Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture

Area of Science:

• Veterinary microbiology
• Equine health research
• Microbiome analysis

Background:

• Gastrointestinal tract diseases (GITDs) are a leading cause of mortality in horses.
• Previous research suggests a link between GITDs and the equine gut microbiome.
• Current sequencing methods lack the taxonomic resolution to identify specific bacterial changes related to GITDs.

Purpose of the Study:

• To compare a novel sequencing approach, TEHC, with conventional 16S rRNA gene amplicon sequencing.
• To evaluate the efficacy of TEHC in characterizing the equine fecal microbiome.
• To determine if TEHC provides a more accurate and comprehensive analysis of horse gut bacteria.

Main Methods:

• Comparison of TEHC and conventional 16S rRNA gene amplicon sequencing.
• Analysis of fecal microbiomes from four horses and one mock microbiome.
• Evaluation using operational taxonomic units (OTUs), relative abundance, and diversity metrics (alpha and beta).

Main Results:

• TEHC yielded significantly more OTUs than conventional sequencing at equal read counts.
• TEHC provided a deeper and more accurate characterization of the fecal microbiome.
• Diversity metrics confirmed a richer microbiome profile with TEHC sequencing.

Conclusions:

• The TEHC strategy offers a more extensive characterization of the equine fecal microbiome.
• TEHC surpasses conventional 16S rRNA gene sequencing for equine microbiome analysis.
• This enhanced characterization may aid in identifying bacterial changes associated with equine GITDs.