the weird microbial composition when using different library preparation kit

Hello, have a good time. I am really new in qiime2.
I have trouble with combining a dataset which were made by 5 sequencing runs. Two sequcing runs use the Truseq nano library preparation kit and the others using nextera library preparation kit.

I run my microbiome pipeline starting from demultiplexed fastq, 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;_ .

my questions are:
(1) how to combine the datasets using different library preparation
(2) how to eliminate bias between each sequencing run
(3) why the D_0_Bacteria;_ has extremely different between two library preparation kit
Could you give me some advices on how to face those situations?

Thanks a lot

Chih-Ying

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