Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.
Authors: Álvarez Narváez Sonsiray, Beaudry Megan S, Norris Connor G, Bartlett Paula B, Glenn Travis C, Sanchez Susan
Journal: Animals : an open access journal from MDPI
Summary
Gastrointestinal tract disorders remain a leading cause of mortality in horses, yet our ability to identify the specific microbial shifts underlying these conditions has been constrained by the limited taxonomic resolution of conventional 16S rRNA sequencing methods. Researchers compared target enrichment by hybridisation capture (TEHC)—a novel sequencing approach—against standard 16S amplicon sequencing using faecal samples from four horses and a commercial microbiome control, analysing both the absolute number of operational taxonomic units detected and the relative abundance profiles generated. TEHC substantially outperformed conventional amplicon sequencing, recovering significantly more OTUs at equivalent sequencing depths and yielding greater microbial richness according to alpha diversity metrics; beta diversity analysis further confirmed that TEHC captured a more complex and differentiated microbiome landscape across samples. These improvements in taxonomic resolution mean that researchers and clinicians may now be better positioned to detect the nuanced bacterial changes associated with disease states, potentially enabling more precise diagnosis and targeted management of gastrointestinal disorders. As microbiome analysis becomes increasingly integrated into equine practice, adoption of higher-resolution sequencing strategies such as TEHC could unlock clinically meaningful insights currently obscured by the limitations of PCR-based approaches.
Read the full abstract on PubMed
Practical Takeaways
- •TEHC offers improved diagnostic potential for investigating microbiome-related gastrointestinal issues in horses by providing greater bacterial species identification than standard methods
- •This enhanced taxonomic resolution may help identify specific microbiome signatures associated with different types of colic and other GITDs, supporting more targeted treatment approaches
- •Adoption of TEHC methodology could improve research quality and clinical insights into how microbiome composition relates to equine health outcomes
Key Findings
- •TEHC (target enrichment by hybridization capture) yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing at equal read depth
- •TEHC provided deeper and more accurate characterization of equine fecal microbiome composition based on relative abundance analysis
- •Alpha and beta diversity metrics demonstrated significantly richer microbiome diversity with TEHC compared to 16S amplicon sequencing
- •TEHC strategy enables more extensive taxonomic resolution for identifying specific bacterial changes associated with equine GITDs