Computational protocol: Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection

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Protocol publication

[…] QIME software was used for the filtering analysis. Low-quality sequences were truncated, and the ends of the corresponding sequences were connected using Flash software. High-quality sequences were classified into multiple operational taxonomic units (OTUs) with UCLUST software based on a similarity greater than 97%. The mean lengths of the sequence reads were classified into different taxonomic categories using MGRAST. The taxon abundance of each sample was categorized with the RDP classifier. The diversity of the two worm groups was analyzed using the Mother software according to the species richness in the list of OTUs. The phylotype richness was evaluated by the Chao/Ace calculation, and the Shannon index of diversity was used as an estimator of both the richness and community evenness. The extent of similarities between different ecosystems was investigated using the UniFrac β-diversity.Statistical analyses were based on the number of sequence reads that belonged to each taxa and were performed as described by Li. SPSS 16.0 software was used for the statistical analyses. Significant differences in basal characteristics between the groups were calculated by one-way analysis of variance and Student’s t test for continuous variables. P < 0.05 was considered statistically significant. […]

Pipeline specifications

Software tools UCLUST, RDP Classifier
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Caenorhabditis elegans, Equus caballus
Diseases Escherichia coli Infections, Infection