The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology

Changes in fecal microbiota during estrous cycle in healthy thoroughbred mares

Gut microbiota plays a crucial role in various physiological processes, including the regulation of the reproductive system and steroid sex hormones. Throughout the normal estrous cycle of healthy mares, the levels of estradiol-17β (E2) and progesterone (P4) in the blood exhibit periodic changes. To investigate the relationship between cyclic changes in steroid sex hormones and the gut microbiome of mares, we analyzed the fecal microbiota composition in healthy mares during the typical estrous cycle. Blood and fecal samples from five healthy mares were collected, E2 and P4 levels in serum were analyzed using radioimmunoassay (RIA), and the gut microbiome was analyzed by 16S rRNA sequencing. The overall richness and composition of the gut microbiota remained relatively stable during the normal estrous cycle in mares. The Linear Discriminant Analysis Effect Size analysis of the microbial composition during the follicular and luteal phases identified the Rhodococcus genus as differentially abundant. These findings indicate that the mare's gut microbiota's significant composition remains consistent throughout the estrous cycle. At the same time, specific low-abundance pathogenic bacteria exhibit changes that align with sexual hormonal fluctuations.

Current Understanding of Equine Gut Dysbiosis and Microbiota Manipulation Techniques: Comparison with Current Knowledge in Other Species

Understanding the importance of intestinal microbiota in horses and the factors influencing its composition have been the focus of many studies over the past few years. Factors such as age, diet, antibiotic administration, and geographic location can affect the gut microbiota. The intra- and inter-individual variability of fecal microbiota in horses complicates its interpretation and has hindered the establishment of a clear definition for dysbiosis. Although a definitive causal relationship between gut dysbiosis in horses and diseases has not been clearly identified, recent research suggests that dysbiosis may play a role in the pathogenesis of various conditions, such as colitis and asthma. Prebiotics, probiotics, and fecal microbiota transplantation to modulate the horse's gastrointestinal tract may eventually be considered a valuable tool for preventing or treating diseases, such as antibiotic-induced colitis. This article aims to summarize the current knowledge on the importance of intestinal microbiota in horses and factors influencing its composition, and also to review the published literature on methods for detecting dysbiosis while discussing the efficacy of gut microbiota manipulation in horses.

Metabolic changes before and after weaning in Dezhou donkey foals in relation to gut microbiota

Weaning is undoubtedly one of the most crucial stages in the growth and development of all mammalian animals, including donkey foals. Weaning is a dynamic and coordinated process of the body, which is closely associated with the health, nutrition, and metabolism of the host. Many studies have shown that the intestinal microbiota and serum metabolites of mammals exhibit different changes during lactation, weaning, and postweaning. However, the alterations in serum metabolites in donkey foals before and postweaning and the correlation between serum metabolites and intestinal microbiota are largely unknown. This study is based on the fecal 16S rRNA and serum metabolomes of Dezhou donkey foals. In total, 10 samples (fecal and serum) were collected during the following three stages: before weaning (F.M.1), during weaning (F.M.3), and postweaning (F.M.6). To study the alterations in intestinal microflora, serum metabolites, and their correlation before and postweaning. We found that with the growth and weaning progress of donkey foals, the intestinal microbiota of donkey foals underwent obvious changes, and the diversity of fecal bacteria increased (Chao1 and Shannon indexes). The main intestinal microbial flora of donkey foals include Bacteroides and Firmicutes. We found many microbiota that are associated with immunity and digestion in the postweaning group, such as Verrucomicrobiales, Clostridia, Oscillospiraceae, Akkermansia, and Rikenellaceae, which can be considered microbial markers for the transition from liquid milk to solid pellet feed. Clostridia and Oscillospiraceae can produce organic acids, including butyric acid and acetic acid, which are crucial for regulating the intestinal microecological balance of donkeys. Furthermore, the metabolome showed that the serum metabolites enriched before and postweaning were mainly related to arachidonic acid metabolism and riboflavin metabolism. Riboflavin was associated with the development of the small intestine and affected the absorption of the small intestine. We also found that the changes in the gut microbiome of the foals were significantly correlated with changes in serum metabolites, including lysophosphatidylcholine (LPC; 12,0) and positively correlated with Lachnoclostridium and Roseburia. To summarize, this study provides theoretical data for the changes in the intestinal microbiome and serum metabolism during the entire weaning period of donkey foals.

Comparison of Intestinal Microbiota of Blue Fox before and after Weaning

Intestinal flora plays an important role in maintaining the internal stability and health of the intestine. Currently, intestinal microbes are considered an important "organ" but are mostly ignored by people. This study evaluated the flora structure of each intestinal segment of blue foxes pre-weaning and explored the differences between the fecal flora and intestinal flora structure of each segment after weaning. Samples of intestinal contents from three blue foxes at 45 days of age (before weaning) and intestinal contents and feces samples from at 80 days (after weaning) were collected for 16s rRNA flora analysis. The species and distribution characteristics of microorganisms in different intestinal segments of blue foxes before and after weaning were different. Except for the rectum, the dominant flora of each intestinal segment of blue fox changed significantly after experiencing weaning, and the fecal flora structure of young fox at the weaning stage did not represent the whole intestinal flora structure but was highly similar to that of the colon and rectum. To sum up, the intestinal flora of blue foxes changed systematically before and after weaning. When performing non-invasive experiments, the microflora structure of the colon and rectum of blue foxes can be predicted by collecting fecal samples.

Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves

BACKGROUND

Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.

RESULTS

Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.

CONCLUSIONS

Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.

Transcriptomic signature related to poor welfare of sport horses

The improvement of horse welfare through housing conditions has become a real issue in recent years and have highlighted the detrimental effect of individual housing of horses on their health and behaviour. In this new study, we analysed the blood transcriptome of 45 sport horses housed individually that were previously examined for their behaviour and gut microbiota. We performed differential and regression analyses of gene expression, followed by downstream bioinformatic analyses, to unveil the molecular pathways related to the behavioural changes associated with welfare impairment in these sport horses. We found that aggressiveness towards humans was the behavioural indicator the most correlated to blood gene expression and that the pathways involved belonged mainly to systemic inflammation. In contrast, the correlations between genes, alert postures and unresponsiveness towards the environment were weak. When blood gene expression profiling was combined with faecal microbiota of a sub-population of horses, stereotypies came out as the most correlated to blood gene expression. This study shows that aggressiveness towards humans and stereotypies are behavioural indicators that covary with physiological alterations. Further studies are needed regarding the biological correlates of unresponsiveness to the environment and alert postures.

Out of the stable: Social disruption and concurrent shifts in the feral mare (Equus caballus) fecal microbiota

The disruption of animals' symbiotic bacterial communities (their microbiota) has been associated with myriad factors including changes to the diet, hormone levels, and various stressors. The maintenance of healthy bacterial communities may be especially challenging for social species as their microbiotas are also affected by group membership, social relationships, microbial transfer between individuals, and social stressors such as increased competition and rank maintenance. We investigated the effects of increased social instability, as determined by the number of group changes made by females, on the microbiota in free-living, feral horses (Equus caballus) on Shackleford Banks, a barrier island off the North Carolina coast. Females leaving their groups to join new ones had fecal microbial communities that were similarly diverse but compositionally different than those of females that did not change groups. Changing groups was also associated with the increased abundance of a several bacterial genera and families. These changes may be significant as horses are heavily dependent upon their microbial communities for nutrient absorption. Though we cannot identify the particular mechanism(s) driving these changes, to the best of our knowledge, ours is the first study to demonstrate an association between acute social perturbations and the microbiota in a free-ranging mammal.

Maternal and infantile gut mycobiome during the weaning period in free ranging Tibetan macaques (Macaca thibetana)

Gut microbiome is critical to the health of mammals. Many previous studies have revealed the gut bacterial microbiomes of mother and infant changed significantly during the weaning period. However, little is known concerning the gut mycobiome of wild primates. Here, we examined the variations on gut mycobiome between weaning and post-weaning for both mother and infant in wild-living Tibetan macaques (Macaca thibetana). Our results showed that the gut mycobiomes of mother and infant were dominated by two phyla Ascomycota and Basidiomycota. For both mother and infant, the ASV richness of gut mycobiome remained relatively steady from weaning to post-weaning periods, while the Shannon indexes increased significant in weaning compared to post-weaning periods. However, no significant difference between mother and infant ASV richness and Shannon indexes during weaning and post-weaning periods respectively. Compared to mothers, we found that much more known taxa of gut fungi were enriched in weaning or post-weaning periods of infants. In particular, we found that the dominant genus Aspergillus was enriched in infants during weaning period. Furthermore, we found that the relative abundance of plant pathogens were significantly higher in the post-weaning period than in the weaning period for infants. Our results indicated that weaning events could affect the gut mycobiome significantly for both mothers and infant in Tibetan macaques, which had a stronger effect on the gut mycobiome of infant monkeys than on their mothers.

Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning

Introduction

A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period.

Methods

A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period.

Results

In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01).

Discussion

Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.

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.

Environmental factors and gut microbiota: Toward better conservation of deer species

Thousands of microbial species inhabiting the animal gut, collectively known as the gut microbiota, play many specific roles related to host nutrient metabolism and absorption, immune regulation, and protection from pathogenic bacteria. Gut microbiota composition is affected by several internal and external factors, such as the host genotype, dietary intake, breeding environment, and antibiotic exposure. As deer species are important members for maintaining ecosystem balance, understanding the effects of multiple factors on the gut microbiota of deer species, particularly endangered ones, is crucial. In this review, we summarize and discuss the factors that significantly affect the gut microbiota of deer and present the impacts of these factors on microbial composition. In particular, we focused on the changes in gut microbiota due to dietary differences under different conditions, including seasonal changes, different geographical locations, and captivity, as well as weaning and pathogen disturbance. Understanding the correlations between gut microbiota composition and its driving factors is important for evaluating and improving the captive breeding environment for better conservation of endangered deer species, and reintroducing wild deer populations in the future.

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.

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.

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

As the initiation point of digestion, the oral microbiome is important in maintaining oral and systemic health. However, the composition of oral microbial communities and the influence of weaning on the oral microbiota of donkey foals remains poorly characterized. The present study used buccal swab samples to determine the changes in oral microbial communities occurring at the time of weaning. A total of 20 oral swab samples were collected from two groups: preweaning donkey foals (PreW group, n = 10) and postweaning donkey foals (PostW group, n = 10). The donkey oral microbiome was analyzed by 16S rRNA gene sequencing using Illumina MiSeq. This study is the first report of the donkey oral microbiome in association with weaning. Compared to the preweaning donkeys, the oral bacteria diversity in the postweaning donkeys was increased, with a higher Simpson index. Changes in the composition of the oral microbiota between the PreW and PostW groups were observed in the present study. At the phylum level, the relative abundance of Firmicutes and Myxococcota was significantly greater in the PostW than in the PreW group. At the genus level, the Gemella, unclassified_o__Lactobacillales, and Lactobacillus were increased in the postweaning donkeys. The donkeys’ oral microbial functions were predicted using PICRUSt, and the functions related to carbohydrate metabolic pathways were significantly enriched in the oral microbiome in the PostW donkeys. In summary, the current study provides a deeper insight into the oral microbiota changes during the weaning period, and the influence of weaning together with the documented changes in diversity and composition will help us to obtain a better understanding of their long-term health impact within the oral cavities of donkey foals. However, a major limitation of the present study was that the samples were obtained from different animals in the PreW and PostW groups, which may have resulted in variability among the different individuals. Further investigation is needed to monitor the shift in oral microbes in the same individuals during the weaning period.

Environmental enrichment changes rabbits' behavior, serum hormone level and further affects cecal microbiota

Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits' ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3-V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.

Gut Microbiota Implications for Health and Welfare in Farm Animals: A Review

Simple Summary

Farm animal health and welfare have been paid increasing concern in the world, which is generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators, such as stress-related hormone, cortisone, and norepinephrine. Gut microbiota as a “forgotten organ” has been reported for its great influence on the host phenotypes through the immune, neural, and endocrine pathways to affect the host health and behavior. In addition, fecal microbiota transplantation as a novel approach is applied to regulating the composition and function of the recipient farm animals. In this review, we summarized recent studies that gut microbiota influenced health, immunity, behavior, and stress response, as well as the progress of fecal microbiota transplantation in farm animals. The review will provide new insights into the measurement of farm animal health and welfare concerning gut microbiota, and the implication of fecal microbiota transplantation to improve productivity, health, and welfare. Above all, this review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Abstract

In the past few decades, farm animal health and welfare have been paid increasing concern worldwide. Farm animal health and welfare are generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators. The gut microbiota has been reported to have a great influence on host phenotypes, possibly via the immune processes, neural functions, and endocrine pathways, thereby influencing host phenotypes. However, there are few reviews regarding farm animals’ health and welfare status concerning the gut microbiota. In this point of view, (1) we reviewed recent studies showing that gut microbiota (higher alpha diversity, beneficial composition, and positive functions) effectively influenced health characteristics, immunity, behaviors, and stress response in farm animals (such as pigs, chickens, and cows), which would provide a novel approach to measure and evaluate the health status and welfare of farm animals. In addition, fecal microbiota transplantation (FMT) as one of the methods can modulate the recipient individual’s gut microbiota to realize the expected phenotype. Further, (2) we highlighted the application of FMT on the improvement of the production performance, the reduction in disease and abnormal behavior, as well as the attenuation of stress in farm animals. It is concluded that the gut microbiota can be scientifically used to assess and improve the welfare of farm animals. Moreover, FMT may be a helpful strategy to reduce abnormal behavior and improve stress adaption, as well as the treatment of disease for farm animals. This review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

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.

Evaluation of changes in microbiota after fecal microbiota transplantation in 6 diarrheic horses

The purpose of this study was to characterize the fecal microbiota of horses with acute and chronic diarrhea before and after fecal microbiota transplantation (FMT). Six client-owned horses with acute and chronic diarrhea received FMT from 2 healthy donor horses. Microbiota analysis using next-generation sequencing was performed on fecal samples collected before and 2 and 7 d after FMT. Signs of diarrhea improved in 4 horses, whereas the remaining 2 horses did not survive. There was a significant difference in the number of bacterial species between donors and recipients (P < 0.05). The Order Lactobacillales and the genera Lactobacillus, Intestinimonas, and Streptococcus were increased in the microbiota of diarrheic horses, and Saccharofermentans genus increased in healthy donors. The results suggest that FMT from the healthy donors was not effective over a 7-day period as it did not change the fecal microbiota of the diarrheic horses. Further research to improve the efficacy of FMT in horses is needed.

Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment

Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.

Comparison of the Fecal Microbiota of Horses with Intestinal Disease and Their Healthy Counterparts

(1) Background: The intestinal microbiota plays an essential role in maintaining the host's health. Dysbiosis of the equine hindgut microbiota can alter the fermentation patterns and cause metabolic disorders. (2) Methods: This study compared the fecal microbiota composition of horses with intestinal disease and their healthy counterparts living in Korea using 16S rRNA sequencing from fecal samples. A total of 52 fecal samples were collected and divided into three groups: horses with large intestinal disease (n = 20), horses with small intestinal disease (n = 8), and healthy horses (n = 24). (3) Results: Horses with intestinal diseases had fewer species and a less diverse bacterial population than healthy horses. Lactic acid bacteria, Lachnospiraceae, and Lactobacillaceae were overgrown in horses with large intestinal colic. The Firmicutes to Bacteroidetes ratio (F/B), which is a relevant marker of gut dysbiosis, was 1.94, 2.37, and 1.74 for horses with large intestinal colic, small intestinal colic, and healthy horses, respectively. (4) Conclusions: The overgrowth of two lactic acid bacteria families, Lachnospiraceae and Lactobacillaceae, led to a decrease in hindgut pH that interfered with normal fermentation, which might cause large intestinal colic. The overgrowth of Streptococcus also led to a decrease in pH in the hindgut, which suppressed the proliferation of the methanogen and reduced methanogenesis in horses with small intestinal colic.

How Can Nutrition Help with Gastrointestinal Tract-Based Issues?

Many horses are fed differently than their wild ancestors. They often have limited access to pasture and are fed conserved forage and concentrates rich in starch and sugars, in only 2 meals per day. Feeding practices in contrast to natural feeding behavior can lead to gastrointestinal issues. Standard nutritional evaluation is warranted because of its important role in prevention and in treatment and management of diseases. When medical and nutritional treatments are combined, success rates are higher. New techniques to characterize equine microbiota have been used, allowing for microbiota manipulation to prevent and treat intestinal diseases.

The Airway Pathobiome in Complex Respiratory Diseases: A Perspective in Domestic Animals

Respiratory infections in domestic animals are a major issue for veterinary and livestock industry. Pathogens in the respiratory tract share their habitat with a myriad of commensal microorganisms. Increasing evidence points towards a respiratory pathobiome concept, integrating the dysbiotic bacterial communities, the host and the environment in a new understanding of respiratory disease etiology. During the infection, the airway microbiota likely regulates and is regulated by pathogens through diverse mechanisms, thereby acting either as a gatekeeper that provides resistance to pathogen colonization or enhancing their prevalence and bacterial co-infectivity, which often results in disease exacerbation. Insight into the complex interplay taking place in the respiratory tract between the pathogens, microbiota, the host and its environment during infection in domestic animals is a research field in its infancy in which most studies are focused on infections from enteric pathogens and gut microbiota. However, its understanding may improve pathogen control and reduce the severity of microbial-related diseases, including those with zoonotic potential.

Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea

(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.

Ages of weaning influence the gut microbiota diversity and function in Chongming white goats

To study the effect of weaning age on the gut microbiota diversity in the lambs of Chongming white goats, fresh feces from the lambs weaned at 30, 45, and 60 days of age were collected 3 days after weaning at 33, 48, and 63 days of age, for microbial composition analysis by 16S rRNA sequencing. The serum concentrations of lipid metabolites were also investigated at the fecal collection dates. Serum and feces from the ewe-reared groups at 33, 48, and 63 days of age were used as controls. The alpha diversity increased significantly after weaning and with the aging of the lambs. Levels of Ruminococcaceae, Lachnospiraceae, and Ruminococcus varied significantly according to the weaning treatment in lambs (P < 0.05). Butyrate-producing gut bacteria such as Ruminococcaceae_UCG-010, Ruminococcaceae_UCG-013, Ruminococcaceae_UCG-014, Ruminococcaceae_UCG-005, Ruminococcaceae_UCG-002, Lachnospiraceae_AC2044_group, and Lachnospiraceae_NK4B4 were identified as significantly increased genera (P < 0.05) in the feces of weaned Chongming white lambs. Additionally, the abundance of fiber degradation-associated bacteria including Ruminococcaceae_UCG-005, Ruminococcus_1, and Ruminococcus_2 significantly increased with lamb weaning age (P < 0.05). Correlation analysis showed that Lachnospiraceae_AC2044_group, norank_f__Bacteroidales_S24-7_group, and Ruminococcaceae_UCG_005 were negatively correlated, and Lachnoclostridium was positively correlated with levels of cholesterol, while Blautia showed positive correlation with low-density lipoprotein cholesterol in serum samples from weaned lambs. This study helped to understand the maturing development of gut microbiota in Chongming white goats under weaning stress. KEY POINTS: • Effects of weaning age on the gut microbiota diversity in Chongming white goat lambs were studied. • Some butyrate-producing gut bacteria were significantly increased after weaned. • Correlations of gut microbiota and lipid metabolites were analyzed.

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse

Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPARγ, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.

Gut microbiota resilience in horse athletes following holidays out to pasture

Elite horse athletes that live in individual boxes and train and compete for hours experience long-term physical and mental stress that compromises animal welfare and alters the gut microbiota. We therefore assessed if a temporary period out to pasture with conspecifics could improve animal welfare and in turn, favorably affect intestinal microbiota composition. A total of 27 athletes were monitored before and after a period of 1.5 months out to pasture, and their fecal microbiota and behavior profiles were compared to those of 18 horses kept in individual boxes. The overall diversity and microbiota composition of pasture and control individuals were temporally similar, suggesting resilience to environmental challenges. However, pasture exposure induced an increase in Ruminococcus and Coprococcus that lasted 1-month after the return to individual boxes, which may have promoted beneficial effects on health and welfare. Associations between the gut microbiota composition and behavior indicating poor welfare were established. Furthermore, withdrawn behavior was associated with the relative abundances of Lachnospiraceae AC2044 group and Clostridiales family XIII. Both accommodate a large part of butyrate-producing bacterial genera. While we cannot infer causality within this study, arguably, these findings suggest that management practices maintained over a longer period of time may moderate the behavior link to the gut ecosystem beyond its resilience potential.

Effect of Intense Exercise on the Level of Bacteroidetes and Firmicutes Phyla in the Digestive System of Thoroughbred Racehorses

Exercise significantly affects the body of both animals and humans, including the composition of the digestive microbiome. This study aimed to determine the changes in the composition of the most numerous bacterial phyla (Firmicutes and Bacteroidetes, as well as the level of the Lactobacillaceae family) in the digestive system of horses under the influence of physical effort. The study included a group of 17 Thoroughbred racehorses at the age of 3 years, fed the same forage, from whom feces samples were collected individually before and 48 h after physical effort. The obtained samples were subjected to DNA isolation and RT-PCR analysis. The results showed a significant increase in the level of both phyla after exercise compared to the state before physical effort; there were no such differences in the level of facultative aerobes, i.e., the Lactobacillaceae family (although a decreasing tendency was found after exercise). In addition, the analysis of the level of the studied phyla indicates individual differences in horses' response to the effort.

Priming for welfare: gut microbiota is associated with equitation conditions and behavior in horse athletes

We simultaneously measured the fecal microbiota and multiple environmental and host-related variables in a cohort of 185 healthy horses reared in similar conditions during a period of eight months. The pattern of rare bacteria varied from host to host and was largely different between two time points. Among a suite of variables examined, equitation factors were highly associated with the gut microbiota variability, evoking a relationship between gut microbiota and high levels of physical and mental stressors. Behavioral indicators that pointed toward a compromised welfare state (e.g. stereotypies, hypervigilance and aggressiveness) were also associated with the gut microbiota, reinforcing the notion for the existence of the microbiota-gut-brain axis. These observations were consistent with the microbiability of behaviour traits (> 15%), illustrating the importance of gut microbial composition to animal behaviour. As more elite athletes suffer from stress, targeting the microbiota offers a new opportunity to investigate the bidirectional interactions within the brain gut microbiota axis.

Dynamic changes in intestinal microbiota in young forest musk deer during weaning

Weaning is an important event for all mammals, including young forest musk deer. However, weaning stress may cause intestinal microbiota-related disorders. Therefore, high-throughput 16S rRNA gene sequencing was applied to study the dynamic changes in intestinal microbiota during pre-weaning (10 days before weaning) and post-weaning (10 days after weaning) in 15 young forest musk deer. We saw that intestinal microbiota diversity in the post-weaning period was significantly higher than that in the pre-weaning period. The most dominant bacterial phyla were similar in the two groups (Firmicutes, Bacteroidetes and Verrucomicrobia). Meanwhile, we applied Linear discriminant analysis effect size (LefSe) to identify the most differentially microbial taxa in the pre-weaning and post-weaning groups. In the post-weaning forest musk deer, the relative abundance of Actinobacteria, Spirochaetes, Ruminococcaceae_UCG-005, Treponema and Prevotella was higher than in the pre-weaning group. However, higher relative abundance of the phyla Bacteroidetes was found in the pre-weaning group compared with that in the post-weaning group. In summary, this research provides a theoretical foundation for the dynamics of young forest musk deer intestinal microbiota during the weaning transition, which may benefit in understanding the growth and health of forest musk deer.

Supplementation of Lactobacillus plantarum or Macleaya cordata Extract Alleviates Oxidative Damage Induced by Weaning in the Lower Gut of Young Goats

Weaning usually leads to stress in livestock, which has a negative impact on their growth and development. Research on oxidative stress and inflammation induced by weaning has not been reported in goats. Here, we focused on oxidative stress profile and inflammation status of the lower gut (jejunum, ileum, and colon) of goats. First, we illustrated the status of antioxidant activity and inflammation in the intestine of young goats on pre-(2 weeks postnatal, 2 wk^pn) or post-(11 wk^pn, weaning at day 45 postnatal)-weaned period of young goats. Malondialdehyde (MDA) was higher (p < 0.0001) in jejunum and ileum of the young goats in 11 wk^pn than that in 2 wk^pn, whereas superoxide dismutase (SOD) activity was lower (p = 0.012) in the lower gut of the young goats with 11 wk^pn than that in 2 wk^pn. Furthermore, we intended to explore the protective influence of a probiotic additive (Lactobacillus plantarum (LAC) P-8, 10 g/d) and a prebiotic additive (Sangrovit^®, Macleaya cordata (MAC) extract 3.75% w/w premix, 0.3 g/d) on intestinal oxidative stress and inflammation status of early-weaned young goats (average weights of 5.63 ± 0.30 kg, weaned on d 45 postnatal). We observed that LAC reduced MDA in jejunum and ileum (p < 0.0001), increased SOD activity in ileum (p < 0.01), and increased glutathione peroxidase (GSH-Px) activity in jejunum (p < 0.05). Similarly, MAC reduced MDA contents (p < 0.0001), increased SOD activities (p < 0.01) in both of ileum and jejunum, and increased GSH-Px activity (p < 0.05) in jejunum. However, there were no differences in feed intake, average daily gain, inflammation parameters (interleukin 2 and interleukin 6), and colon oxidative stress profile (MDA, SOD, or GSH-Px) among treatments. These results provide evidence that weaning induces oxidative damage in the lower gut of young goats, and the oxidative damage in the small intestine can be reduced by adding the addition of LAC or MAC in diets depending on the region of the lower gut.

Domestic Foal Weaning: Need for Re-Thinking Breeding Practices?

Artificial weaning is a standard practice known to be one of the most stressful events in a domestic foal's life. Research has mainly focused on ways to alleviate weaning stress. However, there is still a need for more detailed research on what should constitute best practices with respect to animal welfare. The aim of this review is to address this issue by examining the natural weaning process. We first provide an overview of the scientific literature on the natural temporal dynamics of the dam-offspring bond in horses: it is to be noted that the natural process of weaning is little documented, individual variations have been poorly investigated and immediate effects of weaning on the mare-foal relationship remain unexplored. To partly address these gaps, we performed a study around the weaning period on 16 mare-foal pairs kept with minimal human interference. Most foals were weaned spontaneously when 9-10 months old, with individual variations mainly due to the conception rate of mares. Natural weaning induced no stress response in either partner and was performed without clear signs of rejection by the dams either just before or after. We lastly open up the discussion on the need for rethinking weaning practices under domestic conditions.

Factors Influencing Equine Gut Microbiota: Current Knowledge

Gastrointestinal microbiota play a crucial role in nutrient digestion, maintaining animal health and welfare. Various factors may affect microbial balance often leading to disturbances that may result in debilitating conditions such as colic and laminitis. The invention of next-generation sequencing technologies and bioinformatics has provided valuable information on the effects of factors influencing equine gut microbiota. Among those factors are nutrition and management (e.g., diet, supplements, exercise), medical substances (e.g., antimicrobials, anthelmintics, anesthetics), animal-related factors (breed and age), various pathological conditions (colitis, diarrhea, colic, laminitis, equine gastric ulcer syndrome), as well as stress-related factors (transportation and weaning). The aim of this review is to assimilate current knowledge on equine microbiome studies, focusing on the effect of factors influencing equine gastrointestinal microbiota. Decrease in microbial diversity and richness leading to decrease in stability; decrease in Lachnospiraceae and Ruminococcaceae family members, which contribute to gut homeostasis; increase in Lactobacillus and Streptococcus; decrease in lactic acid utilizing bacteria; decrease in butyrate-producing bacteria that have anti-inflammatory properties may all be considered as a negative change in equine gut microbiota. Shifts in Firmicutes and Bacteroidetes have often been observed in the literature in response to certain treatments or when describing healthy and unhealthy animals; however, these shifts are inconsistent. It is time to move forward and use the knowledge now acquired to start manipulating the microbiota of horses.

Integrative analysis of blood and gut microbiota data suggests a non-alcoholic fatty liver disease (NAFLD)-related disorder in French SLAdd minipigs

Minipigs are a group of small-sized swine lines, which show a broad range of phenotype variation and which often tend to be obese. The SLA^dd (DD) minipig line was created by the NIH and selected as homozygous at the SLA locus. It was brought to France more than 30 years ago and maintained inbred ever since. In this report, we characterized the physiological status of a herd of French DD pigs by measuring intermediate phenotypes from blood and faeces and by using Large White (LW) pigs as controls. Three datasets were produced, i.e. complete blood counts (CBCs), microarray-based blood transcriptome, and faecal microbiota obtained by 16S rRNA sequencing. CBCs and expression profiles suggested a non-alcoholic fatty liver disease (NAFLD)-related pathology associated to comorbid cardiac diseases. The characterization of 16S sequencing data was less straightforward, suggesting only a potential weak link to obesity. The integration of the datasets identified several fine-scale associations between CBCs, gene expression, and faecal microbiota composition. NAFLD is a common cause of chronic liver disease in Western countries and is linked to obesity, type 2 diabetes mellitus and cardiac pathologies. Here we show that the French DD herd is potentially affected by this syndrome.

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

Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.

Development of the equine gut microbiota

Shortly after birth the mammalian gut is colonized, by a transient microbiota, highly susceptible to environment and diet, that eventually stabilizes and becomes the resident gut microbiota. In a window of opportunity during the colonization, oral tolerance is established towards resident bacteria. In this study, the development of the equine gut microbiota was investigated in ten foals from parturition until post weaning. We found great differences in the core species of the gut microbiota composition between time-matched samples on Day 7 and 20 post-partum. Between day 20 and Day 50 post-partum, we saw the gut microbiota became increasingly dominated by fiber fermenting species. After Day 50, no significant changes in species abundance were observed. Gene expression analysis of pro- and anti-inflammatory cytokines in the blood revealed no significant changes before and after weaning. In summary, relative stability of the gut microbiota was reached within 50 days post-partum and, weaning did not have a major impact on the microbial composition.

Inter-breed diversity and temporal dynamics of the faecal microbiota in healthy horses

Understanding gut microbiota similarities and differences across breeds in horses has the potential to advance approaches aimed at personalized microbial modifications, particularly those involved in improving sport athletic performance. Here, we explore whether faecal microbiota composition based on faecal 16S ribosomal RNA gene sequencing varies across six different sport breeds at two time points 8 months apart within a cohort of 189 healthy horses cared for under similar conditions. Lusitano horses presented the smallest and Hanoverians the greatest bacterial diversity. We found subtle but significant differences in β-diversity between Lusitano, Anglo Arabian and the central European breeds, and we reproduced these results across the two time points. Repeat sampling of subjects showed community to be temporally more stable in Lusitano and Anglo Arabian breeds. Additionally, we found that 27 genera significantly varied in abundance across breeds. Overall, 33% of these taxa overlapped with previously identified taxa that were associated with genetic variation in humans or other species. However, a non-significant correlation was observed between microbial composition and the host pedigree-based kinship. Despite a notable variation in the diversity and composition of the faecal microbiota, breed exerted limited effects on the equine faecal microbiota.

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review

There is increasing evidence of a pivotal role of the gut microbiota (GUT-M) in key physiological functions in vertebrates. Many studies discuss functional implications of the GUT-M not only on immunity, growth, metabolism, but also on brain development and behavior. However, while the influence of the microbiota-gut-brain axis (MGBA) on behavior is documented in rodents and humans, data on farm animals are scarce. This review will first report the well-known influence of the MGBA on behavior in rodent and human and then describe its influence on emotion, memory, social and feeding behaviors in farm animals. This corpus of experiments suggests that a better understanding of the effects of the MGBA on behavior could have large implications in various fields of animal production. Specifically, animal welfare and health could be improved by selection, nutrition and management processes that take into account the role of the GUT-M in behavior.

Dysbiosis associated with acute helminth infections in herbivorous youngstock - observations and implications

A plethora of data points towards a role of the gastrointestinal (GI) microbiota of neonatal and young vertebrates in supporting the development and regulation of the host immune system. However, knowledge of the impact that infections by GI helminths exert on the developing microbiota of juvenile hosts is, thus far, limited. This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin). We observed that high versus low parasite burdens (measured via parasite egg counts in faecal samples) were associated with specific compositional alterations of the developing microbiome; in particular, the faecal microbiota of animals with heavy worm infection burdens was characterised by lower microbial richness, and alterations to the relative abundances of bacterial taxa with immune-modulatory functions. Amino acids and glucose were increased in faecal samples from the same cohort, which indicated the likely occurrence of intestinal malabsorption. These data support the hypothesis that GI helminth infections in young livestock are associated with significant alterations to the GI microbiota, which may impact on both metabolism and development of acquired immunity. This knowledge will direct future studies aimed to identify the long-term impact of infection-induced alterations of the GI microbiota in young livestock.

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology

An integrated analysis of gut microbiota, blood biochemical and metabolome in 52 endurance horses was performed. Clustering by gut microbiota revealed the existence of two communities mainly driven by diet as host properties showed little effect. Community 1 presented lower richness and diversity, but higher dominance and rarity of species, including some pathobionts. Moreover, its microbiota composition was tightly linked to host blood metabolites related to lipid metabolism and glycolysis at basal time. Despite the lower fiber intake, community type 1 appeared more specialized to produce acetate as a mean of maintaining the energy supply as glucose concentrations fell during the race. On the other hand, community type 2 showed an enrichment of fibrolytic and cellulolytic bacteria as well as anaerobic fungi, coupled to a higher production of propionate and butyrate. The higher butyrate proportion in community 2 was not associated with protective effects on telomere lengths but could have ameliorated mucosal inflammation and oxidative status. The gut microbiota was neither associated with the blood biochemical markers nor metabolome during the endurance race, and did not provide a biomarker for race ranking or risk of failure to finish the race.

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning

A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.

Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells

Background

The effects of β-glucan on colitis mice are contradictory in previous reports. As a result, it is still unclear whether there is an anti-colitis effect in Ganoderma lucidum polysaccharide (GLP), which is mainly composed of β-glucan. Moreover, the association between GLP function and gut microbiota remains to be elucidated.

Objective

This study aimed to investigate whether GLP consumption improved rat dextran sodium sulfate (DSS)-induced colitis by regulating gut microbiota and altering colonic epithelial expression.

Design

The disease activity index (DAI) scores and the cecal short chain fatty acid (SCFA) levels of DSS-induced colitis rats fed with a GLP diet (Group GLP, n = 6) and a control diet (Group Con, n = 6) were investigated and analyzed. Moreover, the profiles of gut microbiota and colonic epithelial expression were analyzed using metagenomics and transcriptomics.

Results

GLP consumption significantly lowered animal DAI scores by producing more SCFAs by increasing SCFA-producing bacteria such as Ruminococcus_1 and reducing pathogens such as Escherichia-Shigella in both the small intestine and cecum of rat. Moreover, GLP consumption regulated 11 genes, including six upregulated (Ccl5, Cd3e, Cd8a, Il21r, Lck, and Trbv) and five downregulated (Ccl3, Gro, Il11, Mhc2, and Ptgs) genes enriched in six inflammation-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, resulting in enhancement of immunity and reduction of inflammatory response and colonic cancer risk.

Conclusions

GLP consumption alleviated DSS-induced colitis and may have potential for ulcerative colitis relief.

Polygonatum odoratum Polysaccharides Modulate Gut Microbiota and Mitigate Experimentally Induced Obesity in Rats

Increasing evidence suggests that the gut microbiota plays vital roles in metabolic diseases. Polygonatum odoratum extract alleviates hyperglycemia and hyperlipidemia, but the underlying mechanism remains unclear. This study investigated the effects of P. odoratum polysaccharides (POPs) on high-fat diet (HFD)-induced obesity in rats and whether these effects were related to modulation of gut microbiota. POP treatment attenuated weight gain, fat accumulation, epididymal adipocyte size, liver triglycerides, and total liver cholesterol content in HFD-fed rats. POP administration also increased short-chain fatty acids (SCFAs), including isobutyric acid, butyric acid, and valeric acid. POP upregulated the expression of genes involved in adipocyte differentiation (Pparg, Cebpa, Cebpb) and lipolysis (Ppara, Atgl), and downregulated those related to lipid synthesis (Srebpf1, Fabp4, Fas), with corresponding changes in PPARγ and FABP4 protein expression. Finally, POP enhanced species richness and improved the gut microbiota community structure, reducing the relative abundances of Clostridium, Enterococcus, Coprobacillus, Lactococcus, and Sutterella. Principal coordinates analysis (PCoA) revealed a clear separation between HFD-fed rats and all other treatment groups. Correlation analysis identified negative and positive associations between obesity phenotypes and 28 POP-influenced operational taxonomic units (OTUs), including putative SCFA-producing bacteria. Our data suggest that POP supplementation may attenuate features of obesity in HFD-fed rats in association with the modulation of gut microbiota.

Exploring the Prokaryotic Community Associated With the Rumen Ciliate Protozoa Population

Ciliate protozoa are an integral part of the rumen microbiome and were found to exert a large effect on the rumen ecosystem itself as well as their host animal physiology. Part of these effects have been attributed to their ability to harbor a diverse ecto- and endo-symbiotic community of prokaryotic cells. Studies on the relationship between the protozoa population and their associated prokaryotic community in the rumen mainly focused on the methanogens, revealing that protozoa play a major role in enhancing methanogenesis potential. In contrast, little is known about the composition and function of the bacteria associated with rumen protozoa and the extent of this association. In this study, we characterize the prokaryotic communities associated with different protozoa populations and compare their structure to the free-living prokaryotic population residing in the cow rumen. We show that the overall protozoa associated prokaryotic community structure differs significantly compared to the free-living community in terms of richness and composition. The methanogens proportion was significantly higher in all protozoa populations compared to the free-living fraction, while the Lachnospiraceae was the most prevalent bacterial family in the protozoa associated bacterial communities. Several taxa not detected or detected in extremely low abundance in the free-living community were enriched in the protozoa associated bacterial community. These include members of the Endomicrobia class, previously identified as protozoa symbionts in the termite gut. Our results show that rumen protozoa harbor prokaryotic communities that are compositionally different from their surroundings, which may be the result of specific tropism between the prokaryotic community and protozoa.

Rabbit Microbiota Changes Throughout the Intestinal Tract

To gain insight into the importance of carefully selecting the sampling area for intestinal microbiota studies, cecal and fecal microbial communities of Caldes meat rabbit were characterized. The animals involved in the study were divided in two groups according to the feed intake level they received during the fattening period; ad libitum (n = 10) or restricted to 75% of ad libitum intake (n = 11). Cecum and internal hard feces were sampled from sacrificed animals. Assessment of bacterial and archaeal populations was performed by means of Illumina sequencing of 16S rRNA gene amplicons in a MiSeq platform. A total of 596 operational taxonomic units (OTUs) were detected using QIIME software. Taxonomic assignment revealed that microbial diversity was dominated by phyla Firmicutes (76.42%), Tenericutes (7.83%), and Bacteroidetes (7.42%); kingdom Archaea was presented at low percentage (0.61%). No significant differences were detected between sampling origins in microbial diversity or richness assessed using two alpha-diversity indexes: Shannon and the observed number of OTUs. However, the analysis of variance at genus level revealed a higher presence of genera Clostridium, Anaerofustis, Blautia, Akkermansia, rc4-4, and Bacteroides in cecal samples. By contrast, genera Oscillospira and Coprococcus were found to be overrepresented in feces, suggesting that bacterial species of these genera would act as fermenters at the end of feed digestion process. At the lowest taxonomic level, 83 and 97 OTUs in feces and cecum, respectively, were differentially represented. Multivariate statistical assessment revealed that sparse partial least squares discriminant analysis (sPLS-DA) was the best approach for this purpose. Interestingly, the majority of the most discriminative OTUs selected by sPLS-DA were found to be differentially represented between sampling origins in univariate analysis. Our study provides evidence that the choice of intestinal sampling area is relevant due to important differences in some taxa's relative abundance that have been revealed between rabbits' cecal and fecal microbiota. An appropriate sampling intestinal area should be chosen in each microbiota assessment.

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals

BACKGROUND

Even if horses strictly depend on the gut microbiota for energy homeostasis, only a few molecular studies have focused on its characterisation and none on the perinatal gut microbial colonisation process.

OBJECTIVES

To explore the perinatal colonisation process of the foal gut microbial ecosystem and the temporal dynamics of the ecosystem assembly during the first days of life.

STUDY DESIGN

Longitudinal study.

METHODS

Thirteen Standardbred mare-foal pairs were included in the study. For each pair, at delivery we collected the mare amniotic fluid, faeces and colostrum, and the foal meconium. Milk samples and faeces of both mare and foal were also taken longitudinally, until day 10 post-partum. Samples were analysed by means of next-generation sequencing of the 16S rRNA gene on Illumina MiSeq.

RESULTS

Our findings suggest that microbial components derived from the mare symbiont communities establishes in the foal gut since fetal life. After birth, an external transmission route of mare microorganisms takes place. This involves a rapid and dynamic process of assembling the mature foal gut microbiome, in which the founder microbial species are derived from both the milk and the gut microbial ecosystems of the mare.

MAIN LIMITATIONS

The inability to discriminate between live and dead cells, the possible presence of contaminating bacteria in low biomass samples (e.g. meconium and amniotic fluid), the limits of the phylogenetic assignment down to species level, and the presence of unassigned operational taxonomic units.

CONCLUSIONS

Our data highlight the importance of mare microbiomes as a key factor for the establishment of the gut microbial ecosystem of the foal.

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica)

Background: Recent studies have demonstrated an effect of the gut microbiota on brain development and behavior leading to the concept of the microbiota-gut-brain axis. However, its effect on behavior in birds is unknown. The aim of the present study was to determine the effect of the absence of gut microbiota on emotional reactivity in birds by comparing germ-free (GF) quails to those colonized (COL) with gut microbiota. Material and Methods: From hatching, the quails of both groups GF (n = 36) and COL (n = 36) were reared in sterile isolators. The COL quails were colonized at day 2 by introducing a pool of droppings from conventional adult females into the drinking water and feed. The quails were weighed individually on day 2, 6, and 14. From day 8, emotional reactivity was assessed in each group in the isolators through several behavioral tests. Results: GF quails showed a considerable decrease in emotional reactivity demonstrated by spending less time in tonic immobility during the tonic immobility test (242 s ± 31 vs. 331 s ± 32, p ≤ 0.05), traveling a shorter distance (3,897 cm ± 242 vs. 4,827 cm ± 278, p ≤ 0.05) at a lower velocity (6.55 cm/s ± 0.4 vs. 8.1 cm/s ± 0.5, p ≤ 0.05) during the social separation test and spending more time near an object at the beginning of the novel object test (33.7 s ± 6.4 vs. 18.5 s ± 4.1, p ≤ 0.05). No difference in growth was found between the 2 groups. Conclusion: For the first time, this study demonstrates that the absence of gut microbiota reduces emotional reactivity in Japanese quails in situations of fear and social perturbation without influence on growth.

Understanding the Intestinal Microbiome in Health and Disease

This article provides readers with the basic concepts necessary to understand studies using recent molecular methods performed in intestinal microbiome assessment, with special emphasis on the high throughput sequencing. This review also summarizes the current knowledge on this topic and discusses future insights on the interaction between the intestinal microbiome and equine health.