Abstract
Advances have been made to standardize 16S rRNA gene amplicon based studies for inter-study comparisons, yet there are many opportunities for systematic error that may render these comparisons improper and misleading. The fecal microbiome of horses has been examined previously, however, no universal horse fecal collection method and sample processing procedure has been established. This study was initialized in large part to ensure that samples collected by different individuals from different geographical areas (i.e., crowdsourced) were not contaminated due to less than optimal sampling or holding conditions. In this study, we examined the effect of sampling the surface of fecal pellets compared to homogenized fecal pellets, and also the effect of time of sampling after defecation on ‘bloom’ taxa (bloom taxa refers to microbial taxa that can grow rapidly in horse feces post-defecation) using v4 16S rRNA amplicon libraries. A total of 1,440,171 sequences were recovered from 65 horse fecal samples yielding a total of 3,422 OTUs at 97% similarity. Sampling from either surface or homogenized feces had no effect on diversity and little effect on microbial composition. Sampling at various time points (0, 2, 4, 6, 12 h) had a significant effect on both diversity and community composition of fecal samples. Alpha diversity (Shannon index) initially increased with time as regrowth taxa were detected in the amplicon libraries, but by 12 h 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. The results show that immediate sampling of horse feces must be done in order to ensure accurate representation of horse fecal samples. Also, several of the bloom taxa found in this study are known to occur in human and cattle feces post defecation. The dominance of these taxa in feces shortly after defecation suggests that the feces is an important habitat for these organisms, and horse fecal samples that were improperly stored can be identified by presence of bloom taxa.
Highlights
The gut microbiota are viewed as an organ that plays a central role in host physiology, nutrition, immunomodulation, protection from pathogens, and disorders of the gastrointestinal tract of humans [1,2]
The objectives of this study were to examine the technical reproducibility of two collection methods, surface fecal pellet sampling vs. homogenized fecal pellet sampling, and to investigate the identities and timing of potential bloom taxa in horse fecal samples using Next Generation Sequencing (NGS)
A total of 995,902 sequences were clustered to 3422 operational taxonomic units (OTU) with a mean of 15,321 sequences per sample
Summary
The gut microbiota are viewed as an organ that plays a central role in host physiology, nutrition, immunomodulation, protection from pathogens, and disorders of the gastrointestinal tract of humans [1,2]. The nutrition and health of horses is closely tied to their gastrointestinal microbiota [3]. Diets high in starch, fructans, or simple sugars can lead to excess lactic acid production which may result in laminitis or colic [3,9,10]. The addition of oats (high in starch) to a hay diet has been shown to alter both the microbiota composition and function [11]. Use of antimicrobials [12], intense exercising and aerobic conditioning [13], and possibly geography, breed, husbandry, seasonal effects may play roles in shaping the horse gut microbiota [14].The intricate relationship between horse health and gut microbiota has been motivation for Generation Sequencing (NGS) enabled investigations of the equine gut microbiota [11,15,16,17,18]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
