Small‐Molecule Antibiotics from Marine Bacteria and Strategies to Prevent Rediscovery of Known Compounds

Wietz, Matthias; Månsson, Maria; Vynne, Nikolaj Grønnegaard; Gram, Lone

doi:10.1002/9783527665259.ch08

Cited by 7 publications

(6 citation statements)

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“…Several large-scale efforts are under way to find new antibiotic compounds that can be used to fight these strains. However, in many cases, these efforts suffer from frequent rediscovery of compounds previously identified from other strains [ 8 ]. The development of bioinformatics tools to analyse the growing amount of available bacterial genomic sequence information has shown that the number of biosynthetic gene clusters (BGCs) that may encode pathways capable of producing specialized metabolites is much greater than initially thought, even in strains that were already known for their specialized metabolite repertoires [ 9 , 10 ], but also in many other strains from a wide range of taxonomic groups [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

et al. 2017

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BackgroundBacteria of the genus Rhodococcus are well known for their ability to degrade a large range of organic compounds. Some rhodococci are free-living, saprophytic bacteria; others are animal and plant pathogens. Recently, several studies have shown that their genomes encode putative pathways for the synthesis of a large number of specialized metabolites that are likely to be involved in microbe-microbe and host-microbe interactions. To systematically explore the specialized metabolic potential of this genus, we here performed a comprehensive analysis of the biosynthetic coding capacity across publicly available rhododoccal genomes, and compared these with those of several Mycobacterium strains as well as that of their mutual close relative Amycolicicoccus subflavus.ResultsComparative genomic analysis shows that most predicted biosynthetic gene cluster families in these strains are clade-specific and lack any homology with gene clusters encoding the production of known natural products. Interestingly, many of these clusters appear to encode the biosynthesis of lipopeptides, which may play key roles in the diverse environments were rhodococci thrive, by acting as biosurfactants, pathogenicity factors or antimicrobials. We also identified several gene cluster families that are universally shared among all three genera, which therefore may have a more ‘primary’ role in their physiology. Inactivation of these clusters by mutagenesis might help to generate weaker strains that can be used as live vaccines.ConclusionsThe genus Rhodococcus thus provides an interesting target for natural product discovery, in view of its large and mostly uncharacterized biosynthetic repertoire, its relatively fast growth and the availability of effective genetic tools for its genomic modification.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3966-1) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

et al. 2017

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“…In that way, marine Actinobacteria has been isolated from zooplankton, pelagic waters, macroalgae, sponges and sediments discovering several antimicrobial compounds, the majority from the Streptomyces genus such as marinopyrroles, napyradiomycins, Bonactin, Essramycin, Lajollamycin, Etamycin (Wietz et al . ), 1‐Hydroxy‐1‐norresistomycin (Gorajana et al . ), bisantraquinones (Ravikumar et al .…”

Section: Discussionmentioning

confidence: 99%

“…Some of the most common compounds discovered from marine bacteria include marinopyrroles, bisanthraquinones, salinisporamycin, arenimycin, abyssomicin, pentabromopseudilin, indolmycin, violacein, korormycin, tetrabromopyrrole, thiomarinols, bogorol A, macrolactin T, ieodoglucomides A and B, tauramamide, tropodithietic acid (TDA), 2,4‐diacetylphloroglucinol (DAPG), malyngolide, hormothamnin A and ariakemicins A and B (Wietz et al . ).…”

Section: Introductionmentioning

confidence: 97%

Bioprospecting from marine coastal sediments of Colombian Caribbean: screening and study of antimicrobial activity

et al. 2018

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“…Interestingly, 52.7% of all unknown gene clusters were strain-specific (singletons), which represented a total of 106 BGCs (data not included in Figure 4 for clarity purposes; a graphical representation of each singleton is available in Figures S2-S13). One of the biggest setbacks faced when looking for novel metabolites is rediscovering compounds that had previously been described in other strains [46]. Singletons are, therefore, excellent targets for mining the occurrence of new compounds, since they do not seem to be spread across the Streptomyces genus and therefore lowering the risk of rediscovering already known compounds.…”

Section: Secondary Metabolite Analysismentioning

confidence: 99%

A Multidisciplinary Approach to Unraveling the Natural Product Biosynthetic Potential of a Streptomyces Strain Collection Isolated from Leaf-Cutting Ants

et al. 2021

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The rapid emergence of bacterial resistance to antibiotics has urged the need to find novel bioactive compounds against resistant microorganisms. For that purpose, different strategies are being followed, one of them being exploring secondary metabolite production in microorganisms from uncommon sources. In this work, we have analyzed the genome of 12 Streptomyces sp. strains of the CS collection isolated from the surface of leaf-cutting ants of the Attini tribe and compared them to four Streptomyces model species and Pseudonocardia sp. Ae150A_Ps1, which shares the ecological niche with those of the CS collection. We used a combination of phylogenetics, bioinformatics and dereplication analysis to study the biosynthetic potential of our strains. 51.5% of the biosynthetic gene clusters (BGCs) predicted by antiSMASH were unknown and over half of them were strain-specific, making this strain collection an interesting source of putative novel compounds.

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Small‐Molecule Antibiotics from Marine Bacteria and Strategies to Prevent Rediscovery of Known Compounds

Cited by 7 publications

References 272 publications

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

Bioprospecting from marine coastal sediments of Colombian Caribbean: screening and study of antimicrobial activity

A Multidisciplinary Approach to Unraveling the Natural Product Biosynthetic Potential of a Streptomyces Strain Collection Isolated from Leaf-Cutting Ants

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