Computational protocol: Killing Effects of an Isolated Serratia marcescens KH-001 on Diaphorina citri via Lowering the Endosymbiont Numbers

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Protocol publication

[…] To eliminate the low-quality sequences, PyroNoise algorithm in Mothur (version 1.33.3) were used (), and the Quantitative Insights Into Microbial Ecology (QIIME) platform (version 1.8.0) was implemented for Bioinformatics analysis (). Briefly, 16S rRNA operational taxonomic units (OTUs) were clustered using an open-reference OTU picking protocol based on 97% nucleotide similarity with the UCLUST algorithm (), and ChimeraSlayer was applied to remove chimeric sequences (). The relative abundance of each OTU was determined as a proportion of the sum of sequences for every sample, taxonomic relative abundance profiles were generated based on OTU annotation, and the microbial community structure was evaluated by biodiversity. Shannon index, phylogenetic diversity, chao1 index and the observed number of species were used to evaluate α diversity, and the weighted and unweighted UniFrac distances were used to evaluate β diversity using QIIME pipeline. […]

Pipeline specifications

Software tools PyroNoise, mothur, QIIME, UCLUST, ChimeraSlayer
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Serratia marcescens, Diaphorina citri, Escherichia coli, Wolbachia endosymbiont of Armadillidium vulgare str. wVulC
Diseases Drug-Related Side Effects and Adverse Reactions