Non-Microbial profiling

Good morning,
I’m new in bioinformatics.
I’ve read the metaphlan3.0 manual and it says that analysis with metaphlan allows to reach the spice-level resolution for bacteria, archeae, viruses and eukaryotes but my outputs show only bacteria abundance, am I doing something wrong?

The command I use is :

metaphlan file_name.fastq --input_type fastq > output_file_name.txt

Which eukaryotes are included in the database?
Is there any possibility to consult the metaphlan database?
Is it possible to incorporate another database to my analysis?

Thank you for your help.

A list of species included in the database is available in the marker info file here
You cannot incorporated another database to MetaPhlAn, but you can expand it with the new markers for the species of interest.

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Hello Francesco,

Some markers not present in this file are present in the fasta file (mpa_v30_CHOCOPhlAn_201901.fna), can the species they belong to be found by metaphlan3? If yes, under what taxonomy would they appear in the profile tsv file?

Thank you very much for your help,


Hi @AgnesBaud ,
Thanks for reporting this. Could you provide us a list with the markers not present in the markers info file?

Hello @aitor.blancomiguez

Here is the list. I just realized that for all these markers, it’s only a matter of the organism txid at the beginning of the name.

Example: 373404__GeneID:6921131 in fasta is 2006134__GeneID:6921131 in markers_info

markers_in_fasta_but_not_in_markers_info.txt (45.5 KB)

Hi @AgnesBaud
Thanks for reporting this, it seems all the missing markers are discarded markers from viral species (for different reasons). While in the FNA file it should not affect the metaphlan results, but we will remove them from the fasta file in the next db version. Thanks a lot

Hi @aitor.blancomiguez,

Thank you for your answer. So the markers that are in the markers info file but not in the fasta file (these 1961 markers, but also 442 other markers) are all discarded markers that do not affect the metaphlan results? Or are some stored somewhere else?

Thank you very much,

Hi @AgnesBaud , they will not affect at all the metaphlan results

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