Dear Qiime friends,
In order to identify differential abundance taxa between two group (PN (12 sample)and PT(12 sample) using lefse ifor my microbiome study. Dokdo was used to produce a input file (input_table.tsv in attached file) for lefse analysis. After process through the following scripts, 2 and 12 genera were assigned for PN and PT, respectively. Among the fourteen differential abundance genera, these genera show higher sequence frequencies and are present in more samples in their group than the other one, except Rothia, which was chosen as an representative biomarker for PN. (LDA plot show in attached file)
Viewing the input_table.tsv or the taxanomy barplot level 6 output, Rothia present in 4 samples in PN and 10 sample in PT groups with frequencies of (0.19%, 20.52%, 0.90%, 0.70%) and (0.69%,0.44%, 0.48%’ 4.91%, 0.46%, 0.28%, 0.54%, 1.42%, 0.55%,1.42%) in each positive sample, respectively.
I just wonder, whether this look-odd result could be frequently seen in lefse output, and
how should I properly explain the result for Rothia to represent the PN group?
Any suggestion will be highly appreciated.
Sincerely,
Jrhau Lung
(I have learned that different algorithms adopted to deal with the zero inflation for differential abundant taxa determination for microbiome study could assign totally different taxa from the same 16S sequence dataset. But assign a taxa present in more number of samples in another group to represent a group in which it occurs in fewer number of samples still look odd to me).
table.qza (596.6 KB)
silva-taxonomy-138-99-V3-V4.qza (260.5 KB)
sample-metadata.tsv (11.4 KB)
