Microbiome of Gallus gallus domesticus: ceca luminal content
DNA was extracted from samples using the Qiagen DNeasy 96 PowerSoil Pro Kit, with purity assessed by NanoDrop and concentrations quantified using the PicoGreen assay, aiming for 0.2 ng/l. Libraries for shallow shotgun sequencing were prepared with the Illumina NexteraXT DNA Library Preparation Kit. This involved fragmenting 0.25 ng of genomic DNA with transposase, adding unique adapters, and amplifying it via a 12-cycle PCR. Library size and concentration were confirmed using capillary electrophoresis and PicoGreen fluorimetry, respectively. Sequencing was performed on the NovaSeq 6000 system using a 2x150 bp paired-end flow cell and Illuminas 2-color SBS chemistry at the University of Minnesota Genomics Center. Base call files generated by Illumina Real Time Analysis software were used for primary analysis and de-multiplexing with Illuminas bcl-convert v4.0.3.