Major hindgut diversity in horses exposed in major microorganism study
A surprising hindgut diversity among the microorganisms that inhabit the hindgut of thoroughbred horses has been described by researchers, including dozens of new or unnamed bacteria.
The scientists used molecular analysis of faecal samples from five 12-month-old thoroughbreds from the same farm and field in Ireland. The young horses were all reared on permanent mixed ryegrass pasture, with a diet supplemented with proprietary grain-based feeds after weaning, plus trace elements.
Rachel Gilroy and her fellow researchers, writing in the open access journal PeerJnoted the crucial role played by horses around the world, including in racing, as working and companion animals, and as food animals.
Domestication began at least 6000 years ago and led to diversification into many breeds, accompanied by significant biological changes.
As a foraging herbivore, the horse relies on a high cellulose diet of grasses and legumes. However, unlike cattle, horses do not have a rumen to digest complex carbohydrates. Instead, they rely on hindgut fermentation.
It is, they say, an efficient but enigmatic process, much less well understood than ruminal digestion, which relies on a rich microbial community – the hindgut microbiome, encompassing bacteria, archaea and viruses. , as well as fungi and other eukaryotic microbes.
“This ecosystem plays a key role in nutrient assimilation and feed conversion – effectively turning grass into horse flesh and horses,” they said.
The horse’s gut also acts as a reservoir of equine and human pathogens, as well as sources of antimicrobial resistance, as previous research has shown.
Basically, various diseases are associated with disturbances in the microbial ecology of the hindgut in horses, including foal diarrhea, colitis, laminitis, colic, and equine grass disease.
Thus, by better understanding the hindgut microbiome of horses, it is possible to develop interventions that can improve the health and welfare, performance, value and longevity of horses.
The researchers noted that previous studies of the horse’s hindgut microbiome have documented a rich variety of microorganisms, which vary in composition depending on age, breed and disease state. .
However, previous studies have largely relied on methods that fail to provide resolution down to the species or strain level, and do not cover viruses and eukaryotes.
“Thus, despite previous efforts – and building on comparisons with the human microbiome, where new species are still being discovered – the horse hindgut microbiome presents us with a vast landscape of taxonomic, ecological and functional diversity. , explored only superficially, certain to encompass important, as yet unknown roles.
The researchers applied shotgun metagenomics to thoroughbred fecal samples in their study. Metagenomics refers to the study of a collection of genetic material (genomes) from a mixed community of organisms.
Initial analyzes of the resulting data revealed considerable novelty and diversity in the equine fecal microbiome, with over 59% of sequence reads in each sample categorized by the Kraken taxonomic tagging program as “unassigned”. that is, from unknown organisms.
Genetic reads accounted for all three domains of life, as well as viruses, although bacteria predominated, accounting for more than 89% of assigned reads in any sample.
The bacterial reads were mainly Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria.
However, Kraken profiles also provided evidence for over 30 additional bacterial phyla in this ecosystem.
“Many of these appear to be novel in the context of the horse gut, including Deinococcus-Thermus, Thermotogae and the Candidate phylum Cloacimonetes, which has been reported almost exclusively from anaerobic fermenters and the aqueous environment.
Remarkably, two samples showed a very high relative abundance of reads attributed to the genus Acinetobacter, mirroring similar results in two healthy horses in a previous study.
The authors uncovered a host of other findings about bacteria, including around 100 newly named bacterial species.
They also recovered nearly 200 bacteriophage genomes, many of which are new. Bacteriophages are viruses that infect and replicate in bacteria and archaea.
Readings attributed to eukaryotes provided evidence of budding yeasts and apicoplex parasites in these samples.
The authors said their findings reveal new insights into this important ecosystem, while showing the benefits of shotgun metagenomics in carrying out this type of work.
“Exploration of just five fecal samples has led to the discovery – and recovery – of the genomes of nearly 100 new bacterial and archaeal species and nearly 200 bacteriophage genomes, greatly increasing the known microbial diversity of this environment.”
They said that ranking the genomes of these species in publicly available databases will underpin all future studies in this area, improving the quality of reference-based taxonomic assignments.
“Although the limited scope of this study does not allow us to hope to provide a complete view of the taxonomic diversity within the horse gut, it does give us a tantalizing glimpse of the richness that awaits us when such approaches are deployed. more broadly, especially when the integration of long-read sequencing into metagenomics brings the promise of genome assemblies rivaling those of cultured isolates.
“Just as the horse has allowed humans to explore new external landscapes, new sequencing and bioinformatics approaches will allow us to explore the inner world of the equine gut microbiome,” they said.
In conclusion, the authors said their research had generated a “preliminary census” of the Thoroughbred horse gut microbiome and its associated metabolic potential far beyond the scope of that seen in currently available metagenomic studies. Dozens of new genera and species of bacteria have been revealed.
“The assignment of previously unnamed species to Candidatus binomials, as employed here, provides an important precedent for the continued description of these organisms as they are discovered in other biological environments.”
The study team included Gilroy, Anuradha Ravi, Evelien Adriaenssens, Dave Baker and Mark Pallen, all from Quadram Institute Bioscience in Norwich, England; Joy Leng, Roberto La Ragione and Christopher Proudman, all from the University of Surrey; and Aharon Oren, of the Hebrew University of Jerusalem in Israel.
Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ. 2022.
The metagenomic study of the equine faecal microbiome reveals a great taxonomic diversity. PeerJ 10:e13084 DOI 10.7717/peerj.13084