DNA seq of piglets fecal microbiota
Reads were de-multiplexed based on Illumina indexing system. Sequences were analyzed using QIIME 1.5.0 (Caporaso et al., 2010). After filtering based on read quality and length (minimum quality = 25 and minimum length = 200), Operational Taxonomic Units (OTUs) defined by a 97% of similarity were picked using the Uclust v1.2.22 q method (Edgar, 2010) and the representative sequences were submitted to the RDP classifier (Wang et al., 2007) to obtain the taxonomy assignment and the relative abundance of each OTU using the Greengenes 16S rRNA gene database (McDonald et al., 2012). Alpha- and beta-diversity analyses were performed using QIIME 1.