Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.
Abstract: GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the current microbiome sequencing methods has hampered the identification of specific bacterial changes associated with GITDs in horses. Here, we have compared TEHC, a new approach for 16S rRNA gene selection and sequencing, with conventional 16S rRNA gene amplicon sequencing for the characterization of the equine fecal microbiome. Both sequencing approaches were used to determine the fecal microbiome of four adult horses and one commercial mock microbiome. Our results show that TEHC yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing when the same number of reads were used in the analysis. This translated into a deeper and more accurate characterization of the fecal microbiome when the samples were sequenced with TEHC according to the relative abundance analysis. Alpha and beta diversity metrics corroborated these findings and demonstrated that the microbiome of the fecal samples was significantly richer when sequenced with TEHC compared to 16S amplicon sequencing. Altogether, our study suggests that the TEHC strategy provides a more extensive characterization of the fecal microbiome of horses than the current alternative based on the PCR amplification of a portion of the 16S rRNA gene.
Publication Date: 2024-01-29 PubMed ID: 38338088DOI: 10.3390/ani14030445Google Scholar: Lookup
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- Journal Article
Summary
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The research explores a new approach named Target Enrichment by Hybridization Capture (TEHC) for better understanding how changes in horse’s gut microbiome may connect to Gastrointestinal tract diseases (GITDs), which often cause fatalities among horses. The unprecedented high taxonomic resolution of TEHC presents a significant improvement over the existing method, opening up opportunities for more accurate and detailed analyses of horse’s fecal microbiomes.
Context & Purpose of the Research
- Gastrointestinal tract diseases (GITDs) are a leading cause of death among horses, with prior research suggesting a link between these diseases and alterations in the horse’s gut microbiome.
- Existing methods for sequencing the microbiome have been limited in their ability to identify specific bacterial changes related to GITDs due to poor taxonomic resolution.
- This research investigates the effectiveness of the TEHC, an innovative method for 16S rRNA gene selection and sequencing, to ensure a more comprehensive and detailed approach in characterizing the equine fecal microbiome.
The Research Methodologies
- Conventional 16S rRNA gene amplicon sequencing and the newly proposed TEHC were both used to understand the fecal microbiome of four adult horses along with a commercial mock microbiome.
- The two methods were analyzed side-by-side, comparing the number of operational taxonomic units (OTUs) derived from each method.
Key Findings
- The study found that the TEHC method resulted in significantly more OTUs than conventional 16S amplicon sequencing when the same number of reads were used in the analysis.
- This allowed for a more in-depth and precise characterization of the fecal microbiome, with the relative abundance analysis confirming these results.
- Alpha and beta diversity metrics further supported these findings, indicating that the fecal sample’s microbiome was significantly richer when TEHC was used compared to using traditional 16S amplicon sequencing.
Implications of the Study
- Overall, the study suggests that the TEHC strategy provides much more comprehensive characterization of the equine fecal microbiome.
- Such a detailed analysis could enable more accurate identification of specific bacterial changes associated with GITDs in horses and potentially lead to better prevention and treatment strategies for these conditions.
Cite This Article
APA
Álvarez Narváez S, Beaudry MS, Norris CG, Bartlett PB, Glenn TC, Sanchez S.
(2024).
Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.
Animals (Basel), 14(3), 445.
https://doi.org/10.3390/ani14030445 Publication
Researcher Affiliations
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA.
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA.
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA.
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA.
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA.
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA.
Grant Funding
- Animal Health Capacity Grant SNIFA0001344201 / United States Department of Agriculture
Citations
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