Composition of the fecal microbiota of CDX2P-CreERT2;Apcfl/fl mice and CDX2P-CreERT2;Apcfl/fl;Dhpsfl/fl mice
DNA was extracted frozen fecal samples from CDX2P-CreERT2;Apcfl/fl mice and CDX2P-CreERT2;Apcfl/fl;Dhpsfl/fl mice using the QIAamp Fast DNA Stool Mini Kit (Qiagen). DNA was quantified and controlled using Qubit Fluorometric Quantification (Thermo Fisher Scientific) and the V4 region of the 16S rRNA gene was sequenced with the Illumina MiSeq. Sequences were processed with Mothur, version 1.44,7 aligned to the SILVA database release 132, and taxonomically classified with the Ribosomal Database Project classifier 16.8, 9 Non-bacterial sequences and chimeric sequences detected by UCHIME were removed. Operational Taxonomic Unit clustering was performed with VSEARCH, using abundance-based greedy clustering.10 Rarefaction followed by alpha-diversity, and beta-diversity calculations were repeated 1000 times, and the results were averaged.