# Multiple interrelated species (Streptococci) **URL:** \ **Category:** StrainPhlAn\ **Created:** [November 26, 2021, 2:58pm UTC](https://forum.biobakery.org/t/multiple-interrelated-species-streptococci/2839 "2021-11-26T14:58:39Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![AndrewM](https://avatars.discourse-cdn.com/v4/letter/a/c57346/32.png) [@AndrewM](https://forum.biobakery.org/u/AndrewM)\ **Post date:** [November 26, 2021, 2:58pm UTC](https://forum.biobakery.org/t/multiple-interrelated-species-streptococci/2839/1 "2021-11-26T14:58:39Z")
Hello, I’d be very interested to know whether you’ve had experience with samples where multiple inter-related species from the same genus are present. I am very interested in the streptococci in our oral samples, and we have _Streptococcus mitis_ as dominant, but significant contributions from _Strep. pseudopneumoniae_, _parasanguinis_, _infantis_, _oralis_, _pneumoniae_ and _salivarius_ (in order of decreasing abundance). I sense the potential for a few levels of problems. Firstly, the NCBI classification of these organisms (which I think you use) can be discordant with a more genetically informed lineage (GTDB) - or at the very least multiple genomes tagged as the same species by NCBI can get dotted around the tree by GTDB. Here I have indicated where genomes from the prebuilt pangenomes are placed by GTDB (r95): ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/1/13e45d17de5b26c24ad5cf0134e8f6d45b3868ee.png) _Strep. pyogenes_ genomes are admixed with _Strep. mitis_, and _Strep. mitis_ & _Strep. oralis_ are intermixed. There is also considerable sharing of COGs between some Streptococcal species. The Euler diagram shows that this is most notable for _Strep. oralis_ and _Strep. mitis_. ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/8/874bd79a97f939fc52d67fca4d048634738978a9.png) Given that I know _mitis_ dominates in my data, I wonder if the _Strep. oralis_ pangenomes could come out badly. Panphlan could report pangenomes for samples where _S. oralis_ is really below the reportable limit, but those COGs shared with _S. mitis_ are easily detectable. Homing in on specific questions: 1. Have you considered generating pangenomes based on GTDB hierarchies at different resolutions? 2. What might be the best way of mitigating against impacts of shared COGs between species which are both present in samples. I could consider removing the shared COGs from the _S. oralis_ pangenome, as I won’t be able to trust the presence absence data. However I probably don’t need to worry about _S. mitis_ as signal from its genes should dominate. Would this seem sensible, and how easy would it be to edit the _S. oralis_ pangenome in this way? Thanks again for such a useful tool! Andrew ---
**Author:** ![AndrewM](https://avatars.discourse-cdn.com/v4/letter/a/c57346/32.png) [@AndrewM](https://forum.biobakery.org/u/AndrewM)\ **Post date:** [November 29, 2021, 12:30pm UTC](https://forum.biobakery.org/t/multiple-interrelated-species-streptococci/2839/2 "2021-11-29T12:30:43Z")
I should correct the above statement, it’s _Strep. pneumoniae_ that is intermixed with _Strep. mitis_! I wonder if the four outliers could be phenotypically _false positive_ Strep. pneumoniae (if that’s a thing), or atypical pneumococci (as per [Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of "Atypical" pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factor-encoding genes - PubMed](https://pubmed.ncbi.nlm.nih.gov/10678950/)) ---
**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:** [November 29, 2021, 2:56pm UTC](https://forum.biobakery.org/t/multiple-interrelated-species-streptococci/2839/3 "2021-11-29T14:56:52Z")
Hi @AndrewM These are really interesting questions. However, I think for the sake of future users who might have the same questions, the PanPhlAn forum would be more suitable. Could you please re-post the questions there? Thanks ---
**Author:** ![AndrewM](https://avatars.discourse-cdn.com/v4/letter/a/c57346/32.png) [@AndrewM](https://forum.biobakery.org/u/AndrewM)\ **Post date:** [November 29, 2021, 3:13pm UTC](https://forum.biobakery.org/t/multiple-interrelated-species-streptococci/2839/4 "2021-11-29T15:13:40Z")
My mistake, that’s where I meant to put it!