btyper3 3.3.0

In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes

BTyper3

In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes

Overview

BTyper3 is a command-line tool for taxonomically classifying Bacillus cereus group genomes using a standardized nomenclature

The program, as well as the associated databases, can be downloaded from https://github.com/lmc297/BTyper3

Post issues at https://github.com/lmc297/BTyper3/issues

For more information, check out the BTyper3 wiki at https://github.com/lmc297/BTyper3/wiki

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Installation

For more information, check out the BTyper3 wiki

conda (recommended)

To create a conda environment named btyper3 and install BTyper3 and all of its dependencies:

1. Install conda, if necessary

2. Create a new environment named btyper3 by running the following command from your terminal:

conda create -n btyper3

3. Activate your btyper3 environment by running the following command from your terminal:

conda activate btyper3

4. Install BTyper3 by running the following command from your terminal:

conda install -c bioconda btyper3

5. You can now run btyper3! Run the following command from your terminal to view all btyper3 options, or check the BTyper3 wiki for details:

btyper3 --help

6. When you're done with BTyper3, you can deactivate the btyper3 environment by running the following:

conda deactivate

pip

1. To run BTyper3, please download and install the following dependencies, if necessary:

python3

Biopython v. 1.7.4 and up (for python3)

Pandas (for python3)

NumPy (for python3)

BLAST v. 2.9.0+ and up (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)

pyFastANI version 0.3 and up

2. Add BLAST+ to your path, if necessary (to check if BLAST+ is in your path, try running makeblastdb -h and tblastn -h from your command line; you should get a help message for each command, with no error messages)

3. Install via pip:

pip install btyper3  

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News: updates in BTyper3 v3.2.0 and v3.3.0 -- new species just dropped!

The primary function of BTyper3 is to allow users to taxonomically classify B. cereus group genomes using a standardized nomenclature (see here and here for details regarding how the standardized nomenclature was constructed, and how it compares to historical typing methods, respectively). However, we understand that some users may also want to compare their B. cereus group genomes to the type strain genomes of published B. cereus group species. Thus, in BTyper3 v3.2.0, we have added the --ani_typestrains option, which calculates ANI values between a query genome and the genomes of all published B. cereus group species type strains and reports the type strain that produces the highest ANI value.

The type strain genomes used by BTyper3's --ani_typestrains option correspond to the species discussed in Figure 2 of our taxonomy review, plus five species published after the review was published (i.e., Bacillus sanguinis, Bacillus paramobilis, and Bacillus hominis, added in v3.2.0, and "B. arachidis" and B. rhizoplanae, added in v3.3.0). Within the standardized taxonomy that BTyper3 uses for genomospecies assignment:

• All members of Bacillus sanguinis (type strain RefSeq Assembly Accession GCF_018332475.1) belong to B. mosaicus (i.e., B. sanguinis is not considered a novel species in the standardized taxonomy)

• All members of Bacillus paramobilis (type strain RefSeq Assembly Accession GCF_018332495.1) belong to B. mosaicus (i.e., B. paramobilis is not considered a novel species in the standardized taxonomy)

• All members of Bacillus hominis (type strain RefSeq Assembly Accession GCF_018332515.1) belong to B. mycoides (i.e., B. hominis is not considered a novel species in the standardized taxonomy)

• "Bacillus arachidis" (type strain RefSeq Assembly Accession GCF_017498775.1) replaces the putative genomospecies previously referred to as "Unknown Species 17" in the standardized taxonomy

• Bacillus rhizoplanae (type strain RefSeq Assembly Accession GCF_917563915.1) represents a novel genomospecies within the standardized taxonomy and has been added to the database

Importantly, B. cereus group species are often proposed in the literature using unstandardized approaches (e.g., varying genomospecies thresholds, which may produce overlapping genomospecies). We have added the type strain comparison method in BTyper3 v3.2.0, as users may still want to compare a query genome with the type strains of published B. cereus group species. However, interpret results with caution, as some B. cereus group genomes may belong to multiple species using type strain genomes.

For more information, check out our:

• Review of B. cereus group taxonomy/nomenclature

• Standardized nomenclature for the B. cereus group

• Comparison of our standardized nomenclature to other B. cereus group typing methods (e.g., MLST, panC, ANI-based comparisons to species type strain genomes)

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Citation

If you found the BTyper3 tool, its source code, and/or any of its associated databases useful, please cite:

Carroll, Laura M., Martin Wiedmann, Jasna Kovac. 2020. "Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes." mBio 11(1): e00034-20; DOI: 10.1128/mBio.00034-20.

Carroll, Laura M., Rachel A. Cheng, Jasna Kovac. 2020. "No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus group with Historical Typing Methods." Frontiers in Microbiology 11: 580691; DOI: 10.3389/fmicb.2020.580691.

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Quick Start

For detailed information, check out the BTyper3 wiki

Command Structure

btyper3 -i [fasta] -o [output directory] [options...]

For help, type btyper3 -h or btyper3 --help

For your current version, type btyper3 --version

Sample Commands

Perform all default analyses, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path):

btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory

Perform all default analyses, using an assembled genome (complete or draft) in (multi-)FASTA format as input (fastANI is not in the user's path):

btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --fastani_path /path/to/FastANI_executable/fastANI

Perform all default analyses, plus pseudo-gene flow unit assignment AND species type strain comparison, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path):

btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --ani_geneflow True --ani_typestrains True

Perform seven-gene MLST only, using user-supplied MLST gene sequences and the latest version of the PubMLST B. cereus s.l. database (sequences can be in multi-FASTA format, or concatenated into a single sequence in FASTA format):

btyper3 -i /path/to/mlst.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --virulence False --bt False --panC False --download_mlst_latest True

Perform panC group assignment only, using a user-supplied panC gene sequence in FASTA format:

btyper3 -i /path/to/panC.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --virulence False --bt False --mlst False

Perform virulence factor and Bt toxin-encoding gene detection in a plasmid sequence in FASTA format:

btyper3 -i /path/to/plasmid.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --mlst False --panC False

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Disclaimer: BTyper3 is pretty neat! However, no tool is perfect, and BTyper3 cannot definitively prove whether an isolate is pathogenic or not. As always, interpret your results with caution. We are not responsible for taxonomic misclassifications, misclassifications of an isolate's pathogenic potential or industrial utility, and/or misinterpretations (biological, statistical, or otherwise) of BTyper3 results.