the weird microbial composition when using different library preparation kit

[jwdebelius (Justine Debelius)]

Hi @Chih-Ying,

Welcome to the :qiime2: forum!

I can't speak to the differences in Nexera and Treseq nano specifically, but kit effects are a pretty well known issue. You might want to look at the MBQC paper which discusses specific issues related to kit effects. You might also be interested in past contaminant removal threads, although I think this is maybe less relevant:

Discussion: methods for removing contaminants and cross-talk

Thanks for the report @lewisNU! I have not tried this method yet, or heard any reports on the forum from others who have given independent tests of it, so it is very good to hear your results. Just to be clear: decontam is not yet incorporated in QIIME 2 and is not associated with the core :qiime2: development team. I am excited to try this method out and incorporate it into :qiime2: when I can — and am very excited to hear about what others are doing for contaminant detection and removal. W…

Harmonization is a lot harder, and depends on how you plan to analyze your data. You might look at the perc-norm plugin, which may help with some of the normalization, although I'm not sure how you integrate this across analysis.

https://library.qiime2.org/plugins/q2-perc-norm/5/

In other cases, it really depends on what analysis you're planning to do.

@Chih-Ying

however when I check the abundance table on phylum level, D_0_Bacteria;_ has higher abundance in the samples using Truseq nano library preparation kit. In contrast, the samples with nextera library preparation kit have much lower abundance of D_0_Bacteria;_ .

Does the nextera kit have more Archea? Or just more unclassified reads?
Were there any other differences in parameters beteen the two kits?

Best,
Justine