Computational protocol: Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model

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Protocol publication

[…] Paired-end reads were joined using fastq-join from the ea-utils software package. Sequences were analysed using the open source software package Quantitative Insights Into Microbial Ecology (QIIME v. 1.8.0). After demultiplexing and quality filtering of sequences, chimeras were detected and removed using USEARCH 6.1 ( The resulting high quality sequences were processed to generate OTUs with a 97% similarity threshold that were then taxonomically assigned on Greengenes database using UCLUST ( variable number of sequences was obtained per sample (range [20,641–231,849] and [5,804–418,919] for stool and mucosa samples, respectively). Therefore, for fair comparison, the sequence number of each sample was randomly normalized to the same sequencing depth (20,500 sequences per stool sample and 5,800 sequences per mucosal sample). The alpha (Chao 1, Shannon’s diversity index, phylogenetic diversity (PD)) and beta-diversity (Principal Coordinate Analyses (PCoA) on a weighted Unifrac distance matrix analyses) were performed using QIIME. […]

Pipeline specifications

Software tools ea-utils, QIIME, USEARCH, UCLUST, UniFrac
Databases Greengenes
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Homo sapiens, Mus musculus, Escherichia coli
Diseases Inflammatory Bowel Diseases, Drug-Related Side Effects and Adverse Reactions
Chemicals Benzo(a)pyrene, Polycyclic Aromatic Hydrocarbons