Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples.
Authors: Beckers Kalie F, Schulz Christopher J, Childers Gary W
Journal: PloS one
Summary
# Editorial Summary When collecting faecal samples for microbiome analysis across multiple horses and locations, timing and handling procedures significantly impact the validity of results—yet no standardised protocol has existed for equine practitioners and researchers. Beckers and colleagues used 16S rRNA gene sequencing on 65 equine faecal samples to evaluate whether sampling method (surface versus homogenised material) and time elapsed since defecation (0–12 hours) affected microbial detection. Whilst the sampling approach made little difference, the timing proved critical: microbial diversity initially increased over the first few hours as rapidly-growing "bloom" taxa—primarily Bacillaceae, Planococcaceae, and Enterococcaceae families—proliferated, then paradoxically crashed by 12 hours as these few families came to dominate the community. Samples must therefore be processed immediately after collection to accurately represent the horse's actual faecal microbiome; the presence of these bloom taxa in a sample can serve as a marker of improper storage or delayed processing, making it possible to flag compromised data from crowdsourced or multi-site studies. For practitioners involved in microbiome sampling protocols or interpreting faecal analysis results, this work underscores the critical importance of standardised, rapid sample handling to ensure results are biologically meaningful rather than artefactual.
Read the full abstract on PubMed
Practical Takeaways
- •If you're collecting fecal samples for microbiome analysis, collect immediately after defecation and process without delay—samples stored even a few hours will not represent the horse's actual microbiome.
- •For crowdsourced or field-collected samples, presence of Bacillaceae, Planococcaceae, and Enterococcaceae in high abundance is a red flag indicating improper storage or delayed processing.
- •Whether you sample the surface or mix the fecal pellet doesn't matter much, but timing is everything—standardize on immediate collection to ensure valid comparisons between horses and studies.
Key Findings
- •Sampling surface versus homogenized feces had minimal effect on microbial diversity and composition.
- •Time since defecation significantly altered fecal microbiome diversity and composition, with alpha diversity initially increasing then sharply decreasing by 12 hours.
- •Bloom taxa (Bacillaceae, Planococcaceae, Enterococcaceae) rapidly dominated fecal samples within 12 hours of defecation, obscuring true microbiome representation.
- •Immediate sampling of fresh feces is essential for accurate microbiome characterization; delayed or improperly stored samples can be identified by bloom taxa dominance.