Abstract

This dataset comprises paired-end Illumina iSeq 100 16S rRNA gene amplicon reads (V3–V4 region) generated from equine gastrointestinal samples, including nematodes (n=43) and matched host fecal material (n=7) collected from Equus caballus (n=6) and Equus asinus (n=1) at slaughterhouse sampling. Raw sequencing data are provided as demultiplexed FASTQ files, accompanied by a structured metadata table enabling stratification by sample type (nematode vs feces), host species and sex, nematode subfamily/type and sex, gastrointestinal sampling site (caecum vs ventral colon), sampling location, and collection date. Library construction followed PCR amplification with Illumina overhang adapters and dual-indexing (Nextera XT), with pooled sequencing including 5% PhiX.