TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarS...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2019-02-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/6526.pdf |
| _version_ | 1797419661739950080 |
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| author | Pedro Seoane Silvana T. Tapia-Paniagua Rocío Bautista Elena Alcaide Consuelo Esteve Eduardo Martínez-Manzanares M. Carmen Balebona M. Gonzalo Claros Miguel A. Moriñigo |
| author_facet | Pedro Seoane Silvana T. Tapia-Paniagua Rocío Bautista Elena Alcaide Consuelo Esteve Eduardo Martínez-Manzanares M. Carmen Balebona M. Gonzalo Claros Miguel A. Moriñigo |
| author_sort | Pedro Seoane |
| collection | DOAJ |
| description | Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11. |
| first_indexed | 2024-03-09T06:50:29Z |
| format | Article |
| id | doaj.art-bcfa8d08559a4e3cbd37b3dcc147ca88 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:50:29Z |
| publishDate | 2019-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-bcfa8d08559a4e3cbd37b3dcc147ca882023-12-03T10:28:30ZengPeerJ Inc.PeerJ2167-83592019-02-017e652610.7717/peerj.6526TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11Pedro Seoane0Silvana T. Tapia-Paniagua1Rocío Bautista2Elena Alcaide3Consuelo Esteve4Eduardo Martínez-Manzanares5M. Carmen Balebona6M. Gonzalo Claros7Miguel A. Moriñigo8Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, SpainDepartment of Microbiology, Universidad de Málaga, Málaga, SpainAndalusian Platform for Bioinformatics, Universidad de Málaga, Málaga, SpainDepartment of Microbiology and Ecology, Universidad de Valencia, Valencia, SpainDepartment of Microbiology and Ecology, Universidad de Valencia, Valencia, SpainDepartment of Microbiology, Universidad de Málaga, Málaga, SpainDepartment of Microbiology, Universidad de Málaga, Málaga, SpainDepartment of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, SpainDepartment of Microbiology, Universidad de Málaga, Málaga, SpainProbiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.https://peerj.com/articles/6526.pdfProbioticsCultured fishSyntenyWorkflowBioinformaticsShewanella putrefaciens |
| spellingShingle | Pedro Seoane Silvana T. Tapia-Paniagua Rocío Bautista Elena Alcaide Consuelo Esteve Eduardo Martínez-Manzanares M. Carmen Balebona M. Gonzalo Claros Miguel A. Moriñigo TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 PeerJ Probiotics Cultured fish Synteny Workflow Bioinformatics Shewanella putrefaciens |
| title | TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 |
| title_full | TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 |
| title_fullStr | TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 |
| title_full_unstemmed | TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 |
| title_short | TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11 |
| title_sort | tarsynflow a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of shewanella putrefaciens strain pdp11 |
| topic | Probiotics Cultured fish Synteny Workflow Bioinformatics Shewanella putrefaciens |
| url | https://peerj.com/articles/6526.pdf |
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