Understanding the microbial fibre degrading communities & processes in the equine gut

Research Progress on Influencing Factors of Gastrointestinal Microbial Diversity in Equine

Microbiota in the gastrointestinal tract play a crucial role in nutrient digestion, health and so forth in equines. As the research attention on gut microbes has increased, several studies have investigated the composition of the gastrointestinal microbial flora in equines. This article reviews the effects of breed, age, intestinal site, nutritional management and diseases on the gastrointestinal microbiota of horses and donkeys, thus offering references for improving the gastrointestinal microecological environment in these animals and preventing and controlling disease occurrence in them.

Dietary supplementation of new-born foals with free nucleotides positively affects neonatal diarrhoea management

Foals commonly experience diarrhoea in the first weeks of life. Although this condition is rarely life-threatening, it can have significant health consequences. This study investigated whether new-born foals can benefit from a dietary supplement of nucleotides, as already demonstrated in other species. Dietary nucleotides have positive effects on rapidly proliferating tissues and are considered "semi-essential nutrients" since cells have only a limited capacity to synthesize these compounds. The aim of this study was to investigate whether providing foals with a dietary nucleotide supplementation, in the form of an oral paste, was able to affect diarrhoea incidence, systemic immunity, intestinal microbiota and volatile fatty acid production. Thirty new-born standardbred foals, from 3 different premises within the same area, were equally distributed between two groups: one group received an oral paste containing dietary nucleotides (NUCL group), while the other received a placebo paste (CTRL group). Faecal and blood samples were collected on days 1 and 35 after birth. No statistical differences in cytokines (TNF-α, IFN-γ, IL-6, IL-12) or faecal calprotectin levels were found between the two groups, suggesting that the level of nucleotide supplementation used in this study did not have significant effects on the systemic immune system and on the levels of faecal calprotectin. However, the NUCL group showed a lower relative frequency of number of days with diarrhoea (6.12% vs 13.33%; p < 0.001) and greater weight gain compared with the CTRL group (50.3 ± 5.65 kg vs 44.0 ± 8.65 kg; p < 0.05). Total volatile fatty acids, branched volatile fatty acids, acetic acid, propionic acid, butyric acid, succinic acid and iso-butyric acids in faecal samples were all higher in the NUCL group compared with the CTRL group. This outcome may explain an earlier establishment of a gut microbiota in the foals of the NUCL group that was closer to that typical of an adult horse, characterised by predominant fibrolytic populations. Volatile fatty acid production (especially butyric acid) has also been shown to correlate with the intestinal well-being of the horse, supporting the use of dietary nucleotide supplements for improved health and well-being in new-born foals. Although we noted no clear differences in the faecal microbial communities between the two groups, dietary nucleotide supplementation did appear to have a positive clinical outcome, reducing the number of days of diarrhoea and increasing the levels of volatile fatty acids.

In vitro assessment of horse-isolated strains of Lactobacillus acidophilus and Ligilactobacillus equi species for fecal microbiota modulation in horses

Horses are hindgut fermenters that harbor a complex intestinal microbiota (IM) which provides key enzymes aiding in the breakdown of complex carbohydrates present in their herbivorous diet. Therefore, these animals are deeply dependent on their IM for digestion and nutrition. Consequently, IM imbalances may result in alteration of fermentation patterns with impact on the animal health and the risk of disease. In this context, strategies for assisting the maintenance of a healthy IM in horses are of interest. However, there is limited research concerning the use of probiotics to improve hindgut fermentation and diet digestibility, with very few studies focusing on the use of lactobacilli strains from equine origin. Herein, we conducted independent fecal batch fermentations, using feces from "Asturcón" horses as inocula, added individually with four different lactobacilli strains (two strains of Lactobacillus acidophilus and two of Ligilactobacillus equi) isolated from this same horse breed. The impact on the gut microbiota composition was assessed by 16S rRNA gene profiling and the metabolic activity (production of short-chain fatty acids) by gas chromatography. The functionality of the lactobacilli strain was determined by monitoring in real-time gas production and determining changes in pH along incubation. L. acidophilus IPLA20127, promoted an increase in IM diversity and in the relative abundance of Lactobacillus genus, as well as higher butyric and valeric acid levels. This strain shows potential as probiotic supplement, without triggering acidification, nor promoting an increase of gas production or abrupt IM changes in our experimental model.

Influence of Saccharomyces cerevisiae CNCM I-1077 on the fecal pH, markers of gut permeability, fecal microbiota, and markers of systemic inflammation in sedentary horses fed a high-starch diet

Thirty mature Quarter Horse geldings were used in a completely randomized 32-d study to test the hypotheses that supplemental live Saccharomyces cerevisiaeCNCM; I-1077 improves apparent digestion, stabilizes the fecal pH, reduces gut permeability, maintains microbial communities, and decreases inflammation in horses fed a high-starch diet. Horses were stratified by body weight (BW), age, and body condition score (BCS) to one of two treatments: concentrate formulated with 2 g starch · kg BW-1 · meal-1 (control (CON); n = 15) or the same concentrate top-dressed with 25 g/d S. cerevisiae CNCM I-1077 (treatment (SC); n = 15; 8 × 108CFU). Horses were fed individually in stalls every 12 h. Between meals, horses were housed in dry lots with ad libitum access to water and Coastal bermudagrass hay. On days 0 and 32, BW and BCS were recorded, and blood was collected before feeding and 2, 8, 16, and 24 h postmeal on day 32 to analyze serum D-lactate. Fecal samples were collected on days 0, 16, and 32 at 8, 16, and 24 h postmeal for fecal pH and starch content. Intake and fecal production were recorded over 4 d to measure digestibility on days 28-31. Whole blood total bacterial counts and 16S fecal microbiota rRNA sequencing were performed at days 0, 16, and 32. Results revealed an increased ∆BW in SC horses compared with CON horses (P = 0.03), with no change in BCS (P = 0.97). D-lactate tended to be greater in SC horses on day 32 at 16 and 24 h postmeal compared with CON horses (P = 0.10). Concentrations of TNFα and LogCCL2 decreased from day 0 to day 32 regardless of dietary supplementation (P ≤ 0.02). Fold change of percent reads from day 0 in whole blood bacterial 16S rRNA did not differ between groups. Fecal starch was undetectable, and there were no differences in intake or apparent digestibility. Fecal pH tended (P = 0.07) to be lower in CON at 0 h on day 32 (6.03 ± 0.06) than on day 16 (6.14 ± 0.06). Additionally, pH tended (P = 0.09) to be lower in CON (6.03 ± 0.06) than in SC (6.16 ± 0.06) at 0 h on day 32. Supplementation of S. cerevisiae CNCM I-1077 maintained Bacteroidales and reduced acidosis-like bacteria like Streptococcus and potential pathogens like Enterobacteriaceae, Stenotrophomonas, and Rhodococcus at day 16 (P < 0.05). Furthermore, supplementation increased fibrolytic bacteria at day 32, such as Ruminococcus, Fibrobacter, and Succinivibrio (P < 0.05). These results indicate S. cerevisiae CNCM I-1077 increases BW and promotes a more diverse microbiome when horses are fed ad libitum hay and a high-starch concentrate.

Characterization of a novel multifunctional glycoside hydrolase family in the metagenome-assembled genomes of horse gut

The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discovered a hypothetical protein (595 amino acids). This protein exhibits potential CAZymes activity and has a lower similarity to CAZymes, we named it BfLac2275. We purified the protein using prokaryotic expression technology and studied its enzymatic function. The hydrolysis experiment of the polysaccharide substrate showed that the BfLac2275 protein has the ability to degrade α-lactose (156.94 U/mg), maltose (92.59 U/mg), raffinose (86.81 U/mg), and hyaluronic acid (5.71 U/mg). The enzyme activity is optimal at pH 5.0 and 30 ℃, indicating that the hypothetical protein BfLac2275 is a novel and multifunctional CAZymes in the glycoside hydrolases (GHs). These properties indicate that BfLac2275 has broad application prospects in many fields such as plant polysaccharide decomposition, food industry, animal feed additives and enzyme preparations. This study not only serves as a reference for exploring novel CAZymes encoded by gut microbiota but also provides an example for further studying the functional annotation of hypothetical genes in metagenomic assembly genomes.

Fibrobacter sp. HC4, a newly isolated strain, demonstrates a high cellulolytic activity as revealed by enzymatic measurements and in vitro assay

Despite their low quantity and abundance, the cellulolytic bacteria that inhabit the equine large intestine are vital to their host, as they enable the crucial use of forage-based diets. Fibrobacter succinogenes is one of the most important intestinal cellulolytic bacteria. In this study, Fibrobacter sp. HC4, one cellulolytic strain newly isolated from the horse cecum, was characterized for its ability to utilize plant cell wall fibers. Fibrobacter sp. HC4 consumed only cellulose, cellobiose, and glucose and produced succinate and acetate in equal amounts. Among genes coding for CAZymes, 26% of the detected glycoside hydrolases (GHs) were involved in cellulolysis. These cellulases belong to the GH5, GH8, GH9, GH44, GH45, and GH51 families. Both carboxymethyl cellulase and xylanase activities of Fibrobacter sp. HC4 were detected using the Congo red method and were higher than those of F. succinogenes S85, the type strain. The in vitro addition of Fibrobacter sp. HC4 to a fecal microbial ecosystem of horses with large intestinal acidosis significantly enhanced fibrolytic activity as measured by the increase in gas and volatile fatty acids production during the first 48 h. According to this, the pH decreased and the disappearance of dry matter increased at a faster rate with Fibrobacter sp. HC4. Our data suggest a high specialization of the new strain in cellulose degradation. Such a strain could be of interest for future exploitation of its probiotic potential, which needs to be further determined by in vivo studies.IMPORTANCECellulose is the most abundant of plant cell wall fiber and can only be degraded by the large intestine microbiota, resulting in the production of volatile fatty acids that are essential for the host nutrition and health. Consequently, cellulolytic bacteria are of major importance to herbivores. However, these bacteria are challenged by various factors, such as high starch diets, which acidify the ecosystem and reduce their numbers and activity. This can lead to an imbalance in the gut microbiota and digestive problems such as colic, a major cause of mortality in horses. In this work, we characterized a newly isolated cellulolytic strain, Fibrobacter sp. HC4, from the equine intestinal microbiota. Due to its high cellulolytic capacity, reintroduction of this strain into an equine fecal ecosystem stimulates hay fermentation in vitro. Isolating and describing cellulolytic bacteria is a prerequisite for using them as probiotics to restore intestinal balance.

Effects of lysine and threonine on milk yield, amino acid metabolism, and fecal microbiota of Yili lactating mares

The nutritional benefits of mare milk are attracting increasing consumer interest. Limited availability due to low yield poses a challenge for widespread adoption. Although lysine and threonine are often used to enhance protein synthesis and muscle mass in horses, their impact on mare milk yield and nutrient composition remains underexplored. This study investigated the effects of lysine and threonine supplementation on 24 healthy Yili mares, mares at day 30 of lactation, over a 120-day period. The mares were divided into control and three experimental groups (six mares each) under pure grazing conditions. The control group received no amino acid supplementation, while experimental groups received varying daily doses of lysine and threonine: Group I (40 g lysine + 20 g threonine), Group II (60 g lysine + 40 g threonine), and Group III (80 g lysine + 60 g threonine). Supplementation in Group II notably increased milk yield, while Groups I and II showed higher milk fat percentages, and all experimental groups exhibited improved milk protein percentages. Additionally, blood levels of total protein, albumin, triglycerides, and glucose were reduced. Detailed analyses from Group II at peak lactation (day 60) included targeted metabolomics and microbial sequencing of milk, blood, and fecal samples. Amino acid metabolomics assessed amino acid content in mare milk and serum, while 16S rRNA gene sequencing evaluated rectal microbial composition. The results indicated that lysine and threonine supplementation significantly increased levels of threonine and creatine in the blood, and lysine, threonine, glutamine, and alanine in mare milk. Microbial analysis revealed a higher prevalence of certain bacterial families and genera, including Prevotellaceae, p_251_o5, and Rikenellaceae at the family level, and unclassified_p_251_o5, Prevotellaceae_UCG_001, and Rikenellaceae_RC9_gut_group at the genus level. Multi-omics analysis showed positive correlations between specific fecal genera and amino acids in mare milk. For instance, Prevotellaceae_UCG_003, unclassified Bacteroidetes_BS11_gut_group, and Corynebacterium were positively correlated with lysine, while unclassified Prevotellaceae was positively correlated with alanine and threonine, and Unclassified_Bacteroidales_BS11_gut_group was positively correlated with glutamine. In summary, lysine and threonine supplementation in grazing lactating mares enhanced milk production and improved milk protein and fat quality. It is recommended that herders, veterinarians, and technicians consider amino acid content in the diet of lactating mares. The optimal supplementation levels under grazing conditions for Yili horses were determined to be 60 g lysine and 40 g threonine per day. Future research should explore the molecular mechanisms by which these amino acids influence milk protein and lipid synthesis in mare mammary epithelial cells.

Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution

Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.

Microbial community composition in the dung of five sympatric European herbivore species

The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid-Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non-ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non-ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non-ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.

Longitudinal effects of oral administration of antimicrobial drugs on fecal microbiota of horses

BACKGROUND

Antimicrobial drug-associated diarrhea (AAD) is the most common adverse effect in horses receiving antimicrobials. Little information on how oral administration of antimicrobials alters intestinal microbiota in horses is available.

OBJECTIVE

Investigate changes of the fecal microbiota in response to oral administration of antimicrobials.

ANIMALS

Twenty healthy horses.

METHODS

Prospective, longitudinal study. Horses were randomly assigned to 4 groups comprising 4 horses each: group 1 (metronidazole); group 2 (erythromycin); group 3 (doxycycline); group 4 (sulfadiazine/trimethoprim, SMZ-TMP); and group 5 (control). Antimicrobials were administered for 5 days. Fecal samples were obtained before (day 0) and at 1, 2, 3, 4, 5, 6, and 30 days of the study period. Fecal microbiota was characterized by high throughput sequencing of the V4 region of the 16S rRNA.

RESULTS

Horses remained healthy throughout the study. Richness and diversity in doxycycline, erythromycin, and metronidazole, but not SMZ-TMP groups, was significantly lower (P < .05) at multiple time points after administration of antimicrobials compared with samples from day 0. Main changes in the microbiota were observed during the time of antimicrobial administration (day 2-5; weighted and unweighted UniFrac PERMANOVA P < .05). Administration of erythromycin, doxycycline and, to a lesser extent, metronidazole produced a pronounced alteration in the microbiota compared with day 0 samples by decreasing the abundance of Treponema, Fibrobacter, and Lachnospiraceae and increasing Fusobacterium and Escherichia-Shigella.

CONCLUSIONS AND CLINICAL IMPORTANCE

Oral administration of antimicrobials alters the intestinal microbiota of healthy horses resembling horses with dysbiosis, potentially resulting in intestinal inflammation and predisposition to diarrhea.

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.

Effects of Concentrate Feeding Sequence on Growth Performance, Nutrient Digestibility, VFA Production, and Fecal Microbiota of Weaned Donkeys

In this study, effects on the growth performance, nutrient digestibility, volatile fatty acids (VFA) production, and fecal microbiota of weaned donkeys were observed using different concentrate feeding sequences. Fifteen healthy 6-month-old weaned male donkeys with a body weight of 117.13 ± 10.60 kg were randomly divided into three treatment groups, including group C1 (roughage-then-concentrate), group C2 (concentrate-then-roughage), and group C3 (total mixed ration, TMR). The experiment lasted 35 d. We measured nutrient digestion by the acid-insoluble ash method and analyzed the fecal microbiota of the weaned donkeys by high-throughput sequencing of 16s rRNA genes in the V3-V4 region. The results show that group C3 obtained the best growth performance, and the digestibility of crude protein (CP) and crude extract (EE) was significantly higher than that of group C1 (p < 0.05). Acetic acid, isobutyric acid, valeric acid, isovaleric acid, and caproic acid were notably different among all groups (p < 0.05). In addition, we observed that Firmicutes and Bacteroidetes were dominant in the fecal microbes of each group, and Firmicutes was significantly higher in group C3 (p < 0.05). At the genus level, the different genera were Treponema, Rikenellaceae-RC9-gut-group, Unidentified-F082, and Bacteroidales-RF16-group (p < 0.05). The prediction of fecal microbiota function by PICRUSt indicated that different feeding sequences had minimal impact on the function of the fecal microbiota, particularly on the high-abundance pathway. In summary, the concentrate feeding sequence changed the composition of the fecal microbe of weaned donkeys.