Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production
Some microbial species are chemically homogenous, and the same secondary metabolites are found in all strains. In contrast, we previously found that five strains of <em>P. luteoviolacea </em>were closely related by 16S rRNA gene sequence but produced two different antibio...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2012-08-01
|
| Series: | Marine Drugs |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1660-3397/10/8/1729 |
| _version_ | 1798003607544528896 |
|---|---|
| author | Lone Gram Nikolaj G. Vynne Maria Mansson |
| author_facet | Lone Gram Nikolaj G. Vynne Maria Mansson |
| author_sort | Lone Gram |
| collection | DOAJ |
| description | Some microbial species are chemically homogenous, and the same secondary metabolites are found in all strains. In contrast, we previously found that five strains of <em>P. luteoviolacea </em>were closely related by 16S rRNA gene sequence but produced two different antibiotic profiles. The purpose of the present study was to determine whether such bioactivity differences could be linked to genotypes allowing methods from phylogenetic analysis to aid in selection of strains for biodiscovery. Thirteen <em>P. luteoviolacea </em>strains divided into three chemotypes based on production of known antibiotics and four antibacterial profiles based on inhibition assays against <em>Vibrio anguillarum </em>and <em>Staphylococcus aureus</em>. To determine whether chemotype and inhibition profile are reflected by phylogenetic clustering we sequenced 16S rRNA, <em>gyrB </em>and <em>recA </em>genes. Clustering based on 16S rRNA gene sequences alone showed little correlation to chemotypes and inhibition profiles, while clustering based on concatenated 16S rRNA, <em>gyrB</em>,<em> </em>and <em>recA </em>gene sequences resulted in three clusters, two of which uniformly consisted of strains of identical chemotype and inhibition profile. A major time sink in natural products discovery is the effort spent rediscovering known compounds, and this study indicates that phylogeny clustering of bioactive species has the potential to be a useful dereplication tool in biodiscovery efforts. |
| first_indexed | 2024-04-11T12:10:37Z |
| format | Article |
| id | doaj.art-37da9a6c6db74fd3a2ab90c9c7af898f |
| institution | Directory Open Access Journal |
| issn | 1660-3397 |
| language | English |
| last_indexed | 2024-04-11T12:10:37Z |
| publishDate | 2012-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Marine Drugs |
| spelling | doaj.art-37da9a6c6db74fd3a2ab90c9c7af898f2022-12-22T04:24:37ZengMDPI AGMarine Drugs1660-33972012-08-011081729174010.3390/md10081729Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic ProductionLone GramNikolaj G. VynneMaria ManssonSome microbial species are chemically homogenous, and the same secondary metabolites are found in all strains. In contrast, we previously found that five strains of <em>P. luteoviolacea </em>were closely related by 16S rRNA gene sequence but produced two different antibiotic profiles. The purpose of the present study was to determine whether such bioactivity differences could be linked to genotypes allowing methods from phylogenetic analysis to aid in selection of strains for biodiscovery. Thirteen <em>P. luteoviolacea </em>strains divided into three chemotypes based on production of known antibiotics and four antibacterial profiles based on inhibition assays against <em>Vibrio anguillarum </em>and <em>Staphylococcus aureus</em>. To determine whether chemotype and inhibition profile are reflected by phylogenetic clustering we sequenced 16S rRNA, <em>gyrB </em>and <em>recA </em>genes. Clustering based on 16S rRNA gene sequences alone showed little correlation to chemotypes and inhibition profiles, while clustering based on concatenated 16S rRNA, <em>gyrB</em>,<em> </em>and <em>recA </em>gene sequences resulted in three clusters, two of which uniformly consisted of strains of identical chemotype and inhibition profile. A major time sink in natural products discovery is the effort spent rediscovering known compounds, and this study indicates that phylogeny clustering of bioactive species has the potential to be a useful dereplication tool in biodiscovery efforts.http://www.mdpi.com/1660-3397/10/8/1729<em>Pseudoalteromonas luteoviolacea</em>violaceinindolmycinpentabromopseudilinbiodiscovery |
| spellingShingle | Lone Gram Nikolaj G. Vynne Maria Mansson Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production Marine Drugs <em>Pseudoalteromonas luteoviolacea</em> violacein indolmycin pentabromopseudilin biodiscovery |
| title | Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production |
| title_full | Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production |
| title_fullStr | Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production |
| title_full_unstemmed | Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production |
| title_short | Gene Sequence Based Clustering Assists in Dereplication of <em>Pseudoalteromonas luteoviolacea</em> Strains with Identical Inhibitory Activity and Antibiotic Production |
| title_sort | gene sequence based clustering assists in dereplication of lt em gt pseudoalteromonas luteoviolacea lt em gt strains with identical inhibitory activity and antibiotic production |
| topic | <em>Pseudoalteromonas luteoviolacea</em> violacein indolmycin pentabromopseudilin biodiscovery |
| url | http://www.mdpi.com/1660-3397/10/8/1729 |
| work_keys_str_mv | AT lonegram genesequencebasedclusteringassistsindereplicationofltemgtpseudoalteromonasluteoviolacealtemgtstrainswithidenticalinhibitoryactivityandantibioticproduction AT nikolajgvynne genesequencebasedclusteringassistsindereplicationofltemgtpseudoalteromonasluteoviolacealtemgtstrainswithidenticalinhibitoryactivityandantibioticproduction AT mariamansson genesequencebasedclusteringassistsindereplicationofltemgtpseudoalteromonasluteoviolacealtemgtstrainswithidenticalinhibitoryactivityandantibioticproduction |