Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates
Abstract
:1. Introduction
2. Results and Discussion
2.1. Antimicrobial Activities
2.2. Genome Sequencing
2.3. Taxonomy and Phylogeny
2.4. Pan Genome and Core Genome
2.5. Secondary Metabolism Biosynthetic Gene Clusters
2.6. Protein Family (Pfam) Domain Analysis
2.6.1. KS Domains of PKS Gene Clusters
2.6.2. Nrps Gene Clusters
2.6.3. Siderophores, Bacteriocins and Lantibiotics
2.7. Marine Adaptations
3. Materials and Methods
3.1. Sponge Sampling
3.2. Culture Isolation
3.3. DNA Extraction
3.4. 16S rRNA Gene Sequencing
3.5. 16S rRNA Based Phylogenetic Analysis
3.6. Bioactivity Screening
3.7. Whole Genome Sequencing
3.8. Bioinformatic Methods
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Test Strain | Gram Negative Bacteria | Gram Positive Bacteria | Yeasts | ||||
---|---|---|---|---|---|---|---|
E. coli NCIMB 12210 | P. aeruginosa PAO1 | Bacillus pp. | Staphylococcus spp. | L. monocyte genes F2365 | Candida spp. | A. fumigatus ATCC 46645 | |
SM1 * | + | − | + 1,2 | + a | + | + | n.d. |
SM5 * | + | − | + 1,2 | + a | − | − | n.d. |
SM9 * | + | − | − | − | − | − | n.d. |
SM10 * | + | n.d. | − | − | − | − | n.d. |
SM11 * | − | − | + 2 | + a,b | − | − | n.d. |
SM12 * | − | + | − | + a | − | − | n.d. |
SM14 * | − | − | + 1,2 | + a | − | − | n.d. |
SM16 * | − | + | + 2 | + c | − | − | n.d. |
SM17 * | + | − | − | + b | − | + | n.d. |
SM18 * | − | − | + 2 | + b | − | − | n.d. |
FMC008 * | − | + | + 2 | + d | − | − | n.d. |
B226SN101 | − | − | − 3 | − | n.d. | + | + |
B188M101 | − | − | − 3 | − | n.d. | + | + |
Isolate ID | No. of Contigs | Total Length (Mb) |
---|---|---|
B188SM101 | 609 | 8.23 |
B226SN101 | 580 | 8.39 |
SM5 | 469 | 7.62 |
SM10 | 195 | 7.48 |
SM11 | 311 | 8 |
SM12 | 910 | 6.5 |
SM16 | 388 | 8.44 |
SM1 | 1057 | 8.08 |
SM9 | 1592 | 6.47 |
FMC008 | 1369 | 6.5 |
SM18 | 403 | 7.6 |
SM14 | 639 | 6.41 |
SM17 | 674 | 7.106 |
Isolate ID | PKS * | NRPS | PKS/NRPS Hybrid | Bacteriocin | Lantipeptide | Siderophore | Terpene | Butyrolactone | Ectoine | Other | TOTAL |
---|---|---|---|---|---|---|---|---|---|---|---|
B188M101 | 4 | 19 | 4 | 2 | 4 | 2 | 5 | 2 | 2 | 9 | 53 |
B226SN101 | 2 | 20 | 4 | 2 | 3 | 2 | 5 | 2 | 2 | 9 | 51 |
SM5 | 5 | 9 | 5 | 2 | 1 | 1 | 6 | 1 | 1 | 7 | 38 |
SM10 | 16 | 3 | 3 | 5 | 3 | 2 | 4 | 2 | 1 | 5 | 44 |
SM11 | 10 | 11 | 5 | 2 | 3 | 2 | 6 | 2 | 2 | 11 | 54 |
SM12 | 18 | 7 | - | 1 | 3 | 4 | 1 | 1 | 1 | 4 | 40 |
SM16 | 2 | 5 | 6 | 1 | 5 | 2 | 7 | 2 | 2 | 7 | 39 |
SM1 | 4 | 8 | 1 | 2 | 2 | 2 | 4 | 1 | - | 5 | 28 |
SM9 | 3 | 2 | - | 1 | - | 2 | 6 | - | 1 | 1 | 16 |
FMC008 | 1 | 3 | - | 1 | - | 1 | 5 | - | 1 | 3 | 15 |
SM18 | 9 | 9 | 6 | 2 | 2 | 1 | 6 | 1 | 1 | 4 | 41 |
SM14 | 8 | 2 | - | - | 1 | 2 | - | 1 | - | 3 | 17 |
SM17 | 14 | 18 | 2 | 3 | 2 | 3 | 5 | - | 1 | 1 | 49 |
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Jackson, S.A.; Crossman, L.; Almeida, E.L.; Margassery, L.M.; Kennedy, J.; Dobson, A.D.W. Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates. Mar. Drugs 2018, 16, 67. https://doi.org/10.3390/md16020067
Jackson SA, Crossman L, Almeida EL, Margassery LM, Kennedy J, Dobson ADW. Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates. Marine Drugs. 2018; 16(2):67. https://doi.org/10.3390/md16020067
Chicago/Turabian StyleJackson, Stephen A., Lisa Crossman, Eduardo L. Almeida, Lekha Menon Margassery, Jonathan Kennedy, and Alan D.W. Dobson. 2018. "Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates" Marine Drugs 16, no. 2: 67. https://doi.org/10.3390/md16020067