complex and dynamic ecosystem. The equine hindgut microbiota is intimately associated with health and, as such, represents an area which can be beneficially modified. Synbiotics, supplements that combine probiotic micro-organisms with prebiotic ingredients, are a potential means of influencing the hindgut microbiota to promote health and prevent disease. The objective of the current study was to evaluate the influence of an equine probiotic/prebiotic supplement on characteristics of the microbiota and metabolite production in vitro. E...
Lv S, Zhang Y, Zhang Z, Meng S, Pu Y, Liu X, Liu L, Ma Y, Liu W, Jiang L.The gut microbiomes of equine are plentiful and intricate, which plays an important part in the growth. However, there is a relative lack of information on the microbial diversity in the pony's gut. Unassigned: In this article, 118 fecal samples from DeBa pony, NiQi pony and GuZh horse were studied by 16S rRNA amplicon sequencing. Unassigned: Diversity analysis was used to determine the difference of gut microbiota composition among different breeds. Alpha diversity analysis showed that the gut microbiota of NiQi ponies were abundant and various. Beta diversity analysis showed that the microor...
Flickinger EA, Van Loo J, Fahey GC.Inulin and oligofructose are prebiotic oligosaccharides fermented in the large intestine. This article provides an extensive review of the effects of these oligosaccharides on gastrointestinal characteristics (microflora, pathogen control, epithelial cell proliferation, putrefactive compound production, fecal characteristics, and nutrient digestibility) and systemic metabolism of carbohydrates, nitrogen, lipids, and minerals in dogs, cats, horses, calves, pigs, poultry, and rabbits. In addition, intake of inulin and oligofructose and considerations in their supplementation to animal diets are ...
Peachey LE, Molena RA, Jenkins TP, Di Cesare A, Traversa D, Hodgkinson JE, Cantacessi C.A growing body of evidence, particularly in humans and rodents, supports the existence of a complex network of interactions occurring between gastrointestinal (GI) helminth parasites and the gut commensal bacteria, with substantial effects on both host immunity and metabolic potential. However, little is known of the fundamental biology of such interactions in other animal species; nonetheless, given the considerable economic losses associated with GI parasites, particularly in livestock and equines, as well as the global threat of emerging anthelmintic resistance, further explorations of the ...
Hansen NC, Avershina E, Mydland LT, Næsset JA, Austbø D, Moen B, Måge I, Rudi K.It is well known that nutrient availability can alter the gut microbiota composition, while the effect on diversity and temporal stability remains largely unknown. Methods: Here we address the equine caecal microbiota temporal stability, diversity, and functionality in response to diets with different levels of nutrient availability. Hay (low and slower nutrient availability) versus a mixture of hay and whole oats (high and more rapid nutrient availability) were used as experimental diets. Results: We found major effects on the microbiota despite that the caecal pH was far from sub-clinical ac...
Mura E, Edwards J, Kittelmann S, Kaerger K, Voigt K, Mrázek J, Moniello G, Fliegerova K.Anaerobic fungi are potent fibre degrading microbes in the equine hindgut, yet our understanding of their diversity and community structure is limited to date. In this preliminary work, using a clone library approach we studied the diversity of anaerobic fungi along six segments of the horse hindgut: caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC) and rectum. Of the 647 ITS1 clones, 61.7 % were assigned to genus level groups that are so far without any cultured representatives, and 38.0 % were assigned to the cultivated genera Ne...
Álvarez-Narváez S, Berghaus LJ, Morris ERA, Willingham-Lane JM, Slovis NM, Giguere S, Cohen ND.The practice of prophylactic administration of a macrolide antimicrobial with rifampin (MaR) to apparently healthy foals with pulmonary lesions identified by thoracic ultrasonography (i.e., subclinically pneumonic foals) is common in the United States. The practice has been associated epidemiologically with emergence of R. equi resistant to MaR. Here, we report direct evidence of multi-drug resistance among foals treated with MaR. In silico and in vitro analysis of the fecal microbiome and resistome of 38 subclinically pneumonic foals treated with either MaR (n = 19) or gallium maltolate (...
Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Zomer AL.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 ...
Allison MJ, Cook HM.Rates of oxalate degradation by microbes in gastrointestinal contents from rabbits, guinea pigs, swine and a horse increased after additional of oxalate to diets. A similar response was previously observed with ruminal microbes from cattle and sheep. Bacterial that utilize oxalate for growth appear to be selected by increased levels of dietary oxalate.
Dougal K, Harris PA, Girdwood SE, Creevey CJ, Curtis GC, Barfoot CF, Argo CM, Newbold CJ.Twelve mature (aged 5-16 years) horses and ponies of mixed breed and type were fed restricted (1.25% BM Dry matter) quantities of one of two fiber based diets formulated to be iso-caloric. Diet 1 comprised of 0.8% body mass (BM) of chaff based complete feed plus 0.45% BM low energy grass hay (the same hay used for both diets). Diet 2 comprised 0.1% BM of a nutrient balancer plus 1.15% BM grass hay. Fecal samples were collected at week 10 and week 16. DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the bacterial microbiome of the horse. The two most abun...
Stewart HL, Southwood LL, Indugu N, Vecchiarelli B, Engiles JB, Pitta D.The faecal microbiota is emerging as potentially important in intestinal disease. More research is needed to characterise the faecal microbiota from horses with colic. Objective: To compare the relative abundance of bacterial populations comprising the faecal microbiota in horses presenting for colic compared with an elective surgical procedure. Methods: Prospective observational clinical study. Methods: Admission faecal samples were collected from horses presenting for colic and elective surgical procedures. Faecal samples were extracted for genomic DNA, PCR- amplified, sequenced and analysed...
Kuhl J, Winterhoff N, Wulf M, Schweigert FJ, Schwendenwein I, Bruckmaier RM, Aurich JE, Kutzer P, Aurich C.Many foals develop diarrhoea within the first two weeks of life which has been suggested to coincide with postpartum oestrus in their dams. To analyse the pathogenesis of this diarrhoea we have determined faecal bacteria in foals and their dams (n=30 each), and serum IGF-1 and γ-globulins for 6 weeks after birth. In addition, effects of β-carotene supplementation to mares (group 1: 1000 mg/day, n=15, group 2: control, n=15) on diarrhoea in foals were studied. Diarrhoea occurred in 92 and 79% of foals in groups 1 and 2, respectively, but was not correlated with oestrus in mares. Beta-carotene...
Arnold C, Pilla R, Chaffin K, Lidbury J, Steiner J, Suchodolski J.Diarrhea is an adverse effect of antimicrobial therapy in horses. This matched, case-controlled study compared the fecal microbiome and metabolome of horses on antibiotics that developed diarrhea (AAD, = 17) to those that did not develop diarrhea (ABX, = 15) and to a control population not exposed to antibiotics (CON, = 31). Fecal samples were collected from horses that were matched for diet and antimicrobial agent (including dose, route, and duration of therapy). Illumina sequencing of 16S rRNA genes was performed, and QIIME 2.0 was used to generate alpha and beta diversity metrics. Untarg...
Stothart MR, Greuel RJ, Gavriliuc S, Henry A, Wilson AJ, McLoughlin PD, Poissant J.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...
Mach N, Midoux C, Leclercq S, Pennarun S, Le Moyec L, Rué O, Robert C, Sallé G, Barrey E.Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance. Still, the extent of its functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built an integrated horse gut gene catalog comprising ~25 million unique genes and 372 metagenome-assembled genomes. This catalog represents 4179 genera spanning 95 phyla and functional capacities primed to exploit energy from dietary, microbial, and host resources. The holo-omics approach shows that gut microbiomes enriched in Lachnospiraceae...
Peachey LE, Castro C, Molena RA, Jenkins TP, Griffin JL, Cantacessi C.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...
Gao W, Chan Y, You M, Lacap-Bugler DC, Leung WK, Watt RM.This study explored the range of bacterial taxa present within healthy subgingival (below the gum-line) niches in the horse oral cavity using 16S rRNA gene amplicon pyrosequencing. Pooled subgingival plaque samples were collected from approximately 200 sulcus sites from two horses (EQ1, EQ2) for analysis. A total of 14,260 quality-filtered pyrosequencing reads were obtained, which were assigned to 3875 operational taxonomic units (OTUs; 99% identity cut-off); 1907 OTUs for EQ1 and 2156 OTUs for EQ2. Diverse taxa from 12 phyla were identified, including Actinobacteria (3.17%), Bacteroidetes (25...
Destrez A, Grimm P, Julliand V.The bidirectional communication between the central and the enteric nervous system named the gut-brain axis has been widely recognized. The gut microbiota has been implicated in a variety of stress-related conditions including anxiety, depression and irritable bowel syndrome based on rodent studies or correlative analysis in human patients. The aim of the present study was to investigate to what extent changes in behavior during stressful events and in the microbial composition of the colonic ecosystem were associated in horses. The microbiota alterations were induced by a change from a high-f...
Li Y, Zhang K, Liu Y, Li K, Hu D, Wronski T.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 () 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; = 8) in Gansu Province and Kalamaili Nature Reserve (KNR; = 12) in Xi...
Garrett LA, Brown R, Poxton IR.This study compares quantitatively the microbiota of the gastrointestinal tract of healthy horses with that of horses with equine grass sickness (EGS). Faecal and ileal samples were cultured quantitatively on selective and non-selective media. Confirmed anaerobes were identified to species level. Overall faecal counts gave a ratio of aerobes:anaerobes of approximately 1:1. However, the mean counts in healthy horses of 4.4x10(8) aerobes:3.7x10(8) anaerobes per gram wet weight were different from counts in EGS (means were 10-100-fold higher), with statistically significant differences for the an...
Arnold CE, Isaiah A, Pilla R, Lidbury J, Coverdale JS, Callaway TR, Lawhon SD, Steiner J, Suchodolski JS.Antibiotic administration can be a cause of gastrointestinal disease in horses, creating a disruption in the normal population and function of bacteria found in the hindgut. The objective of this study was to describe the changes in the cecal and fecal microbiomes and metabolomes of clinically healthy horses before and after metronidazole administration. Metronidazole (15 mg/kg BID PO) was given to five horses with cecal cannulas. The study was suspended on Day 3 due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before (Days minus52, m28, m14, and 0) and after (Day...
Coleman MC, Whitfield-Cargile CM, Madrigal RG, Cohen ND.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-o...
Wunderlich G, Bull M, Ross T, Rose M, Chapman B.The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 3...
Desrochers AM, Dolente BA, Roy MF, Boston R, Carlisle S.To evaluate the viability of Saccharomyces boulardii after PO administration in clinically normal horses and its efficacy as a treatment for horses with acute enterocolitis. Methods: Prospective study. Methods: 5 clinically normal horses and 14 horses with acute enterocolitis. Methods: Feces were collected from 5 clinically normal horses and submitted for microbial culture for 2 days prior to administration of a lyophilized form of S. boulardii (25 or 50 g, PO, q 12 h) for 10 days. Feces were collected for microbial culture 5 and 10 days after treament initiation and 10 days after treatment wa...
Kunz IGZ, Reed KJ, Metcalf JL, Hassel DM, Coleman RJ, Hess TM, Coleman SJ.The gastrointestinal microbiota (GIM) plays an essential role in maintaining intestinal homeostasis with disruptions having profound effects on the wellbeing of the host animal. Parasitic infection is a long-standing issue for the equine industry, and the use of anthelmintic drugs for parasite control has long been standard practice. The impact of anthelmintic treatment on the GIM in healthy horses is not well known. This study evaluated the hypothesis that anthelmintic administration will alter the equine fecal microbiota in horses without an observed helminth infection. Ten horses were treat...
Woolcock JB, Mutimer MD, Farmer AM.Using a selective medium, the epidemiology of Corynebacterium equi in horses was studied. Twelve horse studs in different geographical locations were investigated. In addition, a group of horses was monitored over a period of time to determine whether faecal carriage of C equi is constant or intermittent. It was found that C equi could be recovered from every property tested and from all horse breeds. The organism was found in mares, stallions, yearlings and two year olds, and foals aged from 10 days to several months. It appears that C equi is widespread and that its occurrence is not related...
Stewart HL, Pitta D, Indugu N, Vecchiarelli B, Hennessy ML, Engiles JB, Southwood LL.Previous studies have identified alterations in the faecal microbiota of horses with colic; however, further work is needed to interpret these findings. Objective: To compare the faecal microbiota of horses presenting for colic at hospital admission, day 1 and day 3/discharge and with different colic duration and lesion locations. Methods: Prospective observational clinical study. Methods: Faecal samples were collected from 17 colic cases at hospital admission, on day 1 and on day 3 post-admission or at the time of hospital discharge if prior to 72 hours. Faecal samples were extracted for gen...
Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ.The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality...
Martin de Bustamante M, Plummer C, MacNicol J, Gomez D.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-th...
Holyoak GR, Premathilake HU, Lyman CC, Sones JL, Gunn A, Wieneke X, DeSilva U.The goal of this study was to understand the composition and existence of the resident uterine microbiome in healthy mares and to establish the presence of a core microbiome for the healthy equine uterus. We analyzed the microbiomes of 35 healthy mares that are long-time residents of three farms in Oklahoma, Louisiana, and Australia as well as that of 19 mares purchased from scattered owners in the Southern Mid-Western states of the United States. Over 6 million paired-end reads of the V4 region of the 16S rRNA gene were obtained resulting in 19,542 unique Amplicon Sequence Variants (ASVs). AS...
Morita H, Nakano A, Shimazu M, Toh H, Nakajima F, Nagayama M, Hisamatsu S, Kato Y, Takagi M, Takami H, Akita H, Matsumoto M, Masaoka T, Murakami M.To detect the predominant lactobacilli in the intestinal flora of healthy thoroughbreds, we isolated lactobacilli from the feces of nine thoroughbreds (five males and four females; 0-15-year-old). The isolated lactobacilli comprise 17 species (37 strains), and they were classified into five groups: Lactobacillus salivarius (6 species), L. reuteri (6 species), Lactobacillus delbrueckii (3 species), L. buchneri (1 species) and L. vitulinus (1 species). On the basis of 16S rRNA gene sequences, we identified 3 other phylogenetic relatives belonging to the genus Lactobacillus. These results suggest...
BMC research notesMarch 12, 2013
Volume 6 91 doi: 10.1186/1756-0500-6-91
Schoster A, Arroyo LG, Staempfli HR, Weese JS.The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gen...
