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

Abstract

In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, 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 sequencing and analysis of these 96 human faecal samples, and the complete datasets from raw to analysed data. We also provide the key steps of the bioinformatic analyses, from library preparation to data filtering and OTUs tables generation. 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.

Figure 1

Schematic representation of the home-made bioinformatics pipeline for the analysis of targeted metagenomic Ion Torrent sequencing data, that included several publicly available tools (e.g. Mothur, EspritTree, QIIME or DESeq2), databases (the Silva small subunit RNA database and Ribosomal Database Project (RDP)) and home-made Perl/Python scripts.

Figure 2

Quality scores across all bases box-and-whiskers plot (FastQC Read Quality reports (Galaxy Version 0.67)). Red line=median value, blue line=mean value, yellow box=inter-quartile range, upper and lower whiskers = 10% and 90% points respectively.