Computational protocol: Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples

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Protocol publication

[…] Quality filtering of sequences was performed using MOTHUR []. An average q score of 25 and a 25 bp window, with a max of 8 bp homopolymer and min read length of 150 bp and one bp difference in primer sequence were used as filtering criteria. Barcodes were used to assign reads to samples, and sequence data from different runs was concatenated into a single file for further analyses. Sequences were clustered into operational taxonomic units (OTU) based on 97% similarity using USEARCH global search algorithm [] against the Greengenes release 13_8 97% OTU database []. Ribosomal gene copy number were estimated using picrust []. […]

Pipeline specifications

Software tools mothur, USEARCH, PICRUSt
Databases Greengenes
Application 16S rRNA-seq analysis
Organisms Equus caballus, Homo sapiens, Bos taurus