Rapid bacterial community profiling of equine microbiomes using Oxford Nanopore sequencing

Published Wed, Jul 22, 2026

foals — Credit: Barnabas Davoti from Pexels

Members of the Horse Microbiome Research Group recently published a new study in the Journal of Medical Microbiology, led by Dr. Joy Leng, who is currently undertaking the Alborada Well Foal 2 project. This research aims to understand how the foal gut microbiome develops by investigating the microbiomes of mares and their foals.

Using samples collected during a pilot study, the team successfully profiled bacterial communities present in equine feces, saliva, skin and milk by sequencing the full-length 16S rRNA gene with Oxford Nanopore technology. Sequencing was performed in-house using the portable MinION Mk1D platform, providing a rapid, cost-effective workflow with data analyzed through Oxford Nanopore's user-friendly EPI2ME software.

The study demonstrated distinct bacterial communities across different anatomical sites, highlighting the ability of long-read sequencing to generate high-quality microbiome profiles quickly and efficiently.

Rapid bacterial community profiling of equine microbiomes using oxford nanopore sequencing — Quality control figures showing the read quality, length and base yield above read length from the report generated from EPI2ME analysis of skin sample 1. Read quality for most of the reads is high. Nearly all of the reads sequenced are 1,500 bp long which is the length of the whole 16S rRNA gene. Credit: *Journal of Medical Microbiology* (2026). DOI: 10.1099/jmm.0.002176

This work showcases the potential of Oxford Nanopore sequencing as a research tool and future clinical tool for rapid bacterial identification and microbiome profiling. It also provides an important foundation for ongoing studies investigating the equine microbiome.

Publication details

J. Leng et al, Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing, Journal of Medical Microbiology (2026). DOI: 10.1099/jmm.0.002176

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Citation: Rapid bacterial community profiling of equine microbiomes using Oxford Nanopore sequencing (2026, July 21) retrieved 22 July 2026 from https://phys.org/news/2026-07-rapid-bacterial-community-profiling-equine.html

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