Clarification on GTDB-Tk Species Assignments within the Streptococcus anginosus Group

Bacterial Taxonomy
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Dear GTDB Team,

I hope this message finds you well.

Thank you for providing an outstanding platform for GTDB. I would appreciate your guidance on a classification question. Using the classify_wf workflow in GTDB-Tk. I analyzed 324 high-quality NCBI assemblies from the Streptococcus anginosus group. GTDB-Tk assigned these genomes to the following species clusters: Streptococcus vaginalis (184 genomes), Streptococcus anginosus (76 genomes), and Streptococcus hominis (64 genomes).

Could you please explain why many genomes were assigned to the S. vaginalis and S. hominis clusters, and outline the criteria GTDB uses to distinguish these from S. anginosus (e.g., representative genomes, ANI thresholds, alignment fraction, or other decision rules)?

Your guidance would be greatly appreciated.

Best regards,
Hasnain

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Hi Hasnain. Please see the discussion about Streptococcus and ANI-based species clustering here: Streptococcus species cluster identity threshold - #3 by ivelsko.

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You may also find this FAQ insightful: https://gtdb.ecogenomic.org/faq#how-are-gtdb-species-clusters-formed

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