# Differentiating between "kSGBs" and "uSGBs" in MetaPhlAn 4

**URL:** <https://forum.biobakery.org/t/differentiating-between-ksgbs-and-usgbs-in-metaphlan-4/6770>\
**Category:** MetaPhlAn\
**Created:** [March 7, 2024, 3:29pm UTC](https://forum.biobakery.org/t/differentiating-between-ksgbs-and-usgbs-in-metaphlan-4/6770 "2024-03-07T15:29:32Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![bmtalbot](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bmtalbot/32/582_2.png) [@bmtalbot](https://forum.biobakery.org/u/bmtalbot)\
**Post date:** [March 7, 2024, 3:29pm UTC](https://forum.biobakery.org/t/differentiating-between-ksgbs-and-usgbs-in-metaphlan-4/6770/1 "2024-03-07T15:29:32Z")

</div>

Hi,

I ran MetaPhlAn 4 (version 4.0.1 (24 Aug 2022)) with the following script:  
metaphlan SAMPLE\_paired\_1.fastq,SAMPLE\_paired\_2.fastq --bowtie2out SAMPLE\_hostremoved.bowtie2.bz2 --nproc 5 --input\_type fastq -t rel\_ab\_w\_read\_stats --unclassified\_estimation --bowtie2db=/home/bmtalbo/miniconda3/envs/metaphlan4/lib/python3.7/site-packages/metaphlan/metaphlan\_databases --index mpa\_vOct22\_CHOCOPhlAnSGB\_202212 -o metaphlan4\_output/$SAMPLE\_profiled\_metagenome.txt

I think it’s really interesting to have the SGBs identified in the output. However, I’m unclear about two things:

1. How can you tell the difference between “kSGBs” and "uSGB"s in the output? As far as I can see, there is only “SGB”, included, sometimes preceeded by “unclassified”. Is that the delimiter?

2. How should I interpret the level of certainty for lower taxonomic grouping (ie a species) for lines where the higher taxonomic order is determined to be “unclassified”? I’m not interested in the strain-level differences for my analysis, but want to accurately identify all my unique species in the sample for alpha and beta diversity measures.

For example:  
k\_\_Bacteria|p\_\_Firmicutes|c\_\_Clostridia|o\_\_Eubacteriales|f\_\_Oscillospiraceae|g\_\_Oscillospiraceae\_unclassified|s\_\_Oscillospiraceae\_bacterium|t\_\_SGB4247

The genus level is “unclassified”, the species name seems like a generic call to then assign a SGB strain. Would this line truly represent a unique species, or is the species level tag redundant to the genus level tag?

As a separate example, but the same issue, I also have this kind of species classification:  
k\_\_Bacteria|p\_\_Firmicutes|c\_\_Clostridia|o\_\_Eubacteriales|f\_\_Oscillospiraceae|g\_\_Oscillospiraceae\_unclassified|s\_\_Oscillospiraceae\_unclassified\_SGB15252|t\_\_SGB15252

In this instance, I would likely consider the species level more a “unique species” with a SGB tag and would probably include it in my taxonomic diversity analysis at the species level.

Thanks for your help!

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [March 11, 2024, 10:52am UTC](https://forum.biobakery.org/t/differentiating-between-ksgbs-and-usgbs-in-metaphlan-4/6770/2 "2024-03-11T10:52:14Z")

</div>

Dear @bmtalbot  
Answering your questions:

1. From the species level taxonomy (s\_\_) you can distinguish k and uSGBs by the inclusion of the “`_SGB`” string in the species name. E.g. `s __Escherichia_coli` → kSGB` s__ Escherichia_SGB10061` → uSGB.
2. In MetaPhlAn 4, the `t__` level is not considered the strain level but the species-level genome bin (SGB) level ([Redirecting](https://doi.org/10.1016/j.cell.2019.01.001)) and thus you can consider the t\_\_ level as species-level taxonomic units.