Raw Data for the Analysis of Fish Gut Microbial Diversity in the Middle Reaches of the Jialing River

This dataset presents raw and processed sequencing data for analyzing the gut microbiota of eight fish species collected from the middle reaches of the Jialing River (a 633-km channelized stretch from Zhaohua to Hechuan) between 2022 and 2024. The studied species are: Leiocassis crassilabris (CCW), Carassius auratus (JY), Cyprinus carpio (LY), Siniperca chuatsi (G), Hemibagrus macropterus (DQH), Hemibarbus maculatus (HH), Ctenopharyngodon idellus (CY), and Xenocypris davidi (HWG).The data were generated by paired-end sequencing (2 × 250 bp) of the bacterial 16S rRNA gene V3-V4 region on an Illumina NextSeq 2000 platform. Raw sequencing reads are stored in the rawData/ directory, containing raw forward (R1.raw.fastq.gz) and reverse reads (R2.raw.fastq.gz) for each sample. These reads were processed using the described pipeline: quality control with Fastp (v0.19.6), assembly with FLASH (v1.2.11), and clustering into operational taxonomic units at 97% similarity using the UPARSE workflow within USEARCH (v7.1). The resulting high-quality, assembled sequences are archived in the valid/ directory (*.fastq.gz). Statistical reports in the reportStat/ directory (e.g., sample_data.stat.txt) document key metrics (e.g., sequence count, length) per sample, with row labels as sample IDs (corresponding to species abbreviations) and column headers as statistical items, measured in counts of sequences or base pairs. The dataset is complete with no missing data.