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

Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth

The gut microbiota (GM) is essential for mammalian health. Although the association between infant GM and breast milk (BM) composition has been well established in humans, such a relationship has not been investigated in horses. Hence, this study was conducted to analyze the GM formation of foals during lactation and determine the presence of low-molecular-weight metabolites in mares' BM and their role in shaping foals' GM. The fecal and BM samples from six pairs of foals and mares were subjected to 16S ribosomal RNA metagenomic and metabolomic analyses, respectively. The composition of foal GM changed during lactation time; hierarchical cluster analysis divided the fetal GM into three groups corresponding to different time points in foal development. The level of most metabolites in milk decreased over time with increasing milk yield, while threonic acid and ascorbic acid increased. Further analyses revealed gut bacteria that correlated with changes in milk metabolites; for instance, there was a positive correlation between Bacteroidaceae in the foal's gut microbiota and serine/glycine in the mother's milk. These findings help improve the rearing environment of lactating horses and establish artificial feeding methods for foals.

Horse Meat Microbiota: Determination of Biofilm Formation and Antibiotic Resistance of Isolated Staphylococcus Spp

Domestic horses could be bred for leisure activities and meat production, as is already the case in many countries. Horse meat is consumed in various countries, including Kazakhstan and Kyrgyzstan, and with the increase in this consumption, horses are registered as livestock by the Food and Agricultural Organization. In this study, horse meat microbiota of horse samples (n = 56; 32 samples from Kazakhstan and 24 samples from Kyrgyzstan) from two countries, Kazakhstan (n = 3) and Kyrgyzstan (n = 1), were investigated for the first time by next-generation sequencing and metabarcoding analysis. The results demonstrated that Firmicutes, Proteobacteria, and Actinobacteria were the dominant bacterial phyla in all samples. In addition, three (5.4%) Staphylococcus strains were isolated from the Uzynagash region, Kazakhstan. Staphylococcus strains were identified as Staphylococcus warneri, S. epidermidis, and S. pasteuri by partial 16S rRNA DNA gene Sanger sequencing. All three Staphylococcus isolates were nonbiofilm formers; only the S. pasteuri was detected as multidrug-resistant (resistant to penicillin, cefoxitin, and oxacillin). In addition, S. pasteuri was found to carry mecA, mecC, and tetK genes. This is the first study to detect potentially pathogenic Staphylococcus spp. in horse meat samples originating from Kazakhstan. In conclusion, it should be carefully considered that undercooked horse meat may pose a risk to consumers in terms of pathogens such as antibiotic-resistant Staphylococcus isolates.

Storage of equine faecal microbiota transplantation solution has minimal impact on major bacterial communities and structure

Management of diarrhoea in horses is usually non-specific and supportive. Faecal microbiota transplantations (FMT) are used to manage dysbiosis in horses with diarrhoea. There are few studies investigating the effects of storage on prepared FMT solutions. This study was an in vitro non-randomised controlled experiment that investigated the effects of FMT solution preparation and storage on the faecal microbiota. Fresh faeces were collected from five healthy adult horses and used for DNA extraction and preparation of FMT. From each FMT, seven aliquots were collected and DNA was extracted immediately after FMT preparation (0 hr), after storage at 4 °C for 24, 48 or 72 hours, and after storage at -20°C for 7 days, 14 days or 28 days. The extracted DNA was used for 16 S rRNA gene sequencing. The relative abundance, alpha diversity and beta diversity between fresh faeces and FMT 0 hr showed no differences (P ≥ 0.05). There were minimal changes in the microbiota of FMT stored at 4°C for up to 72 hours and -20°C for up to 28 days. The results of this study indicate that preparation of equine FMT solution has minimal effect on the microbiota in comparison to fresh faeces. FMT solution can be stored at 4°C for up to 3 days and -20°C for 28 days without major change in microbiota.

Methylated tirilazad may mitigate oligofructose-induced laminitis in horses

Laminitis is a serious health condition that can cause severe pain and lameness in horses. Due to lack of understanding of laminitis, treatments often fail to achieve the desired results. In recent years, we have begun to recognize that laminitis may involve a complex interaction between local and systemic inflammation. Dysbiosis of the gut microbiota has been linked in the development of systemic inflammation, and our previous findings suggest that the development of laminitis is closely linked to the production of harmful metabolites of the gut microbiota. In addition, it was found that localized lesions in the hoof, especially lamellar injuries, are the most direct cause of laminitis. Matrix metalloproteinases have been found to be strongly associated with the development of laminitis. Recent discovery has found that methylated tirilazad has a role in repairing laminar tissue in vitro. However, its efficacy in horses never has been studied. Therefore, we aimed to investigate the efficacy of methylated tirilazad (product name: PTP-102) in the prevention/treatment of oligofructose-induced laminitis. The results showed that oligofructose successfully induced laminitis in horses, resulting in detreated clinical signs. Blood indices (including inflammation-related indices and other related indices) were significantly increased. Observations of dissection and staining showed significant bleeding, swelling, and damage to hoof tissue. Analysis of the gut microbiota showed a significant decrease in abundance and diversity, and a significant increase in the relative abundance of specific bacteria. Following methylated tirilazad intervention, there were a significant improvement in clinical signs, blood markers and lamellar tissue damage. Additionally, methylated tirilazad positively influenced the gut microbiota structure by reducing the relative abundance of genera closely associated with the development of equine laminitis. This suggests that some of the therapeutic mechanism of methylated tirilazad may be linked to its effects on the gut microbiota. Notably, methylated tirilazad had better effect in the treatment group than the prophylactic group, indicating the post-diagnosis utility of methylated tirilazad for laminitis management.

Gut Microbiota Profiling as a Promising Tool to Detect Equine Inflammatory Bowel Disease (IBD)

Gastrointestinal disorders are common and debilitating in horses, but their diagnosis is often difficult and invasive. Fecal samples offer a non-invasive alternative to assessing the gastrointestinal health of horses by providing information about the gut microbiota and inflammation. In this study, we used 16S sequencing to compare the fecal bacterial diversity and composition of 27 healthy horses and 49 horses diagnosed with inflammatory bowel disease (IBD). We also measured fecal calprotectin concentration, a marker of intestinal inflammation, in healthy horses and horses with IBD. We found that microbiota composition differed between healthy horses and horses with IBD, although less than five percent of the variation in microbiota composition was explained by individual health status and age. Several differentially abundant bacterial taxa associated with IBD, age, or body condition were depleted from the most dominant Firmicutes phylum and enriched with the Bacteroidota phylum. An artificial neural network model predicted the probability of IBD among the test samples with 100% accuracy. Our study is the first to demonstrate the association between gut microbiota composition and chronic forms of IBD in horses and highlights the potential of using fecal samples as a non-invasive source of biomarkers for equine IBD.

Oral probiotic administration attenuates postexercise inflammation in horses

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

Reproductive Tract Microbiota of Mares

The female reproductive tract microbiota is a complex community of microorganisms that might be crucial in maintaining a healthy reproductive environment. Imbalances in the bacterial community (dysbiosis) and the reduction of beneficial organisms and pathogen proliferation are associated with disease. Endometritis is a common cause of fertility problems in mares, and it is still challenging to diagnose and treat based on routine culture results of certain microorganisms. Although high-throughput sequencing studies provide helpful information regarding the composition of the reproductive tract microbiota in mares, there are still challenges in defining a "normal" microbiota. The primary objective of this literature review is to summarize the current knowledge regarding the microbiota present in the reproductive tract of mares, including the vagina, cervix, and uterus. The second objective is to describe the relevant factors that can impact the reproductive microbiota of mares, including the estrous cycle stage, the type of species (genera) investigated, season, and geographic location. The rationality of identifying the normal microbiota in the reproductive tract of a mare will likely aid in understanding the impact of the microbiota on the host's reproductive health and contribute to the treatment and prevention of equine sub and infertility issues.

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

Introduction

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

Methods

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

Results and discussion

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

Effect of probiotics and prebiotics on the composition of the equine fecal and seminal microbiomes and sperm quality: A pilot study

Probiotic and prebiotic effects on equine semen and gastrointestinal microbiome composition and sperm quality are unknown. This study aimed to evaluate the effects of pre-, pro- or synbiotic supplementation on fecal and semen microbiome composition and sperm quality parameters of stallions. This Latin square crossover trial involved four miniature pony stallions receiving control diet only, or addition of a pro-, pre- or synbiotic formulation. Full-length 16S rRNA gene amplicon sequencing was used to measure diversity of semen and fecal microbiomes. Total sperm count, total motility, progressive motility, DNA integrity, lipid peroxidation and mitochondrial oxidative stress, biomarkers of sperm quality, were measured after each intervention. A general linear model was employed to analyse and compare microbiome diversity measures and sperm quality data across four time points. Shannon's diversity index (alpha-diversity), and evenness of semen and gastrointestinal microbiomes were significantly different (p<0.001). A trend was observed for prebiotic effects on the diversity indices of the GI microbiome (p= 0.07). No effects of treatments were observed on either semen microbiome or sperm quality. Pre-, pro- and synbiotic supplements showed no negative effect on sperm quality parameters observed. This proof of concept provides preliminary data to inform future studies exploring the relationship between microbiomes and fertility.

Baselining physiological parameters in three muscles across three equine breeds. What can we learn from the horse?

Mapping-out baseline physiological muscle parameters with their metabolic blueprint across multiple archetype equine breeds, will contribute to better understanding their functionality, even across species. Aims: 1) to map out and compare the baseline fiber type composition, fiber type and mean fiber cross-sectional area (fCSA, mfCSA) and metabolic blueprint of three muscles in 3 different breeds 2) to study possible associations between differences in histomorphological parameters and baseline metabolism. Methods: Muscle biopsies [m. pectoralis (PM), m. vastus lateralis (VL) and m. semitendinosus (ST)] were harvested of 7 untrained Friesians, 12 Standardbred and 4 Warmblood mares. Untargeted metabolomics was performed on the VL and PM of Friesian and Warmblood horses and the VL of Standardbreds using UHPLC/MS/MS and GC/MS. Breed effect on fiber type percentage and fCSA and mfCSA was tested with Kruskal-Wallis. Breeds were compared with Wilcoxon rank-sum test, with Bonferroni correction. Spearman correlation explored the association between the metabolic blueprint and morphometric parameters. Results: The ST was least and the VL most discriminative across breeds. In Standardbreds, a significantly higher proportion of type IIA fibers was represented in PM and VL. Friesians showed a significantly higher representation of type IIX fibers in the PM. No significant differences in fCSA were present across breeds. A significantly larger mfCSA was seen in the VL of Standardbreds. Lipid and nucleotide super pathways were significantly more upregulated in Friesians, with increased activity of short and medium-chain acylcarnitines together with increased abundance of long chain and polyunsaturated fatty acids. Standardbreds showed highly active xenobiotic pathways and high activity of long and very long chain acylcarnitines. Amino acid metabolism was similar across breeds, with branched and aromatic amino acid sub-pathways being highly active in Friesians. Carbohydrate, amino acid and nucleotide super pathways and carnitine metabolism showed higher activity in Warmbloods compared to Standardbreds. Conclusion: Results show important metabolic differences between equine breeds for lipid, amino acid, nucleotide and carbohydrate metabolism and in that order. Mapping the metabolic profile together with morphometric parameters provides trainers, owners and researchers with crucial information to develop future strategies with respect to customized training and dietary regimens to reach full potential in optimal welfare.

The semen microbiome of miniature pony stallions

CONTEXT

Little is known about the microbial composition of stallion semen.

AIMS

To describe the microbiota detected in equine semen of healthy miniature pony stallions.

METHODS

Semen specimens were collected using a Missouri artificial vagina at a single time point. PacBio (Pacific Biosciences) genomic DNA sequencing of the 16S rRNA gene was performed on these specimens, following which next-generation microbiome bioinformatics platform QIIME2 was used to process fastq files and analyse the amplicon data. The data were categorised into genus, family, class, order and phylum.

KEY RESULTS

Firmicutes and Bacteroidetes phyla predominated (76%), followed by Proteobacteria (15%). Bacteroidales, Clostridiales and Cardiobacteriales predominated the microbial rank of order (86%). Class was mainly composed of Bacteroidia, Clostridia and Gammaproteobacteria (87%), while family was mainly composed of Porphyromonadaceae , Family_XI and Cardiobacteriaceae (62%). At the level of genus, 80% of the abundance was composed of seven genera, namely Porphyromonas, Suttonella, Peptoniphilus, Fastidiosipila, Ezakiella, Petrimonas and an unknown taxon.

CONCLUSIONS

The findings indicate that specific microbiota may be characteristic of healthy miniature pony stallions' semen with some inter-individual variations observed.

IMPLICATIONS

Larger equine studies involving fertile and infertile subjects could be informed by this study and could explore the relationship of the semen microbiome to male fertility.

Gut Microbiota Exchange in Domestic Animals and Rural-urban People Axis

In recent years, one of the most critical topics in microbiology that can be addressed is microbiome and microbiota. The term microbiome contains both the microbiota and structural elements, metabolites/signal molecules, and the surrounding environmental conditions, and the microbiota consists of all living members forming the microbiome. Among; the intestinal microbiota is one of the most important microbiota, also called the gut microbiota. After colonization, the gut microbiota can have different functions, including resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, and controlling immune function. Recently, studies have shown that the gut microbiota can prevent the formation of fat in the body. In this study, we examined the gut microbiota in various animals, including dogs, cats, dairy cows, sheep, chickens, horses, and people who live in urban and rural areas. Based on the review of various studies, it has been determined that the population of microbiota in animals and humans is different, and various factors such as the environment, nutrition, and contact with animals can affect the microbiota of people living in urban and rural areas.

A diverse microbial community and common core microbiota associated with the gonad of female Parascaris spp

The microbiome plays an important role in health, where changes in microbiota composition can have significant downstream effects within the host, and host-microbiota relationships can be exploited to affect health outcomes. Parasitic helminths affect animals globally, but an exploration of their microbiota has been limited, despite the development of anti-Wolbachia drugs to help control infections with some filarial nematodes. The equine ascarids, Parascaris spp., are considered the most pathogenic nematodes affecting juvenile horses and are also the only ascarid parasite to have developed widespread anthelmintic resistance. The aim of this study was to characterize the microbiota of this helminth, focusing on the female gonad, determine a core microbiota for this organ, identify bacterial species, and show bacterial localization to the female gonad via in situ hybridization (ISH). A total of 22 gonads were isolated from female Parascaris spp. collected from three foals, and 9 female parasites were formalin-fixed and paraffin-embedded for ISH. Next-generation sequencing was performed using V3-V4 primers as well as the Swift Amplicon™ 16S+ ITS Panel. Overall, ten genera were identified as members of the Parascaris spp. female gonad and twelve bacterial species were identified. The most prevalent genus was Mycoplasma, followed by Reyranella, and there were no differences in alpha diversity between parasites from different horses. Specific eubacteria staining was identified in both the intestine and within the gonad using ISH. Overall, this study provided in-depth information regarding the female Parascaris spp. microbiota and was the first to identify the core microbiota within a specific parasite organ.

Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia

Introduction

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.

Methods

We collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and 10 (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1-V2 gene sequencing.

Results

We included 48 samples in the SSG (n = 16 horses), 45 in the 5DG (n = 15), and 20 in the CG (for t0 and t1, n = 10). Two samples of equine patients receiving antibiotic prophylaxis (6.5%) were positive for ESBL-producing Enterobacterales at t0, while this rate increased to 67% at t1 and decreased only slightly at t2 (61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing there was no significant difference between horses suffering from acute colic (5DG, SDImean of 5.90, SSG, SDImean of 6.17) when compared to the CG (SDImean of 6.53) at t0. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2 the onset of microbiome recovery was noticed. Although we did not identify a significant SDImean difference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance of Enterobacteriaceae, especially Escherichia, was noted for both study groups at t1.

Conclusion

Colic surgery and PAP drive the equine gut microbiome towards dysbiosis and reduced biodiversity that is accompanied by an increase of samples positive for ESBL-producing Enterobacterales. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.

Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China

Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.

Conserved core microbiota in managed and free-ranging Loxodonta africana elephants

The gut microbiota plays a crucial role in animal health and homeostasis, particularly in endangered species conservation. This study investigated the fecal microbiota composition of European captive-bred African savanna elephants (Loxodonta africana) housed in French zoos, and compared it with wild African savanna elephants. Fecal samples were collected and processed for DNA extraction and amplicon sequencing of the 16S rRNA gene. The analysis of α and β diversity revealed significant effects of factors such as diet, daily activity, and institution on microbiota composition. Specifically, provision of branches as part of the diet positively impacted microbiota diversity. Comparative analyses demonstrated distinct differences between captive and wild elephant microbiomes, characterized by lower bacterial diversity and altered co-occurrence patterns in the captive population. Notably, specific taxa were differentially abundant in captive and wild elephants, suggesting the influence of the environment on microbiota composition. Furthermore, the study identified a core association network shared by both captive and wild elephants, emphasizing the importance of certain taxa in maintaining microbial interactions. These findings underscore the impact of environment and husbandry factors on elephant gut microbiota, highlighting the benefits of dietary enrichment strategies in zoos to promote microbiome diversity and health. The study contributes to the broader understanding of host-microbiota interactions and provides insights applicable to conservation medicine and captive animal management.

Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces

Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.

Diversity and functional prediction of fungal communities in different segments of mongolian horse gastrointestinal tracts

BACKGROUND

Anaerobic fungi are effective fibre-degrading microorganisms in the digestive tract of horses. However, our understanding of their diversity and community structure is limited, especially in different parts of the gastrointestinal tract.

RESULTS

For the first time, high-throughput sequencing technology was used to analyse and predict fungal microbial diversity in different parts of the gastrointestinal tract of Mongolian horses. The results revealed that the richness and diversity of fungi in the hindgut of Mongolian horses were much higher than those in the foregut. The foregut was dominated by Basidiomycota and Ascomycota, whereas the hindgut was dominated by Neocallimastigomycota and Basidiomycota. At the genus level, the relative abundance of many pathogenic fungi (Cryptococcus, Cladosporium, Alternaria, and Sarocladium) in the foregut was significantly higher than that in the posterior gut, indicating that Mongolian horses have strong disease resistance. The prediction of fungal function also showed significant differences in the fungal flora between the foregut and the hindgut. The fungi in Mongolian horses' foreguts were mainly pathologically nutritive and contained many animal and plant pathogens, particularly in the small intestine (jejunum and ileum). This indicates that the foregut may be the most important immune site in the digestive system of Mongolian horses, which explains the high disease resistance of Mongolian horses. The number of unassigned functional groups in the posterior gut was significantly higher than that in the anterior gut, indicating that the functions of fungal groups in the posterior gut have not been fully explored, and further studies are required in the future.

CONCLUSIONS

Analysis of high-throughput sequencing results revealed that the fungal composition varied greatly among different gastrointestinal tract segments in Mongolian horses, whose hindgut contains many anaerobic fungi involved in plant cellulose degradation. This provides important basic data for studying fungal diversity in the digestive system of healthy horses, which can be used for the health assessment of horses and provides clues for further research on the disease resistance and digestive capacity of horses, as well as a reference for the early diagnosis of intestinal diseases and innovative treatment methods.

Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing

BACKGROUND

Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited.

RESULTS

In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose.

CONCLUSION

According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.

Exploring the Influence of Growth-Associated Host Genetics on the Initial Gut Microbiota in Horses

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 quantitative trait locus (QTL) information related to horse growth. The taxa involved in 31 host-microbiome associations were functionally linked to carbohydrate metabolism, energy metabolic processes, short-chain fatty acid (SCFA) production, and lactic acid production. Abundances of these taxa were affected by specific SNP genotypes. Most growth-associated SNPs are found between genes. The rs69057439 and rs69127732 SNPs are located within the introns of the VWA8 and MFSD6 genes, respectively. These genes are known to affect energy balance and metabolism. These discoveries emphasize the significant effect of host SNPs on the development of the intestinal microbiome during the initial phases of life and provide insights into the influence of gut microbial composition on horse growth.

Equine Gram-Negative Oral Microbiota: An Antimicrobial Resistances Watcher?

Horses are considered as reservoirs of multidrug resistant bacteria that can be spread through the environment and possibly to humans. The aim of this study was to characterize the oral Gram-negative microbiota of healthy horses and evaluate their antimicrobial susceptibility profile in a One Health approach. For this purpose, samples were collected from the gingival margin of healthy horses, free of antimicrobial therapy, cultured in selective mediums, identified, and tested for antimicrobial susceptibility. Fifty-five Gram-negative isolates were identified, with 89.5% being zoonotic and 62% affecting humans, which were also found commonly in the environment. Forty-eight isolates (96%) were MDR. The phenotypic resistance presented as higher to macrolides (81.8%), β-lactams (55.4%), and quinolones (50%), and lower to sulfonamides (27.3%), tetracyclines, and amphenicols (both with 30.9%). In total, 51.5% of the isolates presented resistance to carbapenems. In addition to being the first report on the commensal oral microbiota of horses and respective susceptibility profile, this study highlights the horse as a valuable sentinel that can control the evolution and transmission of multidrug-resistant bacteria between the "One Health triad" since it is in contact with humans, other animals, and the environment, in different geographic locations.

The Fibre Requirements of Horses and the Consequences and Causes of Failure to Meet Them

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). Ulcerations are caused either by increasing acidity in the stomach (from starch ingestion and reduced saliva production) or splashing of acidic juices caused by a lack of a forage barrier prior to exercise or prolonged periods without fibrous feed intake, which allows the stomach to collapse and spread acidic gastric fluids into the upper squamous regions of the stomach. In the hindgut, starch that has escaped digestion in the small intestine causes microbial instability and increased production of volatile fatty acids (VFA) and lactic acid. This puts horses at great risk for acidosis and subsequent laminitis. Shifts in the hindgut microbiota will also affect a horse's behaviour via the gut-brain axis, as well as potentially compromise immune function. Reduced fluid intake caused by reduced saliva production can result in colic. Choosing a fibrous alternative for starch in a high-energy diet greatly reduces the risk of EGUS and acidosis and improves digestion, GIT pH, body condition, behaviour, immune functions, and performance. Providing hay can reduce crib-biting, wood-chewing, coprophagia, the consumption of bedding, aggression, and stress, and subsequently increase social bonding and affiliation with conspecifics. Adequate fibre intake is related to reduced clinical signs of EGUS, reduced reactivity, and better adaptation to weaning. Lignophagia (wood chewing) has also been observed in horses that are foraging, and this is thought to reflect low fibre content in the available forage (for example, early vegetative, lush pasture).

Associations among the genome, rumen metabolome, ruminal bacteria, and milk production in early-lactation Holsteins

A multicenter observational study to evaluate genome-wide association was conducted in early-lactation Holstein cows (n = 293) from 36 herds in Canada, the USA, and Australia. Phenotypic observations included rumen metabolome, acidosis risk, ruminal bacterial taxa, and milk composition and yield measures. Diets ranged from pasture supplemented with concentrates to total mixed rations (nonfiber carbohydrates = 17 to 47, and neutral detergent fiber = 27 to 58% of dry matter). Rumen samples were collected <3 h after feeding and analyzed for pH, ammonia, d- and l-lactate, volatile fatty acid (VFA) concentrations, and abundance of bacterial phyla and families. Eigenvectors were produced using cluster and discriminant analyses from a combination of pH and ammonia, d-lactate, and VFA concentrations, and were used to estimate the probability of the risk of ruminal acidosis based on proximity to the centroid of 3 clusters, termed high (24.0% of cows), medium (24.2%), and low risk (51.8%) for acidosis. DNA of sufficient quality was successfully extracted from whole blood (218 cows) or hair (65 cows) collected simultaneously with the rumen samples and sequenced using the Geneseek Genomic Profiler Bovine 150K Illumina SNPchip. Genome-wide association used an additive model and linear regression with principal component analysis (PCA) population stratification and a Bonferroni correction for multiple comparisons. Population structure was visualized using PCA plots. Single genomic markers were associated with milk protein percent and the center logged ratio abundance of the phyla Chloroflexi, SR1, and Spirochaetes, and tended to be associated with milk fat yield, rumen acetate, butyrate, and isovalerate concentrations and with the probability of being in the low-risk acidosis group. More than one genomic marker was associated or tended to be associated with rumen isobutyrate and caproate concentrations, and the center log ratio of the phyla Bacteroidetes and Firmicutes and center log ratio of the families Prevotellaceae, BS11, S24-7, Acidaminococcaceae, Carnobacteriaceae, Lactobacillaceae, Leuconostocaceae, and Streptococcaceae. The provisional NTN4 gene, involved in several functions, had pleiotropy with 10 bacterial families, the phyla Bacteroidetes and Firmicutes, and butyrate. The ATP2CA1 gene, involved in the ATPase secretory pathway for Ca²⁺ transport, overlapped for the families Prevotellaceae, S24-7, and Streptococcaceae, the phylum Bacteroidetes, and isobutyrate. No genomic markers were associated with milk yield, fat percentage, protein yield, total solids, energy-corrected milk, somatic cell count, rumen pH, ammonia, propionate, valerate, total VFA, and d-, l-, or total lactate concentrations, or probability of being in the high- or medium-risk acidosis groups. Genome-wide associations with the rumen metabolome, microbial taxa, and milk composition were present across a wide geographical and management range of herds, suggesting the existence of markers for the rumen environment but not for acidosis susceptibility. The variation in pathogenesis of ruminal acidosis in the small population of cattle in the high risk for acidosis group and the dynamic nature of the rumen as cows cycle through a bout of acidosis may have precluded the identification of markers for acidosis susceptibility. Despite a limited sample size, this study provides evidence of interactions between the mammalian genome, the rumen metabolome, ruminal bacteria, and milk protein percentage.

Does colonization with MRSA, ESBL - producing Enterobacteriaceae, and/or Acinetobacter baumannii - increase the risk for postoperative surgical site infection?

OBJECTIVE

Evaluation of the role of indicator pathogens in equine surgical site infection (SSI) and other infection-promoting factors.

STUDY DESIGN

Cross-sectional study.

ANIMALS

Horses presenting with an open injury or surgical colic during 1.5 years.

METHODS

A nasal swab and a faecal sample were collected from every patient upon admission. Furthermore, a wound swab was collected from wounds of injured horses. Details on the wounds and procedures were documented. Laparotomy incisions and injuries were monitored for signs suggesting infection.

RESULTS

In total, 156 horses presented because of a surgical colic (n = 48) or open injuries (n = 108). Thirteen surgical colic patients and three injured horses did not survive beyond 24 h, and four injured horses were discharged from the clinic at the day of admission. SSIs occurred in 31 (30.7%) injured horses and 11 (31.4%) horses after laparotomy. Regarding injuries, general anaesthesia increased the risk of developing a WI compared to sedation. Indicator pathogens were cultured from 29/42 SSI. In total, 10/11 infected laparotomy incisions and 19/31 injuries with SSI tested positive for multidrug-resistant pathogens (MDRPs) . Indicator pathogens were not detected at admission in any of the horses that developed incisional SSIs after laparotomy but were detected in two of the injured horses that developed SSIs.

CONCLUSION

MDRPs were identified in almost 70% of the SSI. Less than 5% of the affected animals were colonized with the same pathogen before admission, indicating that colonization with MDR pathogens is only one of the crucial factors for the development of SSI.

CLINICAL SIGNIFICANCE

Colonization with MDRP seems not to predispose horses to MDR SSIs.

Effects of Microencapsulated Essential Oils on Equine Health: Nutrition, Metabolism and Methane Emission

This review examines the available data regarding the positive effects of microencapsulated essential oils (EOs) on the nutrition, metabolism, and possibly the methane emission of horses. A literature review was conducted on the effect of microencapsulated (EOs) on the health of horses. The information comprises articles published in recent years in indexed journals. The results indicate that mixtures of microencapsulated EOs may be beneficial to equine health due to their antimicrobial and antioxidant activity, as well as their effects on enteric methane production, nutrient absorption, and immune system enhancement. Moreover, encapsulation stabilizes substances such as EOs in small doses, primarily by combining them with other ingredients.

Evaluation of Bacterial Composition and Viability of Equine Feces after Processing for Transplantation

Fecal microbiota transplantation (FMT) has been used empirically for decades in equine medicine to treat intestinal dysbiosis but evidence-based information is scarce. This in vitro study aimed at assessing the effect of a commonly used pre-FMT processing method on the bacterial composition and viability of the fecal filtrate. Three samples of fresh equine manure (T₀) were processed identically: the initial manure was mixed with 1 L of lukewarm water and chopped using an immersion blender to obtain a mixture (T₁), which was left uncovered during 30 min (T₂) and percolated through a sieve to obtain a fecal filtrate (T₃). Samples were taken throughout the procedure (Tn) and immediately stored at 4 °C until processing. The 16S rDNA amplicon profiling associated with propidium monoazide treatment was performed on each sample to select live bacteria. Analyses of α and β diversity and main bacterial populations and quantitative (qPCR) analysis were performed and statistically compared (significance p < 0.05) between time points (T₀-T₃). No significant differences in ecological indices or mean estimated total living bacteria were found in the final fecal filtrate (T₃) in regard to the original manure (T₀); however, relative abundances of some minor genera (Fibrobacter, WCHB1-41_ge and Akkermansia) were significantly different in the final filtrate. In conclusion, the results support the viability of the major bacterial populations in equine feces when using the described pre-FMT protocol.

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse

BACKGROUND

As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.

RESULTS

Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.

CONCLUSION

Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome. Video Abstract.

Advanced Strategies of Drug Delivery via Oral, Topical, and Parenteral Administration Routes: Where Do Equine Medications Stand?

While the global market for veterinary products has been expanding rapidly, there is still a lack of specialist knowledge of equine pharmaceutics. In many cases, the basic structure of the gastrointestinal tract (GIT) and integumentary system of the horse shares similarities with those of humans. Generally, the dosage form developed for humans can be repurposed to deliver equine medications; however, due to physiological variation, the therapeutic outcomes can be unpredictable. This is an area that requires more research, as there is a clear deficiency in literature precedence on drug delivery specifically for horses. Through a careful evaluation of equine anatomy and physiology, novel drug delivery systems (NDDSs) can be developed to adequately address many of the medical ailments of the horse. In addition to this, there are key considerations when delivering oral, topical, and parenteral drugs to horses, deriving from age and species variation. More importantly, NDDSs can enhance the duration of action of active drugs in animals, significantly improving owner compliance; and ultimately, enhancing the convenience of product administration. To address the knowledge gap in equine pharmaceutical formulations, this paper begins with a summary of the anatomy and physiology of the equine gastrointestinal, integumentary, and circulatory systems. A detailed discussion of potential dosage-form related issues affecting horses, and how they can be overcome by employing NDDSs is presented.

Characterisation of faecal microbiota in horses medicated with oral doxycycline hyclate

BACKGROUND

Antimicrobial-associated diarrhoea is a common adverse effect of antimicrobial treatment in horses and has been reported following the administration of oral doxycycline. The administration of antimicrobials has also been associated with changes in the equine intestinal microbiota diversity yet has not been explored under doxycycline treatment.

OBJECTIVES

To describe the dynamics of the faecal microbial diversity following a 5-day oral administration of doxycycline in healthy horses with Streptococcus zooepidemicus infected tissue chambers.

STUDY DESIGN

Experimental prospective cohort study in a single horse group.

METHODS

Seven healthy adult horses with S. zooepidemicus infected tissue chambers received oral doxycycline at 10 mg/kg q 12 h for 5-days following the tissue chamber inoculation. Faeces were collected prior to the tissue chamber inoculation and until 28-days post inoculation. Faecal microbiota was characterised by high throughput sequencing of the V4 region of the 16S rRNA gene on the Illumina MiSeq sequencing platform. Bioinformatic analysis was performed with Mothur and statistical analysis were conducted on R Studio.

RESULTS

A significant decrease in alpha diversity, characterised by a decrease of richness and diversity, and a decrease in beta diversity, characterised by changes in relative abundance, occurred after initiation of and during the administration of doxycycline. A decrease in Verrucomicrobia and increase in Firmicutes:Bacteroidetes ratio occurred following the initiation of treatment, with a return to initial Firmicutes:Bacteroidetes ratio during the treatment. It took 23 days after discontinuing the treatment for the faecal microbiota to return close to the initial state.

MAIN LIMITATIONS

Lack of control population within the study.

CONCLUSIONS

Transitory intestinal dysbiosis occurs under oral administration of doxycycline in horses.

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

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

Saccharomyces cerevisiae fermentation product improves robustness of equine gut microbiome upon stress

Introduction

Nutritional and environmental stressors can disturb the gut microbiome of horses which may ultimately decrease their health and performance. We hypothesized that supplementation with a yeast-derived postbiotic (Saccharomyces cerevisiae fermentation product-SCFP) would benefit horses undergoing an established model of stress due to prolonged transportation.

Methods

Quarter horses (n = 20) were blocked based on sex, age (22 ± 3 mo) and body weight (439 ± 3 kg) and randomized to receive either a basal diet of 60% hay and 40% concentrate (CON) or the basal diet supplemented with 21 g/d Diamond V TruEquine C (SCFP; Diamond V, Cedar Rapids, IA) for 60 days. On day 57, horses were tethered with their heads elevated 35cm above wither height for 12 h to induce mild upper respiratory tract inflammation. Fecal samples were collected at days 0, 28, and 56 before induction of stress, and at 0, 12, 24, and 72 h post-stress and subjected to DNA extraction and Nanopore shotgun metagenomics. Within sample (alpha) diversity was evaluated by fitting a linear model and between sample (beta) diversity was tested with permutational ANOVA.

Results

The SCFP stabilized alpha diversity across all time points, whereas CON horses had more fluctuation (P < 0.05) at 12, 24, and 72 h post-challenge compared to d 56. A significant difference between CON and SCFP was observed at 0 and 12 h. There was no difference in beta-diversity between SCFP and CON on d 56.

Discussion

Taken together, these observations led us to conclude that treatment with SCFP resulted in more robust and stable microbial profiles in horses after stress challenge.

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.

Homeostasis of the Intestinal Mucosa in Healthy Horses-Correlation between the Fecal Microbiome, Secretory Immunoglobulin A and Fecal Egg Count

The defensive function of the intestinal mucosa depends both on the ability to secrete immunoglobulin A and communication with the mucus microbiome. In horses, the functioning of this system is also influenced by the presence of nematode eggs. Feces collected from healthy horses were examined to determine the fecal egg count, immunoglobulin A level (ELISA), microbiome composition (Next-Generation Sequencing, NGS, V3−V4 and V7−V9 hypervariable regions of the 16S rRNA gene analysis and short-chain fatty acid (SCFA) production ((high-performance liquid chromatography, HPLC). In the taxonomic analysis within the phylum, the following order of dominance was found: Firmicutes, Bacteroidota, Verrucomicrobiota and Fibrobacterota. The coefficient of phylogenetic diversity of the microbiome positively correlated with both secretory immunoglobulin A (SIgA) [μg/g of feces] (p = 0.0354, r = 0.61) and SIgA [μg/mg of fecal protein] (p = 0.0382, r = 0.6) and with the number of Cyathostomum eggs (p = 0.0023, r = 0.79). Important components of the key microbiome in horses, such as phylum Proteobacteria and species Ruminococcus flavefaciens, were positively correlated with the fecal SIgA (p < 0.05). All the obtained results indicate the existence of significant relationships between the host response (SIgA production) and composition and SCFA production in the microbiome as well as the presence of small strongyles in the digestive tract of horses.

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes

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 taxa are negatively associated with cardiovascular capacity. Conversely, more complex and functionally diverse microbiomes are associated with higher glucose concentrations and reduced accumulation of long-chain acylcarnitines and non-esterified fatty acids in plasma, suggesting increased ß-oxidation capacity in the mitochondria. In line with this hypothesis, more fit athletes show upregulation of mitochondrial-related genes involved in energy metabolism, biogenesis, and Ca²⁺ cytosolic transport, all of which are necessary to improve aerobic work power, spare glycogen usage, and enhance cardiovascular capacity. The results identify an associative link between endurance performance and gut microbiome composition and gene function, laying the basis for nutritional interventions that could benefit horse athletes.

An integrated gene catalog of the gut microbiome in elite endurance horses is build. The holo-omics analyses identify an associative link between endurance performance and gut microbiome composition and gene function.

Gut health of horses: effects of high fibre vs high starch diet on histological and morphometrical parameters

Background

The conventional feeding management of horses is still characterized by high starch and low fibre diets, which can negatively affect horse’s gastrointestinal health. Thus, the aim of this study was to compare the effects of a high-starch (HS) vs. a high-fibre (HF) diet on gut health in horses. A total of 19 Bardigiano horses destined for slaughter and aged 14.3 ± 0.7 months were randomly allotted to two dietary groups: HS (5 fillies and 4 colts,) and HF group (7 fillies and 3 colts). They received the same first-cut meadow hay but different complementary feeds for 72 days: HS group was fed 8 kg/animal/day of a starch-rich complementary feed while HF group was fed 3.5 kg/animal/day of a fibre‐rich complementary feed. At slaughter, stomachs were separated and washed for the evaluation of the glandular and squamous regions. Also, duodenum, jejunum, ileum, apex of the caecum, sternal flexure, pelvic flexure, right dorsal colon, rectum and liver were excised and submitted to histomorphometrical evaluation.

Results

The glandular region of HS group presented more severe gastric mucosa lesions compared to the HF group (P = 0.006). Moreover, a statistical tendency (P = 0.060) was found for the squamous region, presenting a higher score in HS than HF diet. Regarding morphometry, in jejunum villus height to crypt depth (Cd) ratio was influenced by sex, being greater in males than in females (P = 0.037) while in ileum Cd depended on interaction between sex and diet, being greater in males of HS group (P = 0.029). Moreover, in the duodenum and right dorsal colon the severity of the inflammation depended on sex (P = 0.024 and 0.050), being greater in females than in males. On the contrary, in the jejunum and in the pelvic flexure, inflammation was influenced by diet, being more severe in HS than in HF group (P = 0.024 and 0.052).

Conclusions

These results suggested that HS diet provoked more severe mucosa lesions in the glandular region of the stomach and a higher inflammation both in the jejunum and pelvic flexure. The present study can represent a starting point for further investigations on gut health in horses.

The diversity analysis and gene function prediction of intestinal bacteria in three equine species

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) was significantly different (P < 0.05) between the same species in the two wildlife parks, but neither the intestinal bacterial diversity index (Shannon) nor the community composition were significantly different (P > 0.05). The bacterial abundance index (Chao1) was significantly higher in MA than SP (P < 0.05) and highly significantly higher than PZ (P < 0.01); the bacterial diversity index (Shannon) was higher in MA than PZ, but there was no significant difference, but both MA and PZ were significantly higher than SP (P < 0.05). Moreover, the intestinal bacterial community composition was significantly different among the three equine species (P = 0.001). The dominant bacterial phyla for SP, MA, and PZ were Firmicutes and Bacteroidota; among them, the bacterial family with the highest relative abundance was Lachnospiraceae and the bacterial genus was Rikenellaceae_RC9_gut_group. Analysis of the metabolic gene functions of intestinal bacteria revealed that the highest relative abundance at Pathway level 2 was for global and overview maps; at Pathway level 3, the highest relative abundance was for biosynthesis of secondary metabolites. In sum, the intestinal bacterial community composition and diversity of the above three equine species differed significantly, but their metabolic gene functions were similar. Moreover, the results of this manuscript fill the gap in the study of intestinal bacterial diversity in SP, MA, and PZ. It also provides a reference for the study of the dominant bacteria in the intestinal microorganisms of these three equine species and the discovery of novel functional genes.

Feeding a Saccharomyces cerevisiae Fermentation Product (Olimond BB) Does Not Alter the Fecal Microbiota of Thoroughbred Racehorses

Simple Summary

Saccharomyces cerevisiae fermentation products (SCFP) are feed supplements and are widely used in animal nutrition to promote health. The biological effects of SCFP are based on prebiotic mechanisms that directly influence the microbial community of the gut microbiome or postbiotic factors that directly interact with host cells. To show whether the immunomodulatory effects of SCFP feeding are due to an altered composition of gut microbiota, we analyzed the fecal microbiota of racehorses. Horses were fed either the SCFP (Olimond BB) or a placebo product for six weeks, and fecal samples were collected for 16S rRNA gene sequencing. During this period, SCFP feeding only subtly affected the fecal microbiota in bacterial composition and diversity. SCFP and placebo horses differed significantly in the fecal bacterial diversity directly after intramuscular influenza vaccination. Altogether, the findings argue against a strong prebiotic effect of SCFP in racehorses. In contrast, the modulation of vaccine- and host-induced alterations of the microbiome suggests that the main effects of SCFP are due to contained or induced postbiotic components.

Abstract

Feed supplements such as Saccharomyces cerevisiae 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, n = 6) or placebo pellets (PLA, n = 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 feeding period. Rather, the individual animal had the highest impact on fecal microbiota composition. OLI and PLA horses displayed the same changes in numbers of blood leukocyte subpopulations over time. One day after a booster vaccination against equine influenza during the feeding period, the alpha diversity of fecal microbiota of PLA horses was significantly higher compared to OLI horses. This suggests that SCFP feeding altered the vaccination-induced spectrum of released mediators, potentially affecting gut microbiota. The overall non-consistent findings argue against a strong prebiotic effect of Olimond BB on the microbiota in racehorses. Fecal microbiota differences between the groups were also noticed outside the feeding period and, hence, are most likely not caused by the SCFP additive.

Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations

Domesticated horses live under different conditions compared with their extinct wild ancestors. While housed, medicated and kept on a restricted source of feed, the microbiota of domesticated horses is hypothesized to be altered. We assessed the fecal microbiome of 57 domestic and feral horses from different locations on three continents, observing geographical differences. A higher abundance of eukaryota (p < 0.05) and viruses (p < 0.05) and lower of archaea (p < 0.05) were found in feral animals when compared with domestic ones. The abundance of genes coding for microbe-produced enzymes involved in the metabolism of carbohydrates was significantly higher (p < 0.05) in feral animals regardless of the geographic origin. Differences in the fecal resistomes between both groups of animals were also noted. The domestic/captive horse microbiomes were enriched in genes conferring resistance to tetracycline, likely reflecting the use of this antibiotic in the management of these animals. Our data showed an impoverishment of the fecal microbiome in domestic horses with diet, antibiotic exposure and hygiene being likely drivers. The results offer a view of the intestinal microbiome of horses and the impact of domestication or captivity, which may uncover novel targets for modulating the microbiome of horses to enhance animal health and well-being.

Li Ang et al. present an investigation of feral and domesticated horse gut microbiomes across three continents. Their results provide new insight into how changes in horse lifestyle are reflected in the resident gut microbiome.

Horses as a source of bioactive fecal strains Enterococcus mundtii

Bacteriocin-producing bacteria with probiotic character are known as nutritional supplements mainly for livestock. Among those beneficial bacteria we also found enterococci. Because the species strains Enterococcus mundtii also can produce bacteriocins, this study was focused on fecal strains E. mundtii from horses and their bioactivity with a view to their possible future use in breeding. Rectal removal from 47 horses (40 mares and 7 stallions), the Norik breed from Muráň were sampled in eastern Slovakia during November 2019 year. Horses age ranged from five months up to 23 years. Using MALDI-TOF mass spectrometry and 16S rRNA sequences analysis, 14 strains were allotted to the species E. mundtii. Bacteriocin substances produced by the strains EMKD 38/1, EMKD 40/2, EMKD 34/2 and EMKD 41/3 showed inhibitory activity against the most susceptible (principal) indicator strain Enterococcus avium EA5 and against listeriae as well (inhibitory activity from 100 up to 1 600 AU/mL). Only strain EMKD 41/3 possess Ent P and Mundticin KS genes and showed the broadest inhibitory activity. Ent B gene possessing strain EMKD 24/1 inhibited a growth of only indicator strain EA5. Identified E. mundtii tolerate low pH 3 and oxgall/bile. They were hemolysis, gelatinase and DNase negative and mostly susceptible to clinical antibiotics which are properties requested for application potential of strain. Substance from the strain with the broadest antimicrobial spectrum showed its practical/application potential, e.g. for optimizing the host microbiota which is important regarding the maintenance of animal`s health status.

Caecal microbiota in horses with trigeminal‐mediated headshaking

Background

Trigeminal‐mediated headshaking (TMHS) in horses is a form of neuropathic pain of undetermined cause that often results in euthanasia. The role of microbiota in TMHS has not been investigated in diseased horses.

Objective

To investigate if gastrointestinal microbiota in the cecum is different in horses with TMHS compared to a control population, during a summer season with clinical manifestations of disease.

Animals

Ten castrated horses: five with TMHS and five neurologically normal controls.

Methods

All horses were sourced from our institution and kept under the same husbandry and dietary conditions. All horses were fed orchard grass hay for 30 days and then were euthanized due to chronic untreatable conditions including TMHS and orthopedic disease (control group). Caecal samples for microbiota analysis were collected within 20 min after euthanasia. Sequencing was performed using an Illumina MiSeq platform and the microbiome was analyzed.

Results

The caecal microbiota of horses with TMHS was similar to control horses in terms of diversity but differed significantly with Methanocorpusculum spp. having higher abundance in horses with TMHS. 

Conclusions and clinical importance

Methanocorpusculum spp. was more abundant in the cecum of horses with TMHS. However, its role in disease is unknown. Furthermore, it could also represent an incidental finding due to our small population size.

Humans have intestinal bacteria that degrade the plant cell walls in herbivores

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 large intestine, in which fermentation occurs. The digestive process of horses is similar to that of humans, and many of the intestinal bacteria found in horses that degrade plants are also found in humans. Therefore, it is thought that humans also obtain a certain amount of energy from cell wall-derived dietary fiber. However, the intake of dietary fiber by modern humans is low; thus, the amount of calories derived from indigestible plant fiber is considered to be very low. Cellulose in the plant cell wall is often accompanied by hemicellulose, pectin, lignin, suberin, and other materials. These materials are hard to degrade, and cellulose is therefore difficult for animals to utilize. If the cell wall can be degraded to some extent by cooking, it is thought that humans can obtain calories from cell wall-derived dietary fiber. If humans can use the calories from the cell wall for their diet, it may compensate for human food shortages.

Assessment on In Vitro Probiotic Attributes of Lactobacillus plantarum Isolated From Horse Feces

This study was designed to assess in vitro probiotic attributes of potent bacterium isolated from the feces of healthy horse. Initially, a total of eight bacteria were isolated from the feces and evaluated their antibacterial activities against indicator bacterial pathogens using agar well diffusion assay. Results showed significant (P < .05) antibacterial property of Lactobacillus plantarum strain LF4 against pathogens tested with maximum growth inhibitory activity of 320.16 ± 3.4 AU/mL against Staphylococcus aureus. Further, in vitro probiotic properties of strain LF4 were determined using standard methodologies. Strain LF4 maintained its viability towards acidic condition (pH 2.0) and simulated gastric juice (pH 2.0) with total cell counts of 1.6 ± 0.18 and 1.7 ± 0.18 log cfu/mL, respectively. Moreover, the strain was observed resistant to oxgall (0.5% w/v) up to 36 hours. The isolate showed significant (P < .05) hydrophobicity property (60.3 ± 1.6%), auto-aggregation trait (41.31 ± 1.5%), and moderate proteolytic activity. Strain LF4 revealed significant (P < .05) rate of DPPH scavenging (15.3 ± 1.3-69.7 ± 1.3%) and hydroxyl radical scavenging (11.3 ± 1.3 to 56.4 ± 1.3%) in a concentration dependent manner. Additionally, the isolate was observed susceptible to all the conventional antibiotics tested, thereby indicating its safer utilization. In conclusion, findings suggested the colossal applications of L. plantarum strain LF4 as an ideal probiotic bacterium in equine industries.

A review of the resistome within the digestive tract of livestock

Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.

Gut Microbiota Manipulation in Foals-Naturopathic Diarrhea Management, or Unsubstantiated Folly?

Diarrhea in foals is a problem of significant clinical and economic consequence, and there are good reasons to believe microbiota manipulation can play an important role in its management. However, given the dynamic development of the foal microbiota and its importance in health and disease, any prophylactic or therapeutic efforts to alter its composition should be evidence based. The few clinical trials of probiotic preparations conducted in foals to date show underwhelming evidence of efficacy and a demonstrated potential to aggravate rather than mitigate diarrhea. Furthermore, recent studies have affirmed that variable but universally inadequate quality control of probiotics enables inadvertent administration of toxin-producing or otherwise pathogenic bacterial strains, as well as strains bearing transferrable antimicrobial resistance genes. Consequently, it seems advisable to approach probiotic therapy in particular with caution for the time being. While prebiotics show initial promise, an even greater scarcity of clinical trials makes it impossible to weigh the pros and cons of their use. Advancing technology will surely continue to enable more detailed and accurate mapping of the equine adult and juvenile microbiota and potentially elucidate the complexities of causation in dysbiosis and disease. In the meantime, fecal microbiota transplantation may be an attractive therapeutic shortcut, allowing practitioners to reconstruct a healthy microbiota even without fully understanding its constitution.

Changes in the Fecal Microbiota Associated with a Broad-Spectrum Antimicrobial Administration in Hospitalized Neonatal Foals with Probiotics Supplementation

Simple Summary

Post-antibiotic intestinal dysbiosis leads to an overall reduction in bacterial and functional diversity, along with a minor resistance against pathogens. The study aimed to determine the changes on the fecal microbiota in hospitalized neonatal foals administered with broad-spectrum antimicrobials and supplemented probiotics. Fecal samples were collected at hospital admission, at the end of the antimicrobial treatment and at discharge. Seven foals treated with intravenous ampicillin and aminoglycosides for a mean of seven days were included. The results suggest that the fecal microbiota of neonatal foals rapidly returns to a high diversity after treatment. While the findings need to be confirmed in a larger population, the study suggests that in foals, the effect of antimicrobials may be strongly influenced by the changes that occur over time in the developing gut microbiota. Of note, the findings are influenced by the use of probiotics, and whether the changes would be consistent in antimicrobial-administered but not supplemented foals remains to be elucidated.

Abstract

There is a wide array of evidence across species that exposure to antibiotics is associated with dysbiosis, and due to their widespread use, this also raises concerns also in medicine. The study aimed to determine the changes on the fecal microbiota in hospitalized neonatal foals administered with broad-spectrum antimicrobials and supplemented probiotics. Fecal samples were collected at hospital admission (Ta), at the end of the antimicrobial treatment (Te) and at discharge (Td). Feces were analysed by next-generation sequencing of the 16S rRNA gene on Illumina MiSeq. Seven foals treated with IV ampicillin and amikacin/gentamicin were included. The mean age at Ta was 19 h, the mean treatment length was 7 days and the mean time between Te and Td was 4.3 days. Seven phyla were identified: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, TM7 and Verrucomicrobia. At Ta, Firmicutes (48.19%) and Proteobacteria (31.56%) were dominant. The alpha diversity decreased from Ta to Te, but it was the highest at Td. The beta diversity was higher at Ta than at Te and higher at Td than at Te. An increase in Akkermansia over time was detected. The results suggest that the intestinal microbiota of neonatal foals rapidly returns to a high diversity after treatment. It is possible that in foals, the effect of antimicrobials is strongly influenced or overshadowed by the time-dependent changes in the developing gut microbiota.

A Standard Scale to Measure Equine Keeper Status and the Effect of Metabolic Tendency on Gut Microbiome Structure

Simple Summary

Horses with different metabolic tendencies are anecdotally referred to as “easy” or “hard” keepers. Easy keepers tend to gain weight easily while hard keepers require extra feed to maintain condition. Both easy and hard keeper horses carry a managerial and financial burden which can be a dissuading factor for horse shoppers. This research uses energy intake/need and body condition to develop a standard Equine Keeper Status Scale (EKSS) for assigning keeper status. The microbiome compositions based on EKSS assignments are then compared to explore microbiome differences based on metabolic tendencies of each group. The EKSS can be used by owners to accurately assess their horses’ metabolic tendencies and make improved feeding decisions to meet their horses’ needs. Understanding microbiome differences between easy, medium and hard keeper horses points to potential microbial roles in these metabolic tendencies.

Abstract

Thriftiness in horses has been associated with more efficient nutrient harvesting in digestion, absorption and/or utilization, but the relative contribution of the gut microbiome to host metabolic tendency is not well understood. Recognizing the unreliability of owner reported assignment of keeper status, this research describes a novel tool for calculating whether a horse is an easy (EK) or hard (HK) keeper and then characterizes microbiome differences in these groups. The Equine Keeper Status Scale (EKSS) was developed and validated based on data gathered from 240 horses. Estimates of dietary energy intakes and requirements to achieve the optimal BCS score of 5 were used in EKSS assignments. Sixty percent of owners’ characterizations disagreed with EKSS identified keeper assignments. Equine fecal 16S rRNA profiles (n = 73) revealed differences in α and β diversities and taxa abundances based on EKSS assignments. EK communities had more Planctomycetes and fewer Euryarcheaota, Spirochaetes and Proteobacteria than HK indicating functional differences in nutrient harvesting between groups. Differences in the gut microbiomes of horses based on keeper assignment point to host/microbial interactions that may underlie some differences in metabolic tendency. The EKSS enables robust, repeatable determination of keeper status which can be used by researchers and horse owners.

Inflammation-Associated Microbiota Composition Across Domestic Animals

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 microbiota during health and in the context of naturally occurring diseases. This review compiles microbiome genomic data across domestic species and highlights a common occurrence of gut microbiome dysbiosis during idiopathic intestinal inflammation in multiple species, including dogs, cats, horses, cows, and pigs. Current microbiome data obtained from animals with intestinal inflammation are mostly limited to taxonomical analyses in association with broad clinical phenotype. In general, a pathogen or pathosymbiont were not detected. Rather, functional potential of the altered microbiota has been suggested to be one of the key etiologic factors. Among the domestic species studied, canine analyses are currently the most advanced with incorporation of functional profiling of microbiota. Canine IBD parallels features of the disease in humans, thus canines represent a strong natural model for human IBD. While deeper analyses of metagenomic data, coupled with host molecular analyses are needed, comparative studies across domestic species can reveal shared microbial alterations and regulatory mechanisms that will improve our understanding of intestinal inflammation in both animals and humans.

Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México

Baird's tapir (Tapirus bairdii) is the largest native terrestrial mammal in the Neotropics, which is endangered primarily as a consequence of habitat loss and overhunting. Baird's tapir is predominantly nocturnal and exists at low densities which complicates field studies. Baird's tapir is a large-bodied herbivore that plays a key role in maintaining healthy tropical forests through seed dispersal in its feces. Studies of gut microbiome are essential and valuable to assess the health status of the host and the interaction with the environment. In this study, we collected fresh fecal samples of T. bairdii to analyze its gut microbiome during the rainy and dry seasons in the Calakmul region, which is a critical rainforest conservation area in Mexico. The results of a high-throughput 16S rDNA gene sequencing approach suggest that the fecal microbiome of Baird's tapir has no significant differences in composition among seasons. The most common phyla were Firmicutes, Bacteroidetes, Proteobacteria, Kiritimatiellaeota, and Spirochaetes. This study suggests that the stability of the fecal microbiome is related to similar feeding strategies throughout the year, and emphasizes the value of tapir in seed dispersal (and associated microbes) to the well-conserved forests of the Greater Calakmul region as biodiversity hotspots for conservation.