MetaPhlAn4 can not profile eukaryote?

Microbial community profiling MetaPhlAn
1

Hi developers:
Thanks for your effects in developing and maintaining MetaPhlAn4!
Recently, I installed MetaPhlAn4 and downloaded the database “mpa_vOct22_CHOCOPhlAnSGB_202212” to profile several metagenomes from kelp tissues.
However, using the command “metaphlan …/…/2.qc/HK-t_1_kneaddata_paired_1.fastq,…/…/2.qc/HK-t_1_kneaddata_paired_2.fastq --input_type fastq -o K1_t.txt --nproc 30 --stat_q 0.1 --bowtie2out bowtie2out_K1_t.bz2” (–stat_q 0.2 also tried), there are many bacterial taxonomies but no eukaryotic taxonomy (especially the kelp) in the result file.
So, I wonder if MetaPhlAn4 can profile eukaryotes or not. Or, there is no marker of kelp in the MetaPhlAn4 database, so there is no kelp taxonomy in my result file?
Looking forward to your reply!
Thank you!
Sincerely,
Jiulong

2

Dear @Jiulong-Zhao
The database mpa_vOct22 also contains a set of micro-eukaryotic species, you can have a look at the species currently in the database here: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_species.txt.bz2

3

Hi Developers:
I also meet these issues. mpa_vOct22 include the micro-eukaryotic species candida, which I am sure there are many candida species present in my samples, however, the results have not detected the candida when using Metaphlan4 and mpa_vOct22.

4

Hi Developers:
I also meet these issues. mpa_vOct22 include the micro-eukaryotic species candida, which I am sure there are many candida species present in my samples, however, the results have not detected the candida when using Metaphlan4 and mpa_vOct22.

5

Hi @lzh1982 this is a tricky question to assess… False negatives in MetaPhlAn can be due to several factors like low abundance, strains not accounted for the building of the database, biased in the extraction protocols, etc. Have you tried to run other profilers to compare the results?