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Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.

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PJpreprint: Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments. https://t.co/Zx2Fxa5BV1
Streptococcus global genomic similarity https://t.co/vjBxKc6wis
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Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments. https://t.co/UYlTqmykkZ
Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments. https://t.co/g6aMHWHf1s
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Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify close related bacterial strains in complex environments https://t.co/pEdvN5HICj
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PJpreprint: Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify close related bacterial strains in complex environments https://t.co/ZEw0rfVmTv
Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify close related bacterial strains in complex environments https://t.co/sddGFGbb1N #microbiomebot
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Supplemental Information

Genome sequences and their environmental sources used in this work

Information included: Strains names, CDS number, NCBI accession numbers, isolation sources.

DOI: 10.7287/peerj.preprints.26665v2/supp-1

GSS calculations jupyter notebook

Detailed bioinformatic protocols.

DOI: 10.7287/peerj.preprints.26665v2/supp-2

ANI correlogram for the selected 108 streptococci strains

ANI correlogram for the selected 108 streptococci strains.

DOI: 10.7287/peerj.preprints.26665v2/supp-3

Core genome and pan-genome plots for the 108 streptococci strains

Core genome and pan-genome plots for the 108 streptococci strains.

DOI: 10.7287/peerj.preprints.26665v2/supp-4

Global pairwise identity for the core proteome of the streptococci

Global pairwise identity for the core proteome of the streptococci.

DOI: 10.7287/peerj.preprints.26665v2/supp-5

FASTA files for each streptococci species core genome

FASTA files for each streptococci species core genome.

DOI: 10.7287/peerj.preprints.26665v2/supp-6

Metagenomic abundances of Streptococcus in metagenomic samples

Calculated by core genome fragment recruitment, lowest common ancestor (LCA), and 16S rRNA gene abundances.

DOI: 10.7287/peerj.preprints.26665v2/supp-7

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Hugo R Barajas de la Torre conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Miguel Romero performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Shamayim Martínez-Sánchez performed the experiments, analyzed the data, prepared figures and/or tables, approved the final draft.

Luis D Alcaraz conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

Supplemental Information 1. Genome sequences and their environmental sources used in this work. Information included: Strains names, CDS number, NCBI accession numbers, isolation sources.

Supplemental Information 2. GSS calculations jupyter notebook. Detailed bioinformatic protocols.

Supplemental Information 3. Core genome and pan-genome plots for the 108 streptococci strains. Additionally, each streptococci species core genome and orthologous genes shared between strains.

Supplemental Information 4. Global pairwise identity for the core proteome of the streptococci.

Supplemental Information 5. FASTA files for each streptococci species core genome.

Supplemental Information 6. Metagenomic abundances of Streptococcus in metagenomic samples, calculated by core genome fragment recruitment, lowest common ancestor (LCA), and 16S rRNA gene abundances.

Funding

HBT, MR, and SMS had fellowships from CONACyT. LDA got funding from DGAPA-PAPIIT-UNAM TA2001171 and SEP-CONACyT Ciencia Básica 237387. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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