# Diversity missing in profile output

**URL:** <https://forum.biobakery.org/t/diversity-missing-in-profile-output/1615>\
**Category:** MetaPhlAn\
**Created:** [January 27, 2021, 12:10pm UTC](https://forum.biobakery.org/t/diversity-missing-in-profile-output/1615 "2021-01-27T12:10:45Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![catarina](https://avatars.discourse-cdn.com/v4/letter/c/48db29/32.png) [@catarina](https://forum.biobakery.org/u/catarina)\
**Post date:** [January 27, 2021, 12:10pm UTC](https://forum.biobakery.org/t/diversity-missing-in-profile-output/1615/1 "2021-01-27T12:10:45Z")

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I am trying to profile a marine sponge tissue metagenome (illumina highseq reads) and I ran the following command:  
metaphlan DNA\_1.fq,DNA\_2.fq --bowtie2out metaphlan.bowtie2.bz2 --nproc 24 --input\_type fastq -o profiled\_metaphlan.txt

It runs with the warnings:

WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.  
An additional column listing the merged species is added to the MetaPhlAn output.

And the output:

#mpa\_v30\_CHOCOPhlAn\_201901  
#/tools/software/bioinfo-tools/miniconda/miniconda3/envs/metaphlan/bin/metaphlan DNA\_1.fq,DNA\_2.fq --bowtie2out metaphlan.bowtie2.bz2 --nproc 24 --input\_type fastq -o profiled\_metaphlan.txt  
#SampleID Metaphlan\_Analysis  
#clade\_name NCBI\_tax\_id relative\_abundance additional\_species  
k\_\_Eukaryota 2759 100.0  
k\_\_Eukaryota|p\_\_Ascomycota 2759|4890 100.0  
k\_\_Eukaryota|p\_\_Ascomycota|c\_\_Saccharomycetes 2759|4890|4891 100.0  
k\_\_Eukaryota|p\_\_Ascomycota|c\_\_Saccharomycetes|o\_\_Saccharomycetales 2759|4890|4891|4892 100.0  
k\_\_Eukaryota|p\_\_Ascomycota|c\_\_Saccharomycetes|o\_\_Saccharomycetales|f\_\_Saccharomycetaceae 2759|4890|4891|4892|4893 100.0  
k\_\_Eukaryota|p\_\_Ascomycota|c\_\_Saccharomycetes|o\_\_Saccharomycetales|f\_\_Saccharomycetaceae|g\_\_Saccharomyces 2759|4890|4891|4892|4893|4930 100.0  
k\_\_Eukaryota|p\_\_Ascomycota|c\_\_Saccharomycetes|o\_\_Saccharomycetales|f\_\_Saccharomycetaceae|g\_\_Saccharomyces|s\_\_Saccharomyces\_cerevisiae 2759|4890|4891|4892|4893|4930|4932 100.0 k\_\_Eukaryota|p\_\_Ascomycota|c\_\_Saccharomycetes|o\_\_Saccharomycetales|f\_\_Saccharomycetaceae|g\_\_Saccharomyces|s\_\_Saccharomyces\_sp\_boulardii

However I expect a lot more diversity in the sample, especially bacterial members. What could have gone wrong?

Thanks!

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**Author:** ![catarina](https://avatars.discourse-cdn.com/v4/letter/c/48db29/32.png) [@catarina](https://forum.biobakery.org/u/catarina)\
**Post date:** [February 2, 2021, 9:30am UTC](https://forum.biobakery.org/t/diversity-missing-in-profile-output/1615/2 "2021-02-02T09:30:48Z")

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Any chance for an answer? would the warning be indicative of issues in the run that collapse all diversity expected?

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [February 3, 2021, 10:29am UTC](https://forum.biobakery.org/t/diversity-missing-in-profile-output/1615/3 "2021-02-03T10:29:30Z")

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Hi Catarina,  
Sorry for not catching up this before. The warning just indicates that markers for S. cerevisiae may indicate also the presence of S. boulardii, since the species are 5% similar.  
In this case, it is possible that the bacterial community you are analyzing cannot be described by the species present in the MetaPhlAn database