This dataset contains FASTQ files of sequencing data from the study "The Influence of Vaginal Microbiota on Ewe Fertility: A Metagenomic and Functional Genomic Approach" conducted by the same research team. The dataset includes raw metagenomic sequencing reads generated from the vaginal microbiota of ewes using nanopore technology. The data comprises 13 sequencing runs performed with nanopore technology. Each run contains 24 FASTQ files, with each file corresponding to a unique barcode that represents the sequence of a specific sample (see the metadata file for details). Barcode 24 in each run is a control and does not correspond to a biological sample. Run FAW56643 includes 21 samples, so barcodes 22 and 23 are empty and not associated with any sequences. Details of the samples and their corresponding barcodes are provided in the metadata table. The sequencing data have been filtered to remove reads shorter than 200 base pairs to minimize noise and optimize storage efficiency. These data were analyzed to investigate the composition and diversity of microbial communities, their potential influence on reproductive performance, and the genes and pathways associated with these communities.