Piglet colon content, block 8, piglet 3, treatment 4, day0
General amplification and sequencing preparation are as described by Sanschagrin and Yergeau (2014). Amplification of the 16S rRNA gene was performed using the primer pair F343 (5-TACGGRAGGCAGCAG-3) and R533 (5-ATTACCGCGGCTGCTGGC-3), which targets the V3 hypervariable region (Yergeau et al., 2014). All 16S rRNA gene PCR products were run on 1.2% agarose gels and purified using the PureLink Quick Gel Extraction Kit (Invitrogen, Life Technologies). PCR products were quantified using the Qubit dsDNA HS Assay Kit and Qubit Fluorometer (Life Technologies), and combined in equimolar ratios before sequencing. We multiplexed 64 samples for each sequencing run, giving a total of two amplicon pools. Sequencing was performed on an Ion Torrent Personal Genome Machine (Life Technologies) using the 316 Chip and associated kit, following manufacturer protocols.