Species-Level Gut Microbiota Analysis after Antibiotic-Induced Dysbiosis in Horses.
Authors: Di Pietro Rebecca, Arroyo Luis G, Leclere Mathilde, Costa Marcio Carvalho
Journal: Animals : an open access journal from MDPI
Summary
# Editorial Summary Whilst short-read sequencing has dominated equine microbiota research, long-read technologies offer potential for superior species-level classification; this study compared PacBio full-length 16S rRNA sequencing with standard Illumina methods in nine horses before and after oral trimethoprim-sulfadiazine administration (30 mg/kg twice daily for 5 days). Despite its theoretical advantages, PacBio sequencing failed to achieve meaningful species-level identification in equine faecal samples, though it did reveal greater overall bacterial richness and fewer unclassified sequences than Illumina V4 amplicon analysis. Both methods confirmed Bacteroidetes as the dominant phylum, followed by Firmicutes and Fibrobacteres, but PacBio identified a previously uncharacterised Bacteroidales species comprising 13% of the community—a finding warranting further investigation. The results underscore a critical gap in current reference databases for equine microbiota studies, suggesting that improved taxonomic databases tailored specifically to horses are essential before long-read sequencing can reliably guide clinical decision-making around antibiotic use and microbiota recovery.
Read the full abstract on PubMed
Practical Takeaways
- •Antibiotic-induced dysbiosis in horses causes significant microbiota disruption, but current sequencing technologies cannot fully characterize species-level changes—consider microbiota support strategies during and after TMS therapy
- •Improved reference databases for equine microbiota are critically needed; practitioners should be aware that existing sequencing results may underestimate microbial diversity
- •The persistent abundance of Bacteroidetes post-dysbiosis suggests this phylum recovers quickly; understanding this resilience may inform probiotic or dietary interventions
Key Findings
- •PacBio long-read sequencing failed to classify equine intestinal microbiota at the species level despite theoretical advantage over short-read methods
- •Bacteroidetes remained the most abundant phylum after TMS-induced dysbiosis, followed by Firmicutes and Fibrobacteres
- •An unknown Bacteroidales species comprised 13% of the microbiota and warrants further investigation
- •PacBio detected greater bacterial richness and fewer unclassified sequences compared to Illumina sequencing