Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations

Abstract

Domesticated horses live under different conditions compared with their extinct wild ancestors. While housed, medicated and kept on a restricted source of feed, the microbiota of domesticated horses is hypothesized to be altered. We assessed the fecal microbiome of 57 domestic and feral horses from different locations on three continents, observing geographical differences. A higher abundance of eukaryota (p < 0.05) and viruses (p < 0.05) and lower of archaea (p < 0.05) were found in feral animals when compared with domestic ones. The abundance of genes coding for microbe-produced enzymes involved in the metabolism of carbohydrates was significantly higher (p < 0.05) in feral animals regardless of the geographic origin. Differences in the fecal resistomes between both groups of animals were also noted. The domestic/captive horse microbiomes were enriched in genes conferring resistance to tetracycline, likely reflecting the use of this antibiotic in the management of these animals. Our data showed an impoverishment of the fecal microbiome in domestic horses with diet, antibiotic exposure and hygiene being likely drivers. The results offer a view of the intestinal microbiome of horses and the impact of domestication or captivity, which may uncover novel targets for modulating the microbiome of horses to enhance animal health and well-being.

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes

“…1d ). Consistent with two recent metagenomic studies in horses 30 , 32 , Ascomycota (0.56%) and Basidiomycota (0.25%) were among the top annotated Eukaryota phyla in the gut. At the same time, Saccharomycetaceae represented the dominant eukaryote family 30 .…”

“…Consistent with two recent metagenomic studies in horses 30 , 32 , Ascomycota (0.56%) and Basidiomycota (0.25%) were among the top annotated Eukaryota phyla in the gut. At the same time, Saccharomycetaceae represented the dominant eukaryote family 30 . Many genes in the catalog pertained to the Ciliophora phylum ( n = ~ 80,000 genes), stressing the importance and central role protozoa likely play in host function and microbiome metabolism (Fig.…”

“…The great majority of these CAZYmes pertained to glycosyl-transferase (GT, 26.8%, n = 228,878 genes) and glycoside hydrolase (GH, 64.9%, n = 554,661 genes) families, followed by carbohydrate-binding modules (CBM; ~4%, n = 37,474 genes) and polysaccharide lyases (PL) families (~1.6%, n = 13,801; Supplementary Data 6 ). Confirming what has been recently found in horses 30 , the most highly expressed CAZy family genes belonged to the GT2, GH5, and GH9 families, which contain diverse cellulases and hemicelluloses. Genes encoding GH13, GH57, GH77, and CBM48 families, characterized by their starch catalytic activities, were also highly represented in the catalog (Fig.…”

“…Yet, these core genes showed highly conserved abundance rank structure across individuals, representing 29.7 to 38.4% of the overall microbiome abundance. Only 22.5% ( n = 922,362) of the recently published horse gut microbiome gene catalog 30 overlapped with our gene catalog, indicating that the functional potential of gut microbiomes in horses is vast and currently under-sampled.

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Evaluation of the nemabiome approach for the study of equine strongylid communities

“…To overcome the described challenges owing to barcode properties, metagenomic shotgun sequencing on DNA extracted from faeces could resolve the horse gut biodiversity in a single-pot experiment. While gut microbial gene catalogs have been built recently (Ang et al, 2022; Mach et al, 2022), the genomic resources for cyathostomin remain restricted to a few mitochondrial genomes that span the Coronocyclus (Yang et al, 2020), Cyathostomum (Wang et al, 2020), Cylicocyclus (Y. Gao et al, 2017), Cylicostephanus (Gao et al, 2020), and Triodontophorus (J.-F. Gao et al, 2017) genera, and a single heavily fragmented genome assembly for C. goldi (International Helminth Genomes, 2019).…”