Computational protocol: Gut Bacterial Communities in the Giant Land Snail Achatina fulica and Their Modification by Sugarcane-Based Diet

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Protocol publication

[…] All sequences were globally aligned using the MUSCLE software and further refined manually. Distance data were generated from the clone library using the Kimura two-parameter model and analyzed using the computer program MOTHUR to group sequences into operational taxonomic units (OTU), based on a 97% sequence identity cutoff. MEGA4 was used to construct a UPGMA tree, which was bootstrap resampled 1000 times. Unweighted Principal Coordinates Analysis (PCoA) was performed to evaluate similarity among samples using UNIFRAC . […]

Pipeline specifications

Software tools MUSCLE, mothur, MEGA, UniFrac
Applications 16S rRNA-seq analysis, Nucleotide sequence alignment
Organisms Achatina fulica, Homo sapiens