Computational protocol: Health and Disease Imprinted in the Time Variability of the Human Microbiome

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Protocol publication

[…] The bacterial and archaeal taxonomic assignments were obtained by analyzing 16S rRNA sequences, which were clustered into operational taxonomic units (OTUs) with 97% sequence identity by QIIME (). SMS data () were analyzed and assigned at the strain level by the Livermore metagenomic analysis toolkit (LMAT) (), according to their default quality threshold. The genus, with the best balance between error assignment and the number of taxa, was chosen as our reference taxonomic level. We verified that our conclusions were not significantly affected by selecting the family or species as the reference taxonomic level (see ). [...] Reads from the selected studies were first quality filtered with the FastX toolkit (), allowing only those reads scoring over 25 for quality in 75% of the complete sequence. 16S rRNA reads with 97% nucleotide sequence identity were then clustered into OTUs with the QIIME software package () (version 1.8). We used an open reference OTU picking workflow in all cases. The clustering method used was UCLUST, and the OTUs were matched against the Silva database () (version 111, July 2012) and were taxonomically assigned by a UCLUST-based consensus taxonomy assigner. The parameters used in this step were a similarity of 0.97, a prefilter percent identity of 0.6, 20 maximum accepts, and 500 maximum rejects. […]

Pipeline specifications

Software tools QIIME, LMAT, FASTX-Toolkit, UCLUST
Application Metagenomic sequencing analysis
Organisms Homo sapiens
Diseases Epilepsy, Temporal Lobe, Pierre Robin Syndrome