Shotgun metagenomic sequencing of adult Daphnia magna microbiome
100 adult Daphnia magna were ground, passed through a 50% sucrose filter, and centrifuged to isolate bacterial cells. DNA was extracted from the remaining pellet using the Qiagen DNEasy Blood & Tissue Kit, using the complete animal tissue protocol. A sequencing library was prepared using the Illumina Nextera XT protocol. Input DNA was quantified using the Qubit dsDNA system. Libraries were quality checked using the Agilent Technology 2100 Bioanalyzer. Manual normalization of libraries was performed due to final yields <10nM. Paired-end sequencing was performed using a MiSeq v2 reagenet kit.