Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA)

Comparative Analysis of Bacterial Diversity between the Liquid Phase and Adherent Fraction within the Donkey Caeco-Colic Ecosystem

Donkey hindgut is an enlarged fermentative chamber that harbors a highly complex and extremely abundant community of anaerobic bacteria. It can be divided into two different ecological sites: liquid (Lq) phase and adherent fraction (Ad) colonized by bacteria. However, the Ad bacteria have not previously been specifically collected or directly compared with the Lq bacteria. In the present study, the digesta collected from the caecum, ventral colon and dorsal colon of nine Dezhou donkeys was separated into Lq and Ad fractions. The bacterial community structure was comparatively determined using 16S rRNA gene sequences by Illumina MiSeq. The Ad bacteria had a higher bacterial diversity than Lq bacteria due to the higher Chao and ACE index (p < 0.05). The predominant bacteria at the phylum level were Firmicutes (55.4~74.3%) and Bacteroidota (13.7~32.2%) for both the Lq and Ad fraction. The relative abundance of Bacteroidota, Spirochaetota, Fibrobacterota and Patescibacteria in the Ad fraction was greater than Lq (p < 0.05), suggesting that bacteria associated with feed particles were mainly responsible for plant fiber degradation. At the genus level, the abundance of Lactobacillus in Lq was greater than that in the Ad fraction (p < 0.05), indicating that the bacteria in the Lq fraction were better at hydrolyzing readily fermentable carbohydrates. PICRUSt showed that the activities of enzymes related to fiber degradation in the Ad fraction were also greater than Lq. In addition, the hindgut region also had a significant effect on the bacterial community composition. The relative abundance of Rikenellaceae_RC9_gut_group, Clostridium_sensu_stricto_1, Christensenellaceae_R-7_group and norank_Bacteroidales_BS11_gut_group was increased (p < 0.05) along the donkey hindgut. In summary, the present study provides evidence that bacteria adherent to plant biomass were different to those in the liquid phase within the donkey caeco-colic digesta, and bacteria associated with feed particles may mainly be responsible for plant fiber degradation.

Effects of Differences in Fibre Composition and Maturity of Forage-Based Diets on the Microbial Ecosystem and Its Activity in Equine Caecum and Colon Digesta and Faeces

Simple Summary

Horses are herbivores and forage-based diets are a natural choice for them. Traditionally, horse diets have included a large portion of cereals and have been associated with different intestinal problems. Feeding more forage and less concentrate has been shown to promote both physical and mental health and performance in horses. However, the nutritional quality of forage can differ greatly. This study compared the effect of two different forage diets and the more conventional forage and concentrate diets, on the hindgut microorganisms and the environment. No differences were found between the three diets in the concentration of total bacteria, fungi and protozoa, of cellulose-utilising bacteria or in the concentration of short-chain fatty acids. It can be concluded that a forage diet which fulfils the energy and protein requirements without having to add starch rich concentrate can benefit hindgut health. In addition, further studies on plant-fibre and forage diets for horses are of great importance for horse feeding, for advisors, veterinarians and for the diet formulations industry.

Abstract

Fibrous feeds are essential for horses. When developing feeding regimens promoting health and performance, we need to understand the digestion of plant cell walls and the functioning of the hindgut microbial ecosystem. Our objective was to investigate the effect of grass fibre maturity and legume forage on the hindgut microbiota and its activity. Six caecum and colon fistulated geldings were fed three diets differing in fibre composition: concentrate and late harvested grass haylage (35:65 energy ratio) (C); early and late harvested grass haylage (80:20) (G); lucerne and late harvested grass haylage (80:20) (L) for 28 days in a Latin-square design. No differences were measured in total bacteria concentrations, fungi and protozoa numbers nor in cellulolytic bacteria concentrations between the diets. Short-chain fatty acid concentrations did not differ between diets, but a lower (acetate + butyrate)/propionate ratio when the horses were fed Diet C, compared to G and L, was observed, suggesting lower fibrolytic and higher amylolytic activity. The pH increased when the horses were fed Diet L and decreased when fed C and G from caecum to faeces. The buffering capacity (BC) of hindgut digesta was five to fifteen-fold higher than that of the feeds, suggesting a decreased effect of feed BC as digesta travelled through the digestive tract. In conclusion, an early harvested forage opens up the possibility for forage-only diets, providing high energy without the negative effects of concentrate.

The pelvic flexure separates distinct microbial communities in the equine hindgut

As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.

Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme

Obesity is a major health concern in many domesticated equids animals since it is related to metabolic abnormalities such as insulin dysregulation, hyperlipidaemia or laminitis. Ponies especially are known as "easy keepers" and are often affected by obesity and its related metabolic disorders. Research in the last decade indicated that the intestinal microbiota may play an important role in the development of obesity, at least in humans. Therefore, the objective of our study was to characterize changes in the faecal microbiota during a two-year weight gain programme which compared ponies and warmblood horses. For this purpose, 10 Shetland ponies and ten warmblood horses were fed a ration which provided 200% of their maintenance energy requirement over two years. Feed intake, body weight, body condition and cresty neck score were recorded weekly. At three standardized time points faecal samples were collected to characterize the faecal microbiota and its fermentation products such as short chain fatty acids and lactate. Next generation sequencing was used for the analysis of the faecal microbiota. During body weight gain the richness of the faecal microbiota decreased in ponies. Besides changes in the phylum Firmicutes in ponies that were already described in human studies, we found a decrease of the phylum Fibrobacteres in horses and an increase of the phylum Actinobacteria. We were also able to show that the phylum Fibrobacteres is more common in the microbiota of horses than in the microbiota of ponies. Therefore, the fibrolytic phylum Fibrobacteres seems to be an interesting phylum in the equine microbiota that should receive more attention in future studies.

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

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

Interaction between the sequence of feeding of hay and concentrate, and boiling of barley on feed intake, the activity of hydrolytic enzymes and fermentation in the hindgut of Arabian mares

The interaction between the sequence of feeding of hay and concentrate and the hydrothermal processing of barley in alleviating concentrate effects on intake, and hindgut fermentation in horses was tested. Six Arabian mares (4-10 years of age, 410 ± 35 kg body weight) were used to evaluate the effects of feeding sequence (FS) and type of barley (TB) on intake, and faecal volatile fatty acids (VFA), activities of α-amylase (AA: EC 3.2.1.1), carboxymethyl cellulase (CMCase: EC 3.2.1.4), microcrystalline cellulase (MCCase: EC 3.2.1.91) and general filter paper degrading activity (FPD). Mares were offered a ration of air-dried alfalfa and concentrate (70:30 as-fed) in four subsequent periods of 14 days including 8 days of adaptation and 6 days of sampling. In each period and each meal, mares received concentrate either 30 min after (HC) or 30 min before (CH) alfalfa hay. Barley was either milled or boiled in water. Rectal samples were grabbed directly from rectum once per period. Mares subjected to CH had higher dry matter intakes than mares under HC regime. The acetate:propionate ratio (A:P ratio) in rectal content was higher with CH than HC. The AA activity was higher under CH than under HC. Mares fed boiled barley had lower rectal concentrations of VFA and propionate and a higher A:P ratio than mares fed milled barley. Furthermore, the rectal content showed a higher MCCase activity but a lower AA activity when mares were fed boiled compared with milled barley. Interactions between FS and TB were observed with respect to CMCase activity, and concentrations of propionate and valerate. In conclusion, the present results suggest that both, feeding concentrate before hay and boiling the barley, might improve the hindgut environment in Arabian mares, and that the two measures were mostly additive and sometimes even synergistic.

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

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