README file
Data Set Title: Microbiome of Equine Gastrointestinal Nematodes
Data Set Authors: 
Fabio Gentilini (Department of Veterinary Medical Sciences, University of Bologna), ORCID 0000-0002-0970-4827;
Laura Stancampiano (Department of Veterinary Medical Sciences, University of Bologna), ORCID 0000-0001-6271-9887;
Maria Elena Turba (Genefast srl), ORCID 0000-0003-4369-8536.
Data Set Contact Person: 
Fabio Gentilini (Department of Veterinary Medical Sciences, University of Bologna), ORCID 0000-0002-0970-4827, email fabio.gentilini@unibo.it. 
Data Set License: 
this data set is distributed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, https://creativecommons.org/licenses/by/4.0/. 
Publication Year: 2025
Data set Contents
The data set consists of:
•	1 archive in .zip format, named Microbiota-Equus-Nematodes_fastQfiles.zip, containing Illumina-based 16S rRNA gene amplicon sequencing FASTQ data (100 .fastq.gz files)
•	1 metadata file in .xlsx format
Microbiota-Equus-Nematodes_metadata.xlsx
•	1 README file in .rtf format
Microbiota-Equus-Nematodes_README.rtf
Data set Documentation
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.
Content of the files 
•	zip archive Microbiota-Equus-Nematodes_fastQfiles.zip contains 100 raw FASTQ files (in .fastq.gz format) generated by Illumina-based 16S rRNA gene amplicon sequencing. The names of the .fastq.gz files are indicated in the forward-absolute-filepath and reverse-absolute-filepath columns of the file reporting the samples metadata (Microbiota-Equus-Nematodes_metadata.xlsx);
•	file Microbiota-Equus-Nematodes_metadata.xlsx contains the metadata describing the sequenced samples.
File specifications
File format:
•	Raw sequencing data are provided as paired-end FASTQ files (compressed format, .fastq.gz) generated by Illumina sequencing.
•	Each sample is represented by two files corresponding to forward (R1) and reverse (R2) reads.
Sequencing platform:
•	Illumina iSeq 100 System
Target region:
•	V3–V4 region of the 16S rRNA gene
Read length:
•	Paired-end reads (2 × 150 bp, before quality trimming)
Quality control:
•	A 5% PhiX Control v3 (Illumina) spike-in was included to monitor sequencing performance.
Data availability:
•	Raw FASTQ files are deposited without prior host removal or taxonomic filtering to allow independent reprocessing and reproducibility.
Data sources 
The dataset originates from fecal and nematode samples collected from equids, including Equus caballus (n = 6) and Equus asinus (n = 1), at a licensed slaughterhouse.
A total of 50 biological samples were collected, comprising 43 nematode samples and 7 fecal samples.

Methodologies
Reads were generated by Illumina iSeq 100 paired-end sequencing of PCR-amplified V3–V4 regions of the 16S rRNA gene, using dual-indexed libraries prepared with Nextera XT adapters and including a 5% PhiX control spike-in.
List of variables 
Associated metadata are provided in file Microbiota-Equus-Nematodes_metadata.xlsx in tabular format and include the following variables:
•	sample id – unique identifier for each biological sample
•	ID_S_L – Sample identifier at the time of sampling. The first digit indicates the equid number, the letter specifies whether the sample was collected from the caecum or the ventral colon, and the third element is the sequential sampling number for that equid at the same gastrointestinal site.
•	ID_Equid – unique identifier of the equid from which the sample was taken 
•	biome – Sample type (feces or nematode) 
•	h_Tract – Anatomical site (caecum or ventral colon)
•	n_Sex – nematode sex (where available)
•	n_Subfamily and n_Genus – Nematode type (taxonomic or morphological classification, when applicable)
•	forward-absolute-filepath – Illumina run identifier for the sequenced forward read
•	reverse-absolute-filepath – Illumina run identifier for the sequenced reverse read
•	Collection_date – date of collection of the sample
•	Place and Site – Sampling location (location of the slaughterhouse site), E_R means “Emilia-Romagna”
•	host- species – Equus caballus or Equus asinus
Metadata are structured to enable downstream stratification, diversity analyses, and reproducible reanalysis.