Stackebrandt curves show the relationship between average nucleotide identity (ANI) and 16S rRNA gene similarity for bacterial genomes.
"Stackebrandt curves" aren't really a thing; I made up the name. The idea comes from a 1994 paper by Stackebrandt and Goebel1 in which the authors compared 16S rRNA gene similarity and whole-genome similarity for bacteria. In that paper, the authors used DNA-DNA hybridization results rather than ANI as a measure of genome similarity. In a later study, Kim et al.2 found that the earlier results hold true when ANI is used.
To a high degree, 16S gene similarity and full-genome similarity are correlated. However, Stackebrandt and Goebel observed that 16S similarity is sometimes high when full-genome similarity is low. Conversely, full-genome similarity is rarely high if 16S similarity is low. When plotted with 16S similarity on the y-axis and full-genome similarity on the x-axis, the relationship looks like a curve bending along the top of the plot.
Here is an example that follows the classic pattern: Cutibacterium acnes (accession GCF_008728435.1).
The purpose of this software is to generate 16S gene similarity and ANI data for any bacterial genome in NCBI RefSeq. To do this, we download the list of available genomes, build a 16S gene database, find other genomes with similar 16S sequences, then compute the ANI for each one. The program generates a tab-separated output file that can be used to plot your own Stackebrandt curves.
The Python library and command-line program can be installed using pip.
git clone https://github.com/kylebittinger/stackebrandtcurves.git
cd stackebrandtcurves
pip install -e .Besides the python libraries listed in the setup file, this program
requires vsearch and fastANI to be installed. They are both available
through conda, which is our
recommended method for installation.
The stackebrandtcurve program requires one argument, the accesion number
for a bacterial genome assembly in NCBI RefSeq.
stackebrandtcurve GCF_001688845.2If the program has not been run before, it will automatically download
the files it needs to carry out the computation. The default output file
name is assembly_GCF_001688845.2_pctid_ani.txt, but this can be changed
using the --output-file option to the program.
Running stackebrandtcurve --help will produce a full list of available
options.
We welcome ideas from our users about how to improve this software. Please open an issue if you have a question or would like to suggest a feature.