Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species


Joan E. Edwards, S. A. Shetty, P. van den Berg, Faith A. Burden, D. A. van Doorm, W. F. Pellikaan, J. Dijkstra, H. Smidt. 12 February 2020. Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Animal Microbiome. 2:6.

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Publication date: 
12 February 2020
Animal Microbiome
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Background: Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world’s domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra). Results: Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant. Conclusions: Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.

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Anaerobic fungi are a key unexplored taxa for optimizing lignocellulosic fibre utilisation in equines


Joan E. Edwards, David A van Doorn, Wilbert F Pellikaan, Jan Dijkstra, Henk Everts, Faith A. Burden, Hauke Smidt. 21 June 2016. Anaerobic fungi are a key unexplored taxa for optimizing lignocellulosic fibre utilisation in equines. Presented at INRA-Rowett Symposium. (20 June - 23 June 2016). Clermont-Ferrand, France.

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Date presented: 
Tuesday 21 June 2016
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INRA-Rowett Symposium

The hindgut microbiota of equines enables them to utilize forage/grazing based diets which contain a substantial proportion of lignocellulosic fibres. These fibres are a structural barrier that gut bacteria need to overcome when accessing plant nutrients, as well as being a challenging and structurally complex substrate that can be utilized. The limited dietary energy available from these ‘natural’ diets however means that many equines are supplemented with energy-dense concentrate feeds in order to fulfil their dietary energy requirements. Use of energy-dense concentrate feeds however can change the equine hindgut microbiome, and lead to the development of gut-mediated diseases (i.e. fermentative acidosis, laminitis, colic and stomach ulcers). There is therefore a clear need to optimize the utilization of lignocellulosic fibres in the equine hindgut in order to minimize the need for dietary supplementation. The most effective of the fibre-degrading gut microbes, anaerobic fungi (phylum Neocallimastigomycota), are known to be a normal member of the equine gut microbiota. Despite this however, they have been largely overlooked in equine gut microbiology studies to date. Research being conducted within the EU funded EQUIANFUN project will therefore establish baseline knowledge of the phylogeny, community structure, physiology and nutritional impact of anaerobic fungi in the equine hindgut. The insights gained will inform the development of novel strategies to promote indigenous anaerobic fungal communities in the equine hindgut, enabling optimization of the use of dietary forage as an energy source in equids. Reduction of the use of energy–dense diets and applying targeted nutritional strategies for optimizing microbial health may counteract processes in the gastrointestinal tract that have been associated with disease. Anaerobic fungi therefore offer the potential to enable significant advances to be made in the optimisation of the nutrition, health and welfare of all domesticated equids.

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