Computational protocol: Beneficial Effect of Bidens pilosa on Body Weight Gain, Food Conversion Ratio, Gut Bacteria and Coccidiosis in Chickens

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Protocol publication

[…] The gut bacterial DNA collected from the feces of the chickens in Groups 1 to 4 on day 18 or 21 (i.e., day 4 and 7 post infection) were purified and used as templates for PCR amplification with 16S rRNA primers. Following pyrosequencing (Roche 454), chimeric sequences of the 16S rRNA sequences were removed using Chimera Check []. The trimmed sequences over 300 bp were analyzed using RDPipeline as published []. Briefly, 16S rRNA gene sequence alignment (Aligner), 16S rRNA gene sequence clustering (Complete Linkage Clustering), α-diversity index (Shannon Index and Chao1 estimator), rarefaction curve, and phylogenetic analysis (RDP classifier) were conducted. Principle component analysis and clustering analysis for bacterial genera were performed using the prcomp, heatmap3 and ggplot2 functions in R (the R Foundation for Statistical Computing). The hierarchical multi-level pie charts of bacterial compositions of experimental samples based on phylogenetic classifications were constructed using KRONA software []. […]

Pipeline specifications

Software tools RDPipeline, RDP Classifier, Ggplot2, Krona
Applications Miscellaneous, Phylogenetics, 16S rRNA-seq analysis
Organisms Gallus gallus, Bacteria
Diseases Coccidiosis, Gastrointestinal Diseases, Nervous System Diseases, Protozoan Infections