The effects of signalment, diet, geographic location, season, and colitis associated with antimicrobial use or Salmonella infection on the fecal microbiome of horses

Fecal microbiota and concentrations of long-chain fatty acids, sterols, and unconjugated bile acids in cats with chronic enteropathy

Feline chronic enteropathies (FCE) are common causes of chronic gastrointestinal signs in cats and include different diseases such as food-responsive enteropathy (FRE), inflammatory bowel diseases (IBD), and low-grade intestinal T-cell lymphoma (LGITL). Although changes in intestinal microbiota and fecal metabolites have been reported in dogs and humans with chronic enteropathy, research in cats has been limited. Therefore, this study aimed to evaluate the fecal microbiota and lipid-related fecal metabolites in cats with FCE to a clinically healthy comparison group (CG). A total of 34 cats with FCE (13 FRE, 15 IBD, and 6 LGITL) and 27 cats in the CG were enrolled in this study. The fecal microbiota was evaluated by the qPCR-based feline Dysbiosis Index (DI). The feline DI in cats with CE (median: 1.3, range: -2.4 to 3.8) was significantly higher (p < 0.0001) compared to CG (median: - 2.3, Range: -4.3 to 2.3), with no difference found among the FCE subgroups. The fecal abundances of Faecalibacterium (p < 0.0001), Bacteroides (p < 0.0001), Fusobacterium (p = 0.0398), Bifidobacterium (p = 0.0004), and total bacteria (p = 0.0337) significantly decreased in cats with FCE. Twenty-seven targeted metabolites were measured by gas chromatography-mass spectrometry, including long-chain fatty acids (LCFAs), sterols, and bile acids (BAs). Fecal concentrations of 5 of 12 LCFAs were significantly increased in cats with FCE compared to CG. Fecal concentrations of zoosterol (p = 0.0109), such as cholesterol (p < 0.001) were also significantly increased in cats with FCE, but those of phytosterols were significantly decreased in this group. No differences in fecal BAs were found between the groups. Although no differences were found between the four groups, the fecal metabolomic pattern of cats with FRE was more similar to that of the CG than to those with IBD or LGITL. This could be explained by the mild changes associated with FRE compared to IBD and LGITL. The study showed changes in intestinal microbiota and alteration of fecal metabolites in FCE cats compared to the CG. Changes in fecal lipids metabolites suggest a dysmetabolism of lipids, including LCFAs, sterols, and unconjugated BAs in cats with CE.

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.

Intestinal Microbiota Is a Key Target for Load Swimming to Improve Anxiety Behavior and Muscle Strength in Shank 3-/- Rats

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social disorder and stereotypical behavior, and its incidence rate is increasing yearly. It is considered that acritical period for the prognosis of young children with ASD exists, thus early treatment is crucial. Swimming, due to its comforting effect, is often used to induce enthusiasm in young children for completing activities and has a good effect in the treatment of ASD, but the effective path of swimming has yet to be reported. The intestinal microbiota of ASD patients and animal models has been reported to be different from that of healthy controls, and these changes may affect the brain environment. Therefore, whether the intestinal microbiota is involved in the treatment of ASD by early swimming is our concern. In this study, we used 8-day old Shank3 gene knockout rats with 8 weeks of early load swimming training and conducted behavioral, small intestine morphology, and intestinal content sequencing after training. The results showed that early load swimming significantly reduced the stereotyped and anxious behaviors of Shank3-/- rats, increased their muscle strength, increased the length of intestinal villi and the width of the muscular layer after Shank3 knockout, and affected the abundance of intestinal microorganisms. The abundances with statistical significance were Lactobacillus, Lachnospiraceae, and Alloprevotella. To further confirm the role of intestinal microorganisms in it, we designed a 14-day intestinal stool transplantation experiment. Fecal microbiota transplantation demonstrated that load swimming can significantly reduce the anxiety behavior of Shank3 rats, increase their muscle strength, change the structure of the small intestine, and affect the abundance of intestinal contents. The abundance of Epsilonbateraeota, Prevotella, and Bacteroides significantly changed after transplantation. Our findings confirm the possibility of early load swimming therapy for individuals with ASD and explain that the intestinal microbiota is a key pathway for early exercise therapy for patients with ASD.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Achieving pan-microbiome biological insights via the dbBact knowledge base

16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of experiments when interpreting their own findings in a broader context. To bridge this gap, we introduce dbBact - a novel pan-microbiome resource. dbBact combines manually curated information from studies across diverse habitats, creating a collaborative central repository of 16S rRNA amplicon sequence variants (ASVs), which are assigned multiple ontology-based terms. To date dbBact contains information from more than 1000 studies, which include 1500000 associations between 360000 ASVs and 6500 ontology terms. Importantly, dbBact offers a set of computational tools allowing users to easily query their own datasets against the database. To demonstrate how dbBact augments standard microbiome analysis we selected 16 published papers, and reanalyzed their data via dbBact. We uncovered novel inter-host similarities, potential intra-host sources of bacteria, commonalities across different diseases and lower host-specificity in disease-associated bacteria. We also demonstrate the ability to detect environmental sources, reagent-borne contaminants, and identify potential cross-sample contaminations. These analyses demonstrate how combining information across multiple studies and over diverse habitats leads to better understanding of underlying biological processes.

What Is the Microbiota and What Is Its Role in Colic?

The fecal microbiome of the horse is reflective of the large colon and plays an important role in the health of the horse. The microbes of the gastrointestinal tract digest fiber and produce energy for the host. Healthy horses have Firmicutes, Bacteroidetes, and Verrucromicrobia as the most common phyla. During gastrointestinal disease such as colic or colitis, the microbiome shows less diversity and changes in bacterial community composition.

Multidose misoprostol pharmacokinetics and its effect on the fecal microbiome in healthy, adult horses

OBJECTIVE

To compare the pharmacokinetics between repeated doses and to characterize changes in the fecal microbiome after oral and rectal multidose misoprostol administration.

ANIMALS

6 healthy university-owned geldings.

PROCEDURES

In a randomized, crossover study, misoprostol (5 μg/kg) was administered orally or rectally every 8 hours for 10 doses, or not administered (control), with a 21-day washout between treatments. Concentration-versus-time data for dose 1 and dose 10 were subject to noncompartmental analysis. For microbiota analysis using 16S rRNA amplicon sequencing, manure was collected 7 days before study onset, immediately before dose 1, and 6 hours, 7 days, and 14 days after dose 10, with time-matched points in controls.

RESULTS

Repeated dosing-related differences in pharmacokinetic parameters were not detected for either administration route. The area under the concentration-versus-time curve was greater (P < .04) after oral versus rectal administration. The relative bioavailability of rectal administration was 4 to 86% of that of oral administration. Microbial composition, richness, and β-diversity differed among subjects (P < .001 all) while only composition differed between treatments (P ≤ .01). Richness was decreased 6 hours after dose 10 and at the control-matched time point (P = .0109) in all subjects. No other differences for time points, treatments, or their interactions were observed.

CLINICAL RELEVANCE

Differences in systemic exposure were associated with the route of administration but were not detected after repeated administration of misoprostol. Differences in microbiota parameters were primarily associated with interindividual variation and management rather than misoprostol administration.

Fecal Microbiota Comparison between Healthy Teaching Horses and Client-Owned Horses

The objective of this study was to compare the fecal microbiota of 2 healthy teaching horse herds with that of client-owned horses from the same geographic areas. The fecal microbiota of client-owned horses from Ontario Canada (n = 15) and Florida, USA (n = 11) was compared with that teaching horses from the University of Guelph, Ontario, Canada (n = 10) and the University of Florida, Florida, USA (n = 15). The fecal microbiota was characterized by sequencing of bacterial DNA using the V4 hypervariable region of the 16S rRNA gene. The diversity (inverse Simpson index) of the fecal microbiota was significantly higher in teaching than client owned horses from the same geographical area (P < 0.05). The community membership (Jaccard Index) and structure (Yue and Clayton index) of teaching horses was also significantly different from that of client owned horses from the same geographical area (AMOVA P < 0.001). The bacterial membership and structure of the fecal microbiota of Ontario and Florida teaching horses were significantly different, while the bacterial membership, but not the structure of Ontario and Florida client owned horses was significantly different (AMOVA P < 0.001). In all 4 groups of healthy horses, Lachnospiraceae, Ruminococcaceae, Bacteroidales, Clostridiales, and Treponema were detected in high relative abundance. The fecal microbiota of healthy horses from teaching herds kept in the same environment with identical management practices differs significantly from that of horses housed in different facilities with dissimilar management practices. Our results suggest an effect of the environment and management practices on the gastrointestinal microbiota. Researchers should attempt to include healthy horses from the same farm with similar management as control groups when comparing with diseased horses.

Effects of Intravenous Antimicrobial Drugs on the Equine Fecal Microbiome

Alterations in the gastrointestinal microbiota after antimicrobial therapy in horses can result in loss of colonization resistance and changes in bacterial metabolic function. It is hypothesized that these changes facilitate gastrointestinal inflammation, pathogen expansion and the development of diarrhea. The objectives of this study were to determine the effect of intravenous administration of antimicrobial drugs (ceftiofur, enrofloxacin, oxytetracycline) on equine fecal bacterial communities over time, to investigate whether those changes are detectable after 5 days of treatment and whether they persist over time (30 days). Sixteen horses were randomly assigned into 4 treatment groups: group 1 (enrofloxacin, n = 4); group 2 (ceftiofur sodium, n = 4); group 3 (oxytetracycline, n = 4); group 4 (0.9% saline solution, placebo, n = 4). Antimicrobial therapy was administered for 5 days. Fecal samples were obtained before (day 0) and at 3, 5 and 30 days of the study period. Bacterial DNA was amplified using specific primers to the hypervariable region V1−V3 of the 16S rRNA gene using a 454 FLX-Titanium pyrosequencer. Antimicrobial therapy failed to cause any changes in physical examination parameters, behavior, appetite or fecal output or consistency throughout the study in any horse. There was a significant effect of treatment on alpha diversity indices (richness) over the treatment interval for ceftiofur on days 0 vs. 3 (p < 0.05), but not for other antimicrobials (p > 0.05). Microbial composition was significantly different (p < 0.05) across treatment group and day, but not for interactions between treatment and day, regardless of taxonomic level and beta-diversity distance metric. The most significant antimicrobial effects on relative abundance were noted after intravenous administration of ceftiofur and enrofloxacin. The relative abundance of Fibrobacteres was markedly lower on day 3 compared to other days in the ceftiofur and enrofloxacin treatment groups. There was an increase in Clostridia and Lachnospiraceae from day 0 to days 3 and 5 in ceftiofur and enrofloxacin treated groups. These findings showed the negative effect of antimicrobial drugs on bacterial communities associated with gut health (Fibrobacteres and Lachnospiraceae) and indicate that changes in specific taxa could predispose horses to gastrointestinal inflammation and the development of diarrhea.

Impact of Dietary Zinc Chloride Hydroxide and Zinc Methionine on the Faecal Microbiota of Healthy Adult Horses and Ponies

Zinc supplements are often used in equine nutrition to support skin and hoof quality or the immune function. However, no data on the effects of dietary zinc on the intestinal microbiota of horses and ponies are available so far. In the present study, varying dietary zinc concentrations (maintenance (4 mg/kg BW^0.75/day), 120 mg/kg dry matter (DM)/day and 240 mg/kg DM/day) were achieved by the supplementation of either zinc chloride hydroxide or zinc methionine (six treatment periods of 4 weeks each). Eight healthy adult ponies and two healthy adult horses were included, and faecal samples were collected at the end of each treatment period to analyse the microbiota (16S rDNA sequencing) and microbial metabolites. With increasing dietary zinc concentrations, the richness of the faecal microbiota decreased, independently of the zinc compound used. In addition, a decrease of the relative abundance of Bacteroidetes and Fibrobacteres as well as of acetate and total short-chain fatty acids in the faeces of the animals was observed at high zinc intakes. Effects on the bacterial order, family and genus level were also detected, which were partly more pronounced for zinc chloride hydroxide. It can be concluded that high dietary zinc levels decrease the richness and fermentative activity of the faecal microbiota of horses and ponies. Although all animals were healthy throughout the study, the effects could be critical for gut health, and deserve more research. The detected differences between the zinc compounds used indicate differences in the bioavailability of organic and inorganic zinc sources in equines.