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Old 12-17-2015, 07:15 AM   #1
Naphtap
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Location: Ontario

Join Date: Sep 2015
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Default Controls to Consider for Metagenomics Project

Hi all,

I'm currently working on a number of projects where we sequence the 16S genes in environmental samples with the Illumina MiSeq platform. What I'm wondering is whether there's a way to determine whether we captured the entire microbial community by determining the DNA extraction efficiency.

I'm aware of rarefaction curves, but I wanted controls to be sure that we have a high DNA extraction efficiency. I was thinking that we could spike an environmental sample with a known amount of E. coli or some other species and see how much more the E. coli 16S abundances increased after the spiking compared to a sample that wasn't spiked.

I was also wondering if there are other independent experiments that can be correlated with 16S abundances so that we can be more certain that we accurately captured the microbial community in question. I was thinking of qPCRs and fluorescence assays, but are there other assays that can be used?

Thanks!
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