Computational protocol: Sputum Microbiota Associated with New, Recurrent and Treatment Failure Tuberculosis

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Protocol publication

[…] The 454 -generated FASTA file (.fna) and quality score file (.qual) were acquired as raw sequence data. The multiplexed reads were split and assigned to samples based on their unique nucleotide barcode. We screened, trimmed, and filtered the sequences using default settings of QIIME virtual machine version 1.5.0 (http://www.qiime.org) []. Qualified sequence fragments were assigned to taxonomic identities using reference databases from greengenes (http://greengenes.lbl.gov). The differences in taxonomic composition of microbial communities were analyzed by using Kruskal-Wallis test among three or four groups or Mann-Whitney U test between two groups (IBM SPSS Statistics, v20, and GraphPad Prism software Version 6.01). Alpha diversity and beta diversity measures were calculated and plotted using QIIME. Odds ratio (OR) was calculated and Fisher’s exact test was used to determine if the frequency distribution of the presence of a specific microorganism was associated with the TB disease state in STATA (StataCorp LP, version 9.0). […]

Pipeline specifications

Software tools QIIME, SPSS
Application Miscellaneous
Organisms Homo sapiens, Mycobacterium tuberculosis
Diseases Lung Diseases, Tuberculosis