ArticleBMC genomics2016
Gene content dissimilarity for subclassification of highly similar microbial strains.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
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- Development of a Species-Specific PCR Assay forPathogens (Basel, Switzerland) · 2025Article
- Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.Environmental microbiome · 2024Article
- Discovery of novel treponemes associated with pododermatitis in elk (Applied and environmental microbiology · 2024Article
- Article
- On a Non-Discrete Concept of Prokaryotic Species.Microorganisms · 2020Article
- Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter.Genome biology and evolution · 2019Article
- Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.Microbial ecology · 2018Article
- GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the GenusFrontiers in microbiology · 2018Article
- Phenetic Comparison of Prokaryotic Genomes Using k-mers.Molecular biology and evolution · 2017Article
- Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa.Marine drugs · 2017Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgnisms to different taxonomic levels, and it is still not clear that to what extent genomic fluidity should occur to form a microbial taxonomic group.
resultsBy taking advantage of the eggNOG database for orthologous groups, we calculated gene content dissimilarity among different microbial strains based on the orthologous gene profiles and tested the possibility of applying gene content dissimilarity as a quantitative index in classifying microbial taxonomic groups, as well as its potential application in subclassification of highly similar microbial strains. Evaluation of gene content dissimilarity to completed microbial genomes at different taxonomic levels suggested that cutoffs of 0.2 and 0.4 can be respectively used for species and family delineation, and that 0.2 gene content dissimilarity cutoff approximately corresponded to 98 % 16S rRNA gene identity and 94 % ANI for microbial species delineation. Furthermore, application of gene content dissimilarity to highly similar microbial strains suggested it as an effective approach in classifying closely related microorganisms into subgroups.
conclusionsThis approach is especially useful in identifying pathogens from commensals in clinical microbiology. It also provides novel insights into how genomic fluidity is linked with microbial taxonomy.
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