Libraries pooling of microbial DNA


I write to you wondering to know if libraries pooling of bacterial DNA extracted from the gut of different species using 3 different kits will affect metagenomics investigations using QIIME2.

Thank you

Hi @M_F ,
different kits will affect measured compositions of microbiome data (this is not an issue with QIIME 2, it is an issue with how different kits can skew abundances or introduce reagent contaminants).

I recommend reading this paper on the topic: Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium - PubMed

So you could give it a try and see what you see… but it is only worth it if kit is not a covariate with some factor of interest, e.g., control samples use one kit and treated samples use another kit. Otherwise you cannot distinguish treatment vs. kit effects.

Good luck!