Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization

Data from: Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization (Siegwald et al., Sci. Data, 2017). In a previous paper (Audebert et al., Sci Rep, 2016), we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity. We report here on the Ion Torrent targeted metagenomic analysis of these 96 human faecal samples. We provide the key steps of the bioinformatic analyses, and data files extending from raw data to the final BIOM file, through intermediate files from our home-made 16S targeted metagenomic analysis pipeline (i.e. OTU count tables and BIOM file before data normalization). This data represents a valuable resource for the scientific community, enabling re-processing of these targeted metagenomic datasets through various pipelines and a comparative evaluation of microbiota analysis methods.