Diversity missing in profile output

Microbial community profiling MetaPhlAn
1

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!

2

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

3

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