beta-diversity analysis on pathways/functions

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Marco Severgnini

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Nov 13, 2019, 10:28:17 AM11/13/19
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Dear all, I'm performing data analysis on a set of shotgun metagenome samples and, I was able to create tables in .biom format containing counts of reads supporting functions or pathways for each sample. Now I'm wondering if these tables could be analyzed by QIIME and, in particular, if I can apply a "standard" beta-diversity analysis on them, i.e.: calculate inter-sample distances (with non-phylogenetic metrics), perform PCoA, perform "adonis" test to find whether two experimental classes differ etc.

Can this be made for BOTH functions and pathways (thus, grouping functions to upper hierarchical levels) or from an microbial ecology point-of-view I'm trying to do something meaningless or (even worse) wrong?

Thank you in advance for any help.
All the best

Marco

Eric Franzosa

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Nov 18, 2019, 3:44:59 PM11/18/19
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Hi Marco,

Definitely fair to do this sort of analysis on function totals OR function stratifications (but I wouldn't mix them). Many studies have shown that the former tends to be less diverse than the equivalent taxonomic comparison. This is due to a combination of factors, including 1) housekeeping functions (shared by all/most taxa) tending to inflate community similarity at the functional level and 2) functions specialized to a given environment type that can be satisfied by different mixtures of taxa.

Thanks,
Eric



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