Crowdsourcing horse poo for microbial research: Only the freshest will do, study suggests

Fresh is best when it comes to research into fecal microbes in horses, a study shows.
Fresh is best when it comes to research into fecal microbes in horses, a study shows.

The importance to horse health of a well-balanced and stable population of gut bacteria is now well recognised, with a range of studies exploring the issue.

But how consistent have we been when it comes to sampling fecal material for these studies?

Researchers at Southeastern Louisiana University, writing in the open-access peer-reviewed journal PLOS ONE, noted that while the microbial makeup in horse dung had been examined in studies, no universal collection method and sample processing procedure had been established.

The nutrition and health of horses is closely tied to their gastrointestinal microbiota. Horses are herbivores and hindgut fermentors, which rely on their gut microbiota to break down plant structural carbohydrates.

The intricate relationship between horse health and gut microbes has been motivation for studies that use Next Generation DNA Sequencing.

The microbial population in horse dung changes rapidly in the hours following defecation.
The microbial population in horse dung changes rapidly in the hours following defecation.

Kalie Beckers, Christopher Schulz and Gary Childers said their study was launched in large part to ensure that samples collected by different individuals from different geographical areas, in crowdsourced studies, were not contaminated due to less than optimal sampling or holding conditions.

They examined the effect of sampling the surface of fecal pellets compared to homogenized (mixed) fecal pellets, and also the effect of time of sampling after defecation on “bloom” taxa – that is, the microbes that can grow rapidly in horse dung once it has been expelled by the horse.

They found that sampling from either the surface or homogenized feces had no effect on microbial diversity and little effect on microbial composition.

However, sampling at various time points – at 0, 2, 4, 6 and 12 hours after defecation – had a significant effect on both diversity and community composition of fecal samples.

Diversity initially increased with time but by 12 hours the diversity sharply decreased as the community composition became dominated by a few bloom families, including Bacillaceae, Planococcaeae, and Enterococcaceae, and other families to a lesser extent.

“Initially,” they reported, ” the samples are representative of the fecal microbiome, but after exposure to the aerobic environment the bloom taxa begin to increase in abundance while the gut microbes are still present in high relative abundance as well, resulting in the highest observed diversity at intermediate time points.

“By 12 hours, the bloom taxa became dominant, overwhelming the original community resulting in decreased diversity.

“The results show that immediate sampling of horse feces must be done in order to ensure accurate representation of horse fecal samples,” they said.

Several of the bloom microbes found in the study were known to occur in human and cattle feces following defecation, they noted. Their dominance in feces shortly after defecation suggested that feces was an important habitat for these organisms, and horse fecal samples that were improperly stored can be identified by their presence, they said.

“Currently there are multiple equine projects that are turning to crowdsourcing for sample collection, and this study may help researchers make informed decisions when screening samples for integrity.

“This study is a step forward in that direction of standardizing horse fecal microbiome studies, but optimally a central lab resource is desirable to reduce inter-lab bias for the horse gut microbiome.”

Beckers KF, Schulz CJ, Childers GW (2017) Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples. PLoS ONE12(11): e0187044.

The study, published under a Creative Commons License,  can be read here

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