NEBNext Microbiome DNA Enrichment Kit

[Eva_seqs]

Hello,

I am considering to use the new NEBNext Microbiome Enrichment kit on human mucosal and fecal samples. There is a difference in % of human DNA between these two samples, so I am not expecting the same % enrichment between these two samples.

Does anyone have experience with this kit? What is the % enrichment you usually get, for what types of samples? Did anyone look at bias -i.e. is there taxonomic bias in the enrichment?

There is a recent PLoS One paper out on the method, but I was wondering whether anyone has any direct experience.

Thanks!

[SNPsaurus]

My academic lab has tested it a bit for zebrafish gut microbiomes. In our hands DNA quality mattered quite a bit, which is understandable since longer fragments will give you more DNA in the pulldown per methylated site.

[Eva_seqs]

Good to know about DNA quality, thanks. Did you by any chance experiment with different DNA concentrations and host/microbiome ratios?

[SNPsaurus]

We were using real samples, and the microbiome amount was small (maybe 1% of DNA), so I think we used as much input as possible to have reasonable complexity of the bacterial genomes. The kit certainly improved the representation, but it is a trade-off of extra work and cost, so we're still deciding if it is just better to brute-force it and also seeing if we can improve the selection more.

[ianclarke]

Hi Eva

I am the General Manager of NEB Canada. Please contact if you would like additional information on the microbiome kit

Ian