# Scientific names not found in NCBI Taxonomy Browser **URL:** \ **Category:** MetaPhlAn\ **Created:** [February 21, 2023, 9:07pm UTC](https://forum.biobakery.org/t/scientific-names-not-found-in-ncbi-taxonomy-browser/4839 "2023-02-21T21:07:08Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Anderson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/anderson/32/1983_2.png) [@Anderson](https://forum.biobakery.org/u/Anderson)\ **Post date:** [February 21, 2023, 9:07pm UTC](https://forum.biobakery.org/t/scientific-names-not-found-in-ncbi-taxonomy-browser/4839/1 "2023-02-21T21:07:08Z")
I’m using Metaphlan 4.0 and cannot understand what these labels mean in the scientific names below: k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB1534|o\_\_OFGB1534|f\_\_FGB1534|g\_\_GGB3886|s\_\_GGB3886\_SGB5269 k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB1762|o\_\_OFGB1762|f\_\_FGB1762|g\_\_GGB4533|s\_\_GGB4533\_SGB6246 k\_\_Bacteria|p\_\_Bacteroidetes|c\_\_CFGB570|o\_\_OFGB570|f\_\_FGB570|g\_\_GGB1203|s\_\_GGB1203\_SGB1568 k\_\_Bacteria|p\_\_Proteobacteria|c\_\_CFGB4196|o\_\_OFGB4196|f\_\_FGB4196|g\_\_GGB12441|s\_\_GGB12441\_SGB19290 k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB1230|o\_\_OFGB1230|f\_\_FGB1230|g\_\_GGB3008|s\_\_GGB3008\_SGB3999 k\_\_Bacteria|p\_\_Firmicutes|c\_\_CFGB1395|o\_\_OFGB1395|f\_\_FGB1395|g\_\_GGB3388|s\_\_GGB3388\_SGB4476 I’ve searched in the NCBI extensively and I don’t understand where these labels were taken and what they mean (for example: s\_\_GGB3008\_SGB3999). I’m having trouble justifying them in my research. ---
**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:** [February 22, 2023, 10:16am UTC](https://forum.biobakery.org/t/scientific-names-not-found-in-ncbi-taxonomy-browser/4839/2 "2023-02-22T10:16:39Z")
Hi @Anderson The taxonomies you are showing here above correspond to several unknown SGBs (uSGBs), i.e. SGBs defined purely by metagenomic-assembled genomes (MAGs). As the uSGBs by definition do not contain any reference genome in NBCI, some part of their taxonomy are totally unknown and thus, we assign them a numeric identifier. The 6 cases you are showing below are uSGBs that are unknown up to the phylum level, this is, we did not find any reference genome that shared, at least, 70% identity with them, and thus, we are only confident to assign a phylogeny up to the phylum. If you are interested in more details about the SGBs and the MetaPhlAn 4 database, please, have a look at the following works: [https://doi.org/10.1016/j.cell.2019.01.001](https://doi.org/10.1016/j.cell.2019.01.001) > **[Extending and improving metagenomic taxonomic profiling with uncharacterized...](https://www.biorxiv.org/content/10.1101/2022.08.22.504593v1)** > > Metagenomic assembly enables novel organism discovery from microbial communities, but from most metagenomes it can only capture few abundant organisms. Here, we present a method - MetaPhlAn 4 - to integrate information from both metagenome assemblies... ---
**Author:** ![alban\_mathieu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/alban_mathieu/32/573_2.png) [@alban\_mathieu](https://forum.biobakery.org/u/alban_mathieu)\ **Post date:** [June 26, 2024, 12:53pm UTC](https://forum.biobakery.org/t/scientific-names-not-found-in-ncbi-taxonomy-browser/4839/3 "2024-06-26T12:53:54Z")
> [@aitor.blancomiguez](#): > > correspond to several unknown SGBs (uSGBs), i.e. SGBs defined purely by metagenomic-assembled genomes (MAGs). As the uSGBs by definition do not contain any reference genome in NBCI, some part of their taxonomy are totally unknown and thus, we assign them a numeric identifier. The 6 cases you are showing below are uSGBs that are unknown up to the phylum level, this is, we did not find any reference genome that shared, at least, 70% identity with them, and thus, we are only confident to assign a phylogeny up to the phylum. > If you are interested in more details about the SGBs and the MetaPhlAn 4 database, please, have a look at the following works: > [https://doi.org/10.1016/j.cell.2019.01.00](https://doi.org/10.1016/j.cell.2019.01.001) Hello, Thanks for the answer that explains my case also :). But how can I rely on the genomes that have been used ? I would like to take a look at the genome where the genes come from because i have interesting results. ---
**Author:** ![jorondo1](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jorondo1/32/1312_2.png) [@jorondo1](https://forum.biobakery.org/u/jorondo1)\ **Post date:** [March 31, 2025, 6:59pm UTC](https://forum.biobakery.org/t/scientific-names-not-found-in-ncbi-taxonomy-browser/4839/4 "2025-03-31T18:59:07Z")
Hi @aitor.blancomiguez, If I understand the meaning of u[F|G|S]GBs correctly, they represent e.g. Family-level MAG clusters with no reference genome. However, in the taxonomy we also find OFGBs and CFGBs. What do these represent exactly? I am asking because upon comparing various taxonomic profiling tools, at these levels MetaPhlAn identifies ~150 different orders in my dataset, where any other method (Kraken, Sourmash, mOTUs) only finds about 20. Is it simply because any FGB that cannot be assigned to a known order will get a unique OFGB identifier? This would explain why even if in theory many of these FGBs could share the same Order, they are assigned different Order identifiers. Below is a figure of the number of unique taxa found in two separate metagenome datasets (each with ~30ish samples) that illustrates what I’m referring to. For example, in the NAFLD dataset, 122 of the unique 157 order labels are OFGBs. I’m just trying to figure out why. ![Bildschirmfoto 2025-03-31 um 2.58.01 PM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/8/8c8caf60392d268d128c49e38913cc378ed39302.png)