Computational protocol: Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens

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Protocol publication

[…] Sequencing data analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline (v.1.8.0; []). The paired-end reads were stitched together and joined reads were demultiplexed and quality filtered. A de novo operational taxonomic units (OTUs) were formed at 97% similarity using UCLUST []. Representative sequences from each OTU were aligned to 16S reference sequences with PyNAST [] and used to infer a phylogenetic tree with FastTree []. Taxonomic assignments within the GreenGenes taxonomy [12/10 release] [] were generated using uclust consensus taxonomy assigner. The OTU tables were rarefied at 13,265 sequences per sample for alpha and beta diversity. Analyses of community similarity (β-diversity) were performed by calculating pairwise distance using phylogenetic metric UniFrac []. Three measures of alpha diversity were computed including Good’s Coverage, an indicator of sequencing depth, Shannon diversity, an indicator of evenness in community structure, and richness, the number of OTUs observed. OTU abundances were normalized to the total number of reads in each sample (relative abundance), to test the differences in taxon abundances. Phyla/genera appearing in at least 75% of samples were considered. […]

Pipeline specifications

Software tools QIIME, UCLUST, PyNAST, FastTree, UniFrac
Databases Greengenes
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Gallus gallus, Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344, Bacteria
Diseases Muscular Dystrophy, Duchenne
Chemicals Butyrates