Computational protocol: Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδT cells

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Protocol publication

[…] Sequences were analyzed using the mothur pipeline, version 1.33.3 as described previously. Sequences with a distance-based similarity of 97% or greater were grouped into operational taxonomic units (OTU) using the furthest neighbor algorithm and classified using a modified in-house database containing sequences from GreenGenes 99 and retrieved 16S sequences from Genbank; OTU-based microbial diversity was estimated by calculating the Nonparametric Shannon diversity index (α-diversity). Sequence abundance profiles in each sample were used for downstream statistical and modeling analysis. A phylogenetic tree was inferred using Clearcut on the 16S rRNA sequence alignment generated by mothur. […]

Pipeline specifications

Software tools mothur, Clearcut
Databases Greengenes
Application Phylogenetics
Organisms Mus musculus