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

Abstract

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.

Psyllium Supplementation is Associated with Changes in the Fecal Microbiota of Horses

“…In considering Faith's Phylogenetic Diversity, the samples with the richest diversity were those collected during midsupplementation on Day 7. Others have demonstrated that greater diversity was positively correlated with a healthy horse GIT, and our ndings suggest that prophylactic psyllium was bene cial for improving microbial diversity (25,26). However, population changes were not dramatic from the standpoint of percent abundance of comprising microbes.…”

“…Slight increases were seen in Fibrobacteraceae and Paraprevotellaceae in yearlings, which contain essential cellulose-degrading bacteria and bacteria found in the GIT of pasture forage-fed horses, respectively (27,28). In adults, there was a slight reduction in methanogenic archaean Methanocorpusculaceae but slight increases in methanogenic bacteria Methanobacteriaceae, which captures hydrogen and improves fermentation e ciency, and bacterial Moraxellaceae commonly found in younger horses and foals (16,26,27,29). PICRUSt analysis demonstrated that during psyllium supplementation there was increased mycothiol biosynthesis activity in the GIT.…”

Psyllium supplementation is associated with changes in the fecal microbiota of horses

“…In considering Faith's Phylogenetic Diversity, the samples with the richest diversity were those collected during mid-supplementation on Day 7. Greater diversity has been positively correlated with a healthy horse GIT; our findings suggest that prophylactic psyllium was beneficial for improving microbial diversity [29,30]. However, there were no dramatic detectable changes in abundances of microbial populations.…”

Psyllium Supplementation is Associated with Changes in the Fecal Microbiota of Horses

“…In considering Faith's Phylogenetic Diversity, the samples with the richest diversity were those collected during midsupplementation on Day 7. Greater diversity has been positively correlated with a healthy horse GIT; our ndings suggest that prophylactic psyllium was bene cial for improving microbial diversity (29,30). However, there were no dramatic detectable changes in abundances of microbial populations.…”

“…Slight increases were seen in Fibrobacteraceae and Paraprevotellaceae in yearlings, which contain essential cellulose-degrading bacteria and bacteria found in the GIT of pasture forage-fed horses, respectively (31,32). In adults, there was a slight reduction in methanogenic archaea Methanocorpusculaceae but slight increases in methanogenic bacteria Methanobacteriaceae, which captures hydrogen and improves fermentation e ciency, and bacterial Moraxellaceae commonly found in younger horses and foals (20,30,31,32). Increased mycothiol biosynthesis activity in the GIT was demonstrated during psyllium supplementation.…”