Raw multiplexed 16S rRNA sequencing data for a metabarcoding study of gut microbiota in birds sampled across wetland habitats

The avian fecal samples were collected from various marshes in northern France. DNA was extracted from samples using the DNeasy® mericon® Food Kit. Microbial diversity was assessed using primers targeting the V4 hypervariable region of the bacterial 16S rRNA gene: forward (515FY) and reverse (806RB). Libraries were prepared in triplicate using the Nextera XT Index Kit and sequenced on an Illumina NovaSeq 6000 system. The experiment included several controls to monitor contamination and sequencing artifacts: Six negative DNA extraction controls (CEXT) Six aerosol controls (TAER) Two PCR controls (CPCR) Three bioinformatics blanks (BLNK; unused tag combinations to detect false positives caused by tag jumps) A triplicate of one positive control (CPOS), consisting of a mock community from the NGS Standard: 20 Strain Even Mix Genomic Material - MSA-1002 (ATCC) For high-throughput sequencing, we employed a two-step, tailed PCR approach to construct paired-end, ready-to-pool amplicon libraries (Illumina, Inc., United States). The dataset contains raw multiplexed sequencing data, and detailed primer and tag sequences can be found in the provided files (README).