Computational protocol: An In Vitro Model of the Horse Gut Microbiome Enables Identification of Lactate-Utilizing Bacteria That Differentially Respond to Starch Induction

Similar protocols

Protocol publication

[…] Sequences were demultiplexed and trimmed of bar codes and primer sequences, then filtered for quality and reverse and forward reads were assembled into contigs using FastQC []. Sequence processing was done in QIIME [] using the following workflow: Reads were aligned using default parameters (PyNAST) [], operational taxonomic units (otus) were picked at the 97% similarity threshold using the subsampled open-reference option, chimeric sequences were identified using ChimeraSlayer [] and removed, taxonomic assignments were made against the most recent greengenes database (October, 2012) []. Sequence data has been submitted to the NCBI Sequence Read Archive (SRA), Accession number: SRP028582. […]

Pipeline specifications

Software tools FastQC, QIIME, PyNAST, ChimeraSlayer
Databases Greengenes
Application 16S rRNA-seq analysis
Organisms Equus caballus, Escherichia coli, Bacteria
Diseases Acidosis
Chemicals Fatty Acids, Hydrogen Sulfide, Lactic Acid