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PICRUSt functional metagenomic prediction

KM Khin K. Z. Mon
YZ Yuhua Zhu
GC Ganrea Chanthavixay
CK Colin Kern
HZ Huaijun Zhou
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Metagenomic functional features of the microbial community were predicted using phylogenetic investigation communities by reconstruction of unobserved states (PICRUSt)17. Closed-reference OTU picks from QIIME were aligned to search for 16S sequences matching against the green genes reference OTUs at 97% identity. Generated biom file was normalized by dividing each OTU by known/predicted 16S copy number abundance and used for metagenomic prediction with PICRUSt where Kyoto Encyclopedia of Genes and Genomes (KEGG) genes & pathway abundance for each individual sample were generated. Data were then analyzed with Statistical Analysis of Taxonomic and Functional Profiles (STAMP) version 2.1.318. Differentially represented functional pathways (level 3 in hierarchy, representing KEGG pathways) between the two conditions (presented in extended error bar plots) were analyzed with two-sided Welch’s t-test on every pair of means where p <0.05 was considered significant. Confidence intervals of 95% were obtained by inverting the Welch’s tests.

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