ArticlePloS one
Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case.
Article in PloS one. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 46 citations in OpenAlex.
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- Stress-tolerant Bacillus strains for enhancing tomato growth and biocontrol of Fusarium oxysporum under saline conditions: functional and genomic characterization.World journal of microbiology & biotechnology · 2025Article
- Functional and genomic analyses of plant growth promoting traits in Priestia aryabhattai and Paenibacillus sp. isolates from tomato rhizosphere.Scientific reports · 2025Article
- Resolution of MALDI-TOF compared to whole genome sequencing for identification ofFrontiers in microbiology · 2025Article
- Redundant potassium transporter systems guarantee the survival ofFrontiers in microbiology · 2023Article
- Draft Genome Sequence of the Tomato Stem Endophyte Bacillus safensis TS3.Microbiology resource announcements · 2022Article
- Genomic Characterization ofApplied and environmental microbiology · 2022Article
- A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.Communications biology · 2022Article
- Comparative genomic analyses reveal genetic characteristics and pathogenic factors ofFrontiers in microbiology · 2022Article
- Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae.Archives of microbiology · 2021Article
- Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in AntibacterialGenes · 2021Article
- Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches.The plant pathology journal · 2021Article
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- Novel keratinolytic enzymes, discovered from a talented and efficient bacterial keratin degrader.Scientific reports · 2020Article
- Bridging genomics and field research: draft genome sequence of3 Biotech · 2020Article
- Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile.Microbiology resource announcements · 2019Article
- Draft genome analysis of the endophyte,3 Biotech · 2019Article
- Draft genome sequence of3 Biotech · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. In this study, first, a whole-genome in silico approach was used to accurately demarcate B. pumilus group strains, as a case of highly phylogenetically related taxa, at the species level. In order to achieve that and consequently to validate or correct taxonomic identities of genomes in public databases, an average nucleotide identity correlation, a core-based phylogenomic and a gene function repertory analyses were performed. Eventually, more than 50% such genomes were found to be misclassified. Hierarchical clustering of gene functional repertoires was also used to infer ecotypes among B. pumilus group species. Furthermore, for the first time the machine-learning algorithm Random Forest was used to rank genes in order of their importance for species classification. We found that ybbP, a gene involved in the synthesis of cyclic di-AMP, was the most important gene for accurately predicting species identity among B. pumilus group strains. Finally, principal component analysis was used to classify strains based on the distances between their ybbP genes. The methodologies described could be utilized more broadly to identify other highly phylogenetically related species in metagenomic or epidemiological assessments.
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