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.
Lan Y, Li Y, Yu G, Zhang Z, Irshad I.Accumulating studies indicated that gut microbial changes played key roles in the progression of multiple diseases, which seriously threaten the host health. Gut microbial dysbiosis is closely associated with the development of diarrhea, but gut microbial composition and variability in diarrheic horses have not been well characterized. Here, we investigated gut fungal compositions and changes in healthy and diarrheic horses using amplicon sequencing. Results indicated that the alpha and beta diversities of gut fungal community in diarrheal horses changed significantly, accompanied by distinct ...
Hu D, Wang C, Ente M, Zhang K, Zhang D, Li X, Li K, Chu H.Intestinal microbiota play an important role in the survival of the host. However, no study to date has elucidated the adjustment of intestinal microbiota of the host during rewilding. Thus, this study aims to describe the intestinal bacterial community of reintroduced Przewalski’s horse (RPH) after being released into their original habitat for approximately 20 years in comparison with that of captive Przewalski’s horse (CPH), sympatric domestic horse (DH) and Mongolian wild ass (MWA) by sequencing the 16S rRNA gene. The results showed that the prevalent bacterial communities were differe...
Ayoub C, Arroyo LG, MacNicol JL, Renaud D, Weese JS, Gomez DE.The association of microbiota with clinical outcomes and the taxa associated with colitis in horses remains generally unknown. Objective: Describe the fecal microbiota of horses with colitis and investigate the association of the fecal microbiota with the development of laminitis and survival. Methods: Thirty-six healthy and 55 colitis horses subdivided into laminitis (n = 15) and non-laminitis (n = 39, 1 horse with chronic laminitis was removed from this comparison) and survivors (n = 27) and nonsurvivors (n = 28). Methods: Unmatched case-control study. The Illumina MiSeq platform tar...
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...
Guo R, Zhang S, Chen J, Shen W, Zhang G, Wang J, Zhang F, Pan Q, Xie T, Ai D, Dong J, Suo J, Sun Y, Liu S.Donkeys' gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts-stomach, small intestine, cecum, and rectum-were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flo...
Stothart MR, McLoughlin PD, Poissant J.Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral ...
O'Reilly GC, Holman DB, Muscat K, Muscatello G, Parra MC, Meale SJ, Chaves AV.A foal undergoes considerable growth and development from birth to weaning, progressing from a milk-based diet to complete herbivory. The symbiotic relationships between bacteria, archaea and fungi substantiate this energy demand by colonising the hindgut and remaining flexible throughout the diet transitions. A total of 70 faecal samples were collected from 14 mares and their foals across five studs in NSW as they aged from 0 to 5 months old. DNA was extracted from faecal samples and underwent amplification and sequencing of the 16S rRNA gene V4 hypervariable region of archaea and bacteria, a...
Paul LJ, Ericsson AC, Andrews FM, McAdams Z, Keowen ML, St Blanc MP, Banse HE.The purpose of this study was to characterize the relationship of diet and management factors with the glandular gastric mucosal microbiome. We hypothesize that the gastric mucosal microbial community is influenced by diet and management factors. Our specific objective is to characterize the gastric mucosal microbiome in relation to these factors. 57 client-owned horses in the southern Louisiana region with and without equine glandular gastric disease. Diet and management data were collected via a questionnaire. Gastroscopy was used for evaluation of equine gastric ulcer syndrome and collectio...
Bao W, Yu J, He Y, Liu M, Yang X.The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) w...
Ayoub C, Arroyo LG, Renaud D, Weese JS, Gomez DE.The objective of this study was to compare the fecal microbiota of two 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 mi...
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...
Collinet A, Grimm P, Jacotot E, Julliand V.Large intestine barrier disturbances can have serious consequences for the health of horses. The loss of mucosal integrity that leads to increased intestinal permeability may result from a local inflammatory immune response following alterations of the microbiota, known as dysbiosis. Therefore, our research aimed to identify noninvasive biomarkers for studying the intestinal permeability and the local inflammatory immune response in horses. Regarding the biomarkers used in other mammalian species, we measured the concentrations of lipopolysaccharides (LPS), reflected by 3-OH C14, C16, and C18 ...
MacNicol JL, Renwick S, Ganobis CM, Allen-Vercoe E, Weese JS, Pearson W.The equine gastrointestinal (GI) microbiota is intimately related to the horse. The objective of the current study was to evaluate the microbiome and metabolome of cecal inoculum maintained in an anaerobic chamber or chemostat batch fermenter, as well as the fecal slurry maintained in an anaerobic chamber over 48 h. Cecal and fecal content were collected from healthy adult horses immediately upon death. Cecal fluid was used to inoculate chemostat vessels (chemostat cecal, = 11) and vessels containing cecal fluid (anaerobic cecal, = 15) or 5% fecal slurry (anaerobic fecal, = 6) were maintain...
Cai C, Zhao M, Yao F, Zhu R, Cai H, Shao S, Li XZ, Zhou T.Deoxynivalenol, a mycotoxin that may present in almost all cereal products, can cause huge economic losses in the agriculture industry and seriously endanger food safety and human health. Microbial detoxifications using microbial consortia may provide a safe and effective strategy for DON mitigation. In order to study the interactions involving DON degradation and change in microbial flora, four samples from different natural niches, including a chicken stable (expJ), a sheep stable (expY), a wheat field (expT) and a horse stable (expM) were collected and reacted with purified DON. After being...
Li J, Zhu Y, Mi J, Zhao Y, Holyoak GR, Yi Z, Wu R, Wang Z, Zeng S.Endometrial and vaginal microbiomes are critical in the study of endometritis, which is an important cause of infertility in donkeys. Our objective was to investigate the difference of the endometrial and vaginal microbiomes between healthy donkey jennies (group C) and jennies with endometritis (group E). Endometrial and vaginal swab samples were collected, and the 16 s rRNA gene amplicon high-throughput sequencing technique was applied to identify the microbial composition in the samples. A similar microbial composition pattern was found between endometrial and vaginal samples, which indica...
Wen X, Luo S, Lv D, Jia C, Zhou X, Zhai Q, Xi L, Yang C.The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional...
Wang Y, Li X, Chen X, Kulyar MF, Duan K, Li H, Bhutta ZA, Wu Y, Li K.It is critical to characterize changes in the structure and composition of the host fungal community in natural infection, because it gives the possible overview of gut microbiome in host homeostasis and disease progression. A total of 168 rectal fecal samples were collected and examined using nPCR. The positive samples were double-checked using 18S rDNA high-throughput sequencing. After confirmation, ITS high-throughput sequencing was utilized to investigate the fungal community's response to natural infection. Results showed that a total of three positive samples (1.79%) were identified wi...
Hu D, Tang Y, Wang C, Qi Y, Ente M, Li X, Zhang D, Li K, Chu H.The microbiota and its metabolites play an important role in regulating the host metabolism and immunity. However, the underlying mechanism is still not well studied. Thus, we conducted the LC-MS/MS analysis and RNA-seq analysis on with and without horse botfly infestation to determine the metabolites produced by intestinal microbiota in feces and differentially expressed genes (DEGs) related to the immune response in blood and attempted to link them together. The results showed that parasite infection could change the composition of microbial metabolites. These identified metabolites could b...
Weinert-Nelson JR, Biddle AS, Williams CA.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 (...
de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL.The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon seque...
Hu R, Yao R, Li L, Xu Y, Lei B, Tang G, Liang H, Lei Y, Li C, Li X, Liu K, Wang L, Zhang Y, Wang Y, Cui Y, Dai J, Ni W, Zhou P, Yu B, Hu S.With the rapid development of high-throughput sequencing technology, the amount of metagenomic data (including both 16S and whole-genome sequencing data) in public repositories is increasing exponentially. However, owing to the large and decentralized nature of the data, it is still difficult for users to mine, compare, and analyze the data. The animal metagenome database (AnimalMetagenome DB) integrates metagenomic sequencing data with host information, making it easier for users to find data of interest. The AnimalMetagenome DB is designed to contain all public metagenomic data from animals,...
Hernández-Quiroz F, Murugesan S, Flores-Rivas C, Piña-Escobedo A, Juárez-Hernández JI, García-Espitia M, Chávez-Carbajal A, Nirmalkar K....Horses are non-ruminant, herbivorous mammals, been used through history for various purposes, with a gut microbiota from cecum to the colon, possessing remarkable fermentative capacity. We studied the fecal microbiota of Azteca, Criollo, Frisian, Iberian, Pinto, Quarter and Spanish horse breeds living in Mexico by next-generation DNA sequencing of 16S rRNA gene libraries. Dominant phyla Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, Fibrobacteres, Actinobacteria and Verrucomicrobia have different relative abundances among breeds, with contrasted alpha and beta diversities as well. He...
Lucassen A, Hankel J, Finkler-Schade C, Osbelt L, Strowig T, Visscher C, Schuberth HJ.Feed supplements such as fermentation products (SCFP) alter immune responses in horses. The purpose of this study was to analyze whether a prebiotic activity of the SCFP alters the gut microbiome in horses. Racehorses were fed either SCFP (Olimond BB, OLI, = 6) or placebo pellets (PLA, = 5) for 43 days. Fecal microbiota analysis was performed using 16S rRNA gene sequencing. The numbers and function of circulating immune cell subpopulations were analyzed by flow cytometry. SCFP supplementation resulted in non-consistent differences in fecal microbiota between the PLA and OLI during the feedi...
Gurgul A, Szmatoła T, Ocłoń E, Jasielczuk I, Semik-Gurgul E, Finno CJ, Petersen JL, Bellone R, Hales EN, Ząbek T, Arent Z, Kotula-Balak M....In recent years, a vast amount of sequencing data has been generated and large improvements have been made to reference genome sequences. Despite these advances, significant portions of reads still do not map to reference genomes and these reads have been considered as junk or artificial sequences. Recent studies have shown that these reads can be useful, e.g., for refining reference genomes or detecting contaminating microorganisms present in the analyzed biological samples. A special case of this is RNA sequencing (RNA-Seq) reads that come from tissue transcriptomes. Unmapped reads from RNA-...
Tang L, Gao Y, Yan L, Jia H, Chu H, Ma X, He L, Wang X, Li K, Hu D, Zhang D.The gut microbiome offers important ecological benefits to the host; however, our understanding of the functional microbiome in relation to wildlife adaptation, especially for translocated endangered species, is lagging. In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. The composition and function of the microbiome of sympatric Przewalski's horses and Asiatic wild asses in desert steppe were compared for the first time using the metagenomic shotgun sequencing approach....
Zhang Z, Gao X, Dong W, Huang B, Wang Y, Zhu M, Wang C.Equines and ruminants have evolved as grazing herbivores with specialized gastrointestinal tracts capable of utilizing a wide range of fibrous feeds. In China, agricultural by-products, including corn straw, wheat straw, peanut vine, wheat husk, rice husk, and grass hay, have been extensively included in both equine and ruminant diets. These plant materials, which are composed predominantly of cellulose, hemicellulose, noncellulosic polysaccharides, and lignin, are largely undegradable by equines and ruminants themselves. Their breakdown is accomplished by communities of resident microorganism...
Kinoshita Y, Niwa H, Uchida-Fujii E, Nukada T, Ueno T.Antimicrobial administration can lead to imbalances of gastrointestinal microbiota, called dysbiosis. Dysbiosis sometimes results in diarrhea and enteritis in horses. Fecal microbiota transplantation (FMT) is used to treat affected horses, but whether it is effective as a prophylactic approach for dysbiosis in horses receiving antimicrobials remains unknown. The aim of this study was to assess the efficacy of simultaneous FMT against metronidazole-induced dysbiosis in horses. Changes in the ratios of bacterial families, determined by metagenomic analysis, were similar between the metronidazole...
Li Y, Lan Y, Zhang S, Wang X.Increasing evidence reveals the importance of gut microbiota in animals for regulating intestinal homeostasis, metabolism, and host health. The gut microbial community has been reported to be closely related to many diseases, but information regarding diarrheic influence on gut microbiota in horses remains scarce. This study investigated and compared gut microbial changes in horses during diarrhea. The results showed that the alpha diversity of gut microbiota in diarrheic horses decreased observably, accompanied by obvious shifts in taxonomic compositions. The dominant bacterial phyla (, and )...
Voss SJ, McGuinness DH, Weir W, Sutton DGM.The role of the equine gastrointestinal microbiota in the pathogenesis of equine glandular gastric disease (EGGD) is poorly understood. To investigate whether the glandular gastric microbiota is altered in horses with EGGD. Prospective longitudinal study. Five Thoroughbred racehorses from one training center 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 gen...
Liepman RS, Swink JM, Habing GG, Boyaka PN, Caddey B, Costa M, Gomez DE, Toribio RE.Alterations in the gastrointestinal microbiota after antimicrobial therapy in horses can result in loss of colonization resistance and changes in bacterial metabolic function. It is hypothesized that these changes facilitate gastrointestinal inflammation, pathogen expansion and the development of diarrhea. The objectives of this study were to determine the effect of intravenous administration of antimicrobial drugs (ceftiofur, enrofloxacin, oxytetracycline) on equine fecal bacterial communities over time, to investigate whether those changes are detectable after 5 days of treatment and whether...
Tillotson K, Traub-Dargatz JL, Dickinson CE, Ellis RP, Morley PS, Hyatt DR, Magnuson RJ, Riddle WT, Bolte D, Salman MD.To determine the percentage of broodmares and foals that shed Clostridium perfringens in their feces and classify the genotypes of those isolates. Methods: Prospective cross-sectional study. Methods: 128 broodmares and their foals on 6 equine premises. Methods: Anaerobic and aerobic bacteriologic cultures were performed on feces collected 3 times from broodmares and foals. All isolates of C. perfringens were genotyped. Results: Clostridium perfringens was isolated from the feces of 90% of 3-day-old foals and 64% of foals at 8 to 12 hours of age. A lower percentage of broodmares and 1- to 2-mon...
Tang L, Li Y, Srivathsan A, Gao Y, Li K, Hu D, Zhang D.Captivity maybe the only choice for survival of many endangered vertebrates, and understanding its broad effects is important for animal management and conservation, including breeding endangered species for subsequent release. Extreme environmental changes during captivity may influence survival ability in the wild. Captivity decreases gut bacterial diversity in a wide range of animals. However, most studies directly compare animals living in captivity with those in the wild, and there is a lack of understanding of effects of gradient shift in lifestyle during species reintroduction based on ...
Daly K, Shirazi-Beechey SP.Nine oligonucleotide probes complementary to conserved regions of small subunit rRNA from phylogenetically defined clusters of intestinal anaerobic bacteria were designed and evaluated for use in quantitative analysis of intestinal microflora. Optimum wash temperatures (T(w)) were determined according to the temperature of dissociation (T(d)) of each probe and target group specificity was demonstrated by comparing hybridisation to target and non-target rRNA immobilised on nylon membranes. Three probes are targeted to phylogenetic clusters of Clostridiaceae, clusters III, IV and IX, with three ...
Perry E, Cross TL, Francis JM, Holscher HD, Clark SD, Swanson KS.The effects of travel stress on the equine cecal microbiota are poorly understood. We hypothesized that travel would affect the equine cecal microbiota. Cecally-cannulated horses (n = 6) were randomly assigned to one of two groups, travel (n = 3) and control (n = 3). Horses received a basal diet (Strategy, Purina Animal Nutrition) with 1.2% body weight mixed grass/alfalfa. Travel horses were transported to an unfamiliar location, stalled to simulate weekend horse show conditions, and then returned to the Southern Illinois University Equine Center. Control horses remained at the equine cente...
Scott EM, Arnold C, Dowell S, Suchodolski JS.Next generation sequencing (NGS) studies have demonstrated a rich and diverse ocular surface-associated microbiota in people that was previously undetected by traditional culture-based methods. The ocular surface microbiome of horses has yet to be investigated using NGS techniques. This study aimed to determine the bacterial composition of the ocular surface microbiome in healthy horses, and to identify whether there are microbial community changes over time and following topical antibiotic use. One eye of 12 horses was treated 3 times daily for 1 week with neomycin-polymyxin-bacitracin ophtha...
Schoster A, Kunz T, Lauper M, Graubner C, Schmitt S, Weese JS.Overgrowth of enteric clostridia in dysbiosis in horses with colic is presumed but scarcely investigated. The objective was to provide prevalence data of Clostridium difficile and Clostridium perfringens in horses with and without gastrointestinal disease in Switzerland, and investigate microbiota differences between C. difficile shedders and non-shedders. Fecal samples were taken from healthy horses (n = 103), horses with colic (n = 98) and horses with diarrhea (n = 151). Colic horses were sampled on three days. Selective enrichment culture and molecular typing for C. difficile an...
Stothart MR, McLoughlin PD, Poissant J.Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral ...
Tanabe S, Suzuki T, Wasano Y, Nakajima F, Kawasaki H, Tsuda T, Nagamine N, Tsurumachi T, Sugaya K, Akita H, Takagi M, Takagi K, Inoue Y, Asai Y....We previously isolated the commensal bacteria lactobacilli and bifidobacteria from the Thoroughbred intestine and prepared the horse probiotics LacFi(TM), consisting of Lactobacillus ruminis KK14, L. equi KK 15, L. reuteri KK18, L. johnsonii KK21, and Bifidobacterium boum HU. Here, we found that the five LacFi(TM) constituent strains remarkably suppressed pro-inflammatory interleukin-17 production in mouse splenocytes stimulated with interleukin-6 and transforming growth factor-β. The protective effects of the probiotic on impaired intestinal barrier function were evaluated in Caco-2 cells tr...
Li Y, Ma Q, Shi X, Liu G, Wang C.Evidence has shown that gut microbiota play a key role in host metabolism and health; however, little is known about the microbial community in the donkey hindgut as well as the interactions that occur between gut microbes and the host. This study aimed to explore the gut microbiome differences by analyzing the microbial community and differentially expressed genes (DEGs) related to lipid metabolism and the immune system along the donkey hindgut. The hindgut tissues (cecum, ventral colon, and dorsal colon) were separated, and the contents of each section were collected from six male donkeys fo...
Liepman RS, Swink JM, Habing GG, Boyaka PN, Caddey B, Costa M, Gomez DE, Toribio RE.Alterations in the gastrointestinal microbiota after antimicrobial therapy in horses can result in loss of colonization resistance and changes in bacterial metabolic function. It is hypothesized that these changes facilitate gastrointestinal inflammation, pathogen expansion and the development of diarrhea. The objectives of this study were to determine the effect of intravenous administration of antimicrobial drugs (ceftiofur, enrofloxacin, oxytetracycline) on equine fecal bacterial communities over time, to investigate whether those changes are detectable after 5 days of treatment and whether...
Sykora S, Pieber K, Simhofer H, Hackl V, Brodesser D, Brandt S.Red complex bacteria, i.e. Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, are involved in the onset and progression of periodontal disease in man, yet seldom inhabit the oral cavity of healthy individuals. Periodontal disease is also encountered in horses, with equine odontoclastic tooth resorption and hypercementosis (EOTRH) constituting a particular form of disease. However, only little is known about the oral microbiome of healthy and periodontitis-affected equids. Objective: We aimed to test the hypothesis that red complex bacteria are also associated with EOTRH-re...
Dong HJ, Ho H, Hwang H, Kim Y, Han J, Lee I, Cho S.Equine gastric ulcer syndrome is one of the most frequently reported diseases in thoroughbred racehorses. Although several risk factors for the development of gastric ulcers have been widely studied, investigation of microbiological factors has been limited. In this study, the presence of Helicobacter spp. and the gastric microbial communities of thoroughbred racehorses having mild to severe gastric ulcers were investigated. Although Helicobacter spp. were not detected using culture and PCR techniques from 52 gastric biopsies and 52 fecal samples, the genomic sequences of H. pylori and H. ganm...
Lwin KO, Matsui H.Comparative analysis of methanogen compositions in the feces of horse and pony was carried out by constructing the α -subunit of methyl coenzyme-M reductase (mcrA) gene and 16S ribosomal RNA gene (16S rRNA) clone libraries. The mcrA clone library analysis indicated that Methanomicrobiales was predominant in both horse and pony. Furthermore, most of the clones of the 16S rRNA gene library showed that Methanomicrobiales was also predominant in horse and pony, but the LIBSHUFF analysis showed that the horse and pony libraries were significantly different (P < 0.05). Most of operational taxono...
Bailey SR, Rycroft A, Elliott J.Acute laminitis can be induced experimentally in horses by the administration of carbohydrate, resulting in fermentation within the cecum and ischemia-reperfusion of the digits. The products of fermentation that trigger acute laminitis are as yet unknown; however, compounds such as amines might play a role due to their potential vasoactive properties. The objectives of this study were to quantify the amines present in equine cecal contents and to use a model of carbohydrate overload in vitro to test the hypothesis that carbohydrate fermentation is associated with increased amine production. Ce...
Leclere M, Costa MC.Gastrointestinal microbiota can be influenced by several factors, including diet and systemic inflammation, and in turn could act as a modulator of the allergic response. Fecal microbiota of horses with asthma has not been described. Objective: Analyze the bacterial fecal microbiota of horses with and without asthma under different environment and diet conditions, during both remission and exacerbation. Methods: Prospective observational study. Feces from 6 asthmatic and 6 healthy horses were collected under 3 different conditions: on pasture, housed indoors receiving good quality hay ("good h...
Harlow BE, Donley TM, Lawrence LM, Flythe MD.The goal was to determine the effect of starch source (corn, oats and wheat) and concentration on: (i) total amylolytic bacteria, Group D Gram-positive cocci (GPC), lactobacilli and lactate-utilizing bacteria, and (ii) fermentation by equine microbiota. Results: When faecal washed cell suspensions were incubated with any substrate amylolytics increased over time. However, at 24 h there were 10 and 1000-fold more amylolytics with corn than wheat or oats respectively. Predominant amylolytics isolated were Enterococcus faecalis (corn, wheat) and Streptococcus bovis (oats). GPC increased with any ...
Qin S, Huang Z, Wang Y, Pei L, Shen Y.Inflammatory bowel disease (IBD) is a refractory disease that endangers both humans and animals. In recent times, Lactobacillus have been used to treat animal diseases. It may be a good choice to try to isolate Lactobacillus with probiotic potential to treat IBD. Equine, as a kind of hindgut fermentation animal has rich intestinal microflora, but data regarding this is scarce. The isolation of Lactobacillus with probiotic potential from equine may become a new method for the treatment of IBD. Four isolates of Lactobacillus were isolated from fresh feces of healthy male adult horses and analyze...
Hu R, Yao R, Li L, Xu Y, Lei B, Tang G, Liang H, Lei Y, Li C, Li X, Liu K, Wang L, Zhang Y, Wang Y, Cui Y, Dai J, Ni W, Zhou P, Yu B, Hu S.With the rapid development of high-throughput sequencing technology, the amount of metagenomic data (including both 16S and whole-genome sequencing data) in public repositories is increasing exponentially. However, owing to the large and decentralized nature of the data, it is still difficult for users to mine, compare, and analyze the data. The animal metagenome database (AnimalMetagenome DB) integrates metagenomic sequencing data with host information, making it easier for users to find data of interest. The AnimalMetagenome DB is designed to contain all public metagenomic data from animals,...
Faubladier C, Julliand V, Danel J, Philippeau C.The present study aimed at (1) describing age-related changes in faecal bacterial functional groups involved in carbohydrate degradation and in their activities in foals (n 10) from birth (day (d) 0) to 6 months (d180) and (2) investigating the effect of maternal supplementation (five mares per treatment) from d - 45 to d60 with fermented feed products on response trends over time of the foal bacterial carbohydratedegrading capacity. Maternal supplementation with fermented feed products stimulated foal growth from d0 to d60 and had an impact on the establishment of some digestive bacterial gro...
Fujimori S.The cell walls of plants are mainly made of cellulose and contain a large number of calories. However, the main component, cellulose, is an indigestible plant fiber that is thought to be difficult for humans to use as energy. Herbivores acquire energy through the degradation of cell wall-derived dietary fiber by microorganisms in the digestive tract. Herbivores, especially horses, have a highly developed cecum and large intestine, and plants are fermented for their efficient use with the help of microorganisms. Humans also have an intestinal tract with a wide lumen on the proximal side of the ...
Hashimoto-Hill S, Alenghat T.Domestic animals represent important resources for understanding shared mechanisms underlying complex natural diseases that arise due to both genetic and environmental factors. Intestinal inflammation, particularly inflammatory bowel disease (IBD), is a significant health challenge in humans and domestic animals. While the etiology of IBD is multifactorial, imbalance of symbiotic gut microbiota has been hypothesized to play a central role in disease pathophysiology. Advances in genomic sequencing and analytical pipelines have enabled researchers to decipher the composition of the intestinal mi...
Bond SL, Workentine M, Hundt J, Gilkerson JR, Léguillette R.Prolonged exposure to environmental antigens or allergens elicits an immune response in both healthy horses and those with mild asthma. Corticosteroids often are used to treat lower airway inflammation. Objective: To investigate the changes in equine herpesvirus (EHV)-1,2,4,5 glycoprotein B gene expression and changes in respiratory bacterial and fungal communities after nebulized dexamethasone treatment of horses with asthma. Methods: Horses with naturally occurring mild asthma (n = 16) and healthy control horses (n = 4). Methods: Prospective, randomized, controlled, blinded clinical trial. P...
Tyma JF, Epstein KL, Whitfield-Cargile CM, Cohen ND, Giguère S.OBJECTIVE To determine the effects of oral omeprazole administration on the fecal and gastric microbiota of healthy adult horses. ANIMALS 12 healthy adult research horses. PROCEDURES Horses were randomly assigned to receive omeprazole paste (4 mg/kg, PO, q 24 h) or a sham (control) treatment (tap water [20 mL, PO, q 24 h]) for 28 days. Fecal and gastric fluid samples were collected prior to the first treatment (day 0), and on days 7, 28, 35, and 56. Sample DNA was extracted, and bacterial 16S rRNA gene sequences were amplified and sequenced to characterize α and β diversity and differential ...
Berg EL, Fu CJ, Porter JH, Kerley MS.Short-chain fructooligosaccharides (FOS) were supplemented to the diets of nine quarter horses ranging in age from 489 to 539 d with initial BW averaging 400.6 +/- 21.2 kg. The objectives of this study were to determine the effects of dietary FOS on the fecal responses in terms of pH, the microbial population, and VFA concentrations. The horses were used in a 3 x 3 replicated Latin square design, fed according to NRC requirements, and their individual diets were supplemented with no FOS (CON), 8 g of FOS/d (LOW), or 24 g of FOS/d (HIGH) over three 10-d feeding periods. On the last 3 d of each ...
Whitfield-Cargile CM, Chamoun-Emanuelli AM, Cohen ND, Richardson LM, Ajami NJ, Dockery HJ.Non-steroidal anti-inflammatory drugs (NSAIDs) are routinely used in both veterinary and human medicine. Gastrointestinal injury is a frequent adverse event associated with NSAID use and evidence suggests that NSAIDs induce gastrointestinal microbial imbalance (i.e., dysbiosis) in both animals and people. It is unknown, however, whether cyclooxygenase (COX)-2-selective NSAIDs induce dysbiosis, or if this phenomenon occurs in horses administered any class of NSAIDs. Therefore, our objectives were to determine whether the composition and diversity of the fecal microbiota of adult horses were alt...
Li N, Xie Q, Chen Q, Evivie SE, Liu D, Dong J, Huo G, Li B.Studies on the possible alternative supplements to breastmilk are gaining research interests. Although milk from cow, goat, and mare is nutritious, its effects on the relationship between the immune system, metabolites, and gut microbiota remain unclear. This study aimed to comprehensively evaluate the effects of cow, goat, and mare milk on the immune system, metabolites, and gut microbiota of mice colonized by healthy infant feces using human milk as a standard. We examined the serum biochemistry parameters, immunity indicators, T cells, gut microbiota abundance, and metabolites. Results show...
Bordin AI, Suchodolski JS, Markel ME, Weaver KB, Steiner JM, Dowd SE, Pillai S, Cohen ND.Rhodococcus equi is an important pathogen of foals. Enteral administration of live, virulent R. equi during early life has been documented to protect against subsequent intrabronchial challenge with R. equi, indicating that enteral mucosal immunization may be protective. Evidence exists that mucosal immune responses develop against both live and inactivated micro-organisms. The extent to which live or inactivated R. equi might alter the intestinal microbiome of foals is unknown. This is an important question because the intestinal microbiome of neonates of other species is known to change over...
Coverdale JA.Intensive management practices in the horse industry present a unique challenge to the microbiome of the large intestine. Common management practices such as high-concentrate diets, low forage quality, meal feeding, and confinement housing have an impact on intestinal function, specifically large intestinal fermentation. The microbiome of the equine large intestine is a complex and diverse ecosystem, and disruption of microbiota and their environment can lead to increased incidence of gastrointestinal disorder. Digestion in the horse can be improved through a variety of approaches such as feed...
Xing J, Liu G, Zhang X, Bai D, Yu J, Li L, Wang X, Su S, Zhao Y, Bou G, Dugarjaviin M.The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3-V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age...
Walshe N, Mulcahy G, Crispie F, Cabrera-Rubio R, Cotter P, Jahns H, Duggan V.Cyathostomins are prevalent and pathogenic intestinal helminths of horses, causing acute and chronic disease, including acute larval cyathostominosis, which has a mortality rate of 50%. Factors determining individual susceptibility to acute larval cyathostominosis are unknown. Investigation of these factors could lead to novel treatment and prevention strategies. Objective: To investigate clinicopathological and faecal microbiota changes associated with disease in individual horses in an acute larval cyathostominosis outbreak. Methods: Case series. Methods: The study population was a herd of 2...
