Journal article
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen
Region Sjælland1
University of California at San Diego2
University of Copenhagen3
Big Data 2 Knowledge, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4
Network Reconstruction in Silico Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark5
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark6
The mitis group of streptococci (MGS) is a member of the healthy human microbiome in the oral cavity and upper respiratory tract. Troublingly, some MGS are able to escape this niche and cause infective endocarditis, a severe and devastating disease. Genome-scale models have been shown to be valuable in investigating metabolism of bacteria.
Here we present the first genome-scale model, iCJ415, for Streptococcus oralis SK141. We validated the model using gene essentiality and amino acid auxotrophy data from closely related species. iCJ415 has 71-76% accuracy in predicting gene essentiality and 85% accuracy in predicting amino acid auxotrophy.
Further, the phenotype of S. oralis was tested using the Biolog Phenotype microarrays, giving iCJ415 a 82% accuracy in predicting carbon sources. iCJ415 can be used to explore the metabolic differences within the MGS, and to explore the complicated metabolic interactions between different species in the human oral cavity.
Language: | English |
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Publisher: | Frontiers Media S.A. |
Year: | 2020 |
Pages: | 116 |
ISSN: | 16648021 |
Types: | Journal article |
DOI: | 10.3389/fgene.2020.00116 |
ORCIDs: | Palsson, Bernhard O. |