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Microbial Genomics logo Microbial Genomics

Volume 10, Issue 9

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Open Access

Abstract

is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based classifications using 2276 publicly available genome assemblies and 48 981 publicly available full-length 16S rRNA sequences from , Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14 239 distinct sequences that resolves three major lineages of , but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for , demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the community.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S , evolution , phylogeny , taxonomy , Actinomycetales and Streptomyces
Funding
This study was supported by the:
  • University of Strathclyde
    • Principal Award Recipient: AngelikaBeata Kiepas
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-09-10
2025-11-11

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16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces
M Gen 10, 001287 (2024); https://doi.org/10.1099/mgen.0.001287
/content/journal/mgen/10.1099/mgen.0.001287
/content/journal/mgen/10.1099/mgen.0.001287
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