title: Effects of Eimeria maxima and Clostridium perfringens infections on cecal
design: Total DNA from the cecal contents was extracted with a QIAamp PowerFecal DNA Kit (Qiagen Inc, Qiagen, Valenica, CA). The hypervariable V3 -V4 regions (E. coli position 341 to 805) of the 16S rRNA genewere directly amplified from 10ng of total DNA using PAGE-purified Illumina platform-compatible adaptor oligos that contain features such as sequencing primers, sample-specific barcodes, and 16S PCR primers (forward primer, 341/357F: NNNNCCTACGGGNGGCWGCAG; reverse primer, 805/785R: GACTACHVGGGTATCTAATCC) as described elsewhere. After purification and quantification, amplicons from individual samples were pooled in equal mass (molar) ratios, and the library pool was sequenced using an Illumina MiSeq sequencer as previously described