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.

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

“…In the initial study, Blastocystis -colonized patients exhibited a higher abundance of Ruminococcaceae and Prevotellaceae at the family level, whereas Lactobacillaceae, Enterococcaceae, Streptococcaceae and Enterobacteriaceae were enriched in Blastocystis -free patients. Of note, in this initial study, to analyze the Ion Torrent sequencing data, a homemade pipeline was developed using various publicly available tools such as Mothur [13] or EspritTree [29], databases such as the Silva small subunit RNA database and Ribosomal Database Project (RDP) and Perl/Python scripts [12].…”

“…Previously published datasets of a case-control study [12] evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile were used in this work.…”

“…The association between the sample name, sample ID (index), and Blastocystis sp. colonization status and group is available in Reference [12].…”

Pathogens, microbiome and the host: emergence of the ecological Koch's postulates

“…Very recently, a member of the eukaryome, Tritrichomonas musculis, was shown to activate the epithelial inflammasome and to induce protection against bacterial mucosal infection (Chudnovskiy et al 2016). Other protists, such as Giardia (Barash et al 2017) and possibly Blastocystis (Audebert et al 2016;Siegwald et al 2017), have also been shown to change the resident prokaryotic microbiota. However, data remain conflicting, pointing towards the fact that shifts in the microbiota through given eukaryotes might be strain specific.…”

Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome

“…Table 4 reveals that most reads ( >99%) identified from silkworm gut metagenome belong to the domain Bacteria. Taxonomic diversity was analysed not only with shotgun metagenomic data by different tools (BlastP against Nr database and MG-RAST against GenBank), but also by direct 16 S rRNA sequencing 32 , which showed the same tendency ( Table 5 ). Enterococcus , Acinetobacter , Bacillus and Enterobacter are dominant species in both strains ( Fig.…”