Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts
Abstract
:1. Introduction
2. Results and Discussion
2.1. Diversity of Invertebrate-Associated Bacteria
2.2. Data Processing and Data Clean-Up
2.3. Multivariate Analysis for Strain Selection
2.4. Chemical Diversity of Natural Products in Outlying Bacterial Extracts
2.4.1. Dereplication of Bacillus sp. 4115
Bacterial Strain | (a) Total number of features (m/z) | (b) Total number of features (m/z) after removal of features (m/z) from medium | (c) Total number of features identified by dereplication with AntiMarin | |||
---|---|---|---|---|---|---|
Positive ion mode | Negative ion mode | Positive ion mode | Negative ion mode | Putatively identified (positive and negative modes) | Unidentified (positive and negative modes) | |
Bacillus sp. 4115 | 1220 | 1037 | 359 (29.4% remaining) | 438 (42.2% remaining) | 270 (51.3%) | 526 (48.7%) |
Vibrio splendidus strain LGP32 | 2767 | 654 | 1102 (39.8% remaining) | 617 (94.3% remaining) | 699 (40.7%) | 1019 (59.3%) |
Rhodococcus sp. ZS402 | 1198 | 2361 | 659 (55% remaining) | 1715 (72.6% remaining) | 519 (28%) | 1855 (72%) |
Peak ID | ESI
Mode | m/z | Rt (min) | Molecular Formula
(Isotope Fit Score A0 to A3) | RDB | Hits | Fragmentation Data | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fragment ions MS2 +Ve | Chemical Formula | RDB | Fragment ions MS3 +Ve | Molecular Formula | RDB | ||||||||
1 | Pos | 445.29092 | 17.5 | C22H40O7N2 (99.49%) | 4 | No hits | 427.27921 399.28485 314.19589 232.15408 214.14343 186.14862 | C22H39O6N2 C21H39O5N2 C16H28O5N C11H22O4N C11H20O3N C10H20O2N | 5
4 4 2 3 2 | 168.13794
72.08067 | C10H18ON
C4H10N | 3
1 | |
2 | Pos | 459.30646 | 18.6 | C23H42O7N2 (71.70%) | 4 | No hits | 441.29553 413.30063 328.21176 228.15930 200.16431 | C23H41O6N2 C22H41O5N2 C17H30O5N C12H22O3N C11H22O2N | 5
4 4 3 2 | 146.11752
86.09630 | C7H16O2N
C5H12N | 1
1 | |
3 | Pos | 1036.69141 | 30.5 | C53H93O13N7 (99.82%) | 11 | Pumilacidin B// (surfactin-1) or other cyclic peptide | 1018.67596 937.61896 685.44714 667.43732 455.28571 | C53H92O12N7 C48H85O12N6 C33H61O9N6 C33H59O8N6 C22H39O6N4 | 12
10 7 8 6 | 568.36853
342.20117 | C28H50O7N5 C16H28O5N3 | 7
5 | |
4 | Pos | 1050.70771 | 31.4 | C54H95O13N7 (99.79%) | 11 | Pumilacidin A// or other cyclic peptide | 1032.69104 937.61823 699.46234 681.45282 455.28555 | C54H94O12N7 C48H85O12N6 C34H63O9N6 C34H61O8N6 C22H39O6N4 | 12
10 7 8 6 | 568.36816
342.20087 | C28H50O7N5 C16H28O5N3 | 7
5 | |
5 | Pos | 875.53519 | 33.5 | C43H77O15N3 (98.53%) | 7 | No hits | 710.38348 685.41257 659.46952 654.51534 647.45954 615.44423 610.48905 | C32H58O15N2 C31H61O14N2 C31H67O12N2 C34H72O10N C34H65O10N C29H63O11N2 C32H68O9N | 5
3 1 1 3 1 1 | ||||
6 | Pos | 1078.73917 | 34.5 | C56H99O13N7 (99.80%) | 11 | Pumilacidin C// or other cyclic peptide | 1061.72498 966.65216 699.46283 681.45337 455.28549 | C55H99O13N6 C49H88O12N7 C34H63O9N6 C34H61O8N6 C22H39O6N4 | 10
10 7 8 6 | 568.36859
342.20135 | C28H50O7N5C
16H28O5N3 | 7
5 | |
7 | Pos | 889.55163 | 34.5 | C42H76O14N6 (84.86%) | 8 | No hits | 861.55371 817.49072 803.47546 790.47894 776.46429 757.47034 690.39093 676.41254 662.39655 590.33954 563.32874 | C41H77O13N6 C38H69O13N6 C37H67O13N6 C37H68O13N5 C36H66O13N5 C36H65O11N6 C31H56O12N5 C31H58O11N5 C30H56O11N5 C26H48O10N5 C25H47O10N4 | 7
8 8 7 7 8 7 6 6 6 5 | 449.26096
463.27667 577.34413 477.25619 | C19H37O8N4 C20H39O8N4 C26H49O10N4 C20H37O9N4 | 4
4 5 5 | |
8 | Pos | 903.56635 | 35.6 | C43H78O14N6 (99.76%) | 8 | No hits | 817.49097 804.49593 790.47988 718.42297 704.40740 690.42803 676.41285 604.35589 590.34010 577.34508 491.27243 463.27740 | C38H69O13N6 C38H70O13N5 C37H68O13N5 C33H60O13N5 C32H58O12N5 C32H60O11N5 C31H58O11N5 C27H50O10N5 C26H48O10N5 C26H49O10N4 C21H39O9N4 C20H39O8N4 | 8
7 7 7 7 6 6 6 6 5 5 4 | 364.20825 | C15H30O7N3 | 3 |
2.4.2. Dereplication of Vibrio splendidus Strain LGP32
2.4.3. Dereplication of Rhodococcus sp. ZS402
3. Experimental Section
3.1. Sample Collection and Bacterial Isolation
Peak ID | ESI Mode | m/z | Rt (min) | Molecular Formula (Isotope Fit Score A0 to A3) | RDB | Hits | Fragment Ions MS2 | Molecular Formula | RDB | Fragment ions MS3 | Molecular Formula | RDB |
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | P | 219.12266 | 9.8 | C10H18O5 (99.97%) | 2 | (4E)-6,7,9-Trihydroxydec-4-enoic acid | 173.08047 133.08556 115.07513 87.04388 73.06467 | C8H13O4 C6H13O3 C6H11O2 C4H7O2 C4H9O | 3 1 2 2 1 | |||
2 | P | 305.1590 | 12.9 | C14H24O7 (99.99%) | 3 | No hits | 259.11685 219.12209 173.08040 155.06985 133.08549 115.07516 87.04391 | C12H19O6 C10H19O5 C8H13O4 C8H11O3 C6H13O3 C6H11O2 C4H7O2 | 4 2 3 4 1 3 2 | |||
3 | P | 408.22407 | 15.2 | C18H33O9N (Ammonium adduct of C18H31O9) (60.57%) | 3 | No hits | 392.19974 305.15979 259.11786 219.12292 | undetermined C14H25O7 C12H19O6 C10H19O5 | 3 4 2 | |||
3 | P | 408.22407 | 15.2 | C19H29O5N5 (99.50%) | 8 | No hits | 392.19969 305.15978 259.11783 219.12292 | undetermined C15H21O3N4 C13H15O2N4 C10H1905 | 8 9 2 | 173.08086 155.07023 133.08593 115.07541 | C8H13O4 C8H11O3 C6H1303 C6H11O2 | 3 4 1 2 |
4 | P | 494.25967 | 17.0 | C22H39O11N (Ammonium adduct of C22H37O11) (99.97%) | 4 | No hits | 477.23270 | C22H37O11 | 5 | 459.22238 431.19101 373.18582 345.15396 305.15924 259.11740 219.12263 155.07021 | C22H35O10 C20H31O10 C18H29O8 C16H25O8 C14H25O7 C12H19O6 C10H19O5 C8H11O3 | 6 6 5 5 3 4 2 3 |
5 | P | 580.2965 | 18.5 | C26H45O13N (Ammonium adduct of C26H43O13) (99.96%) | 5 | No hits | 563.26880 477.23288 431.19122 345.15424 305.15945 | C26H43O13 C22H37O11 C20H31O10 C16H25O8 C14H25O7 | 6 5 6 5 3 | 259.11752 219.12265 155.07025 | C12H19O6 C10H19O5 C8H11O3 | 4
2 4 |
6 | P | 448.2180 | 18.8 | C20H33O10N (Ammonium adduct of C20H30O10) (91.50%) | 5 | No hits | 431.18991 345.15372 259.11725 241.10663 155.07002 | C20H31O10 C16H25O8 C12H19O6 C12H17O5 C8H11O3 | 6 5 4 5 4 | |||
7 | P | 534.2550 | 19.4 | C24H39O12N (Ammonium adduct of C24H37O12) (99.13%) | 6 | No hits | 517.22723 431.19070 345.15402 259.11737 241.10681 155.07013 | C24H37O12 C20H31O10 C16H25O8 C12H19O6 C12H17O5 C8H11O | 7 6 5 4 5 4 | |||
7 | P | 534.2550 | 19.4 | C25H35O8N5 (71.66%) | 11 | Oxyplicacetin; 3′-Hydroxy-plicacetin | 517.22723 431.19070 345.15402 259.11737 241.10681 | C25H33O8N4 C21H27O6N4 C17H21O4N4 C10H17O5N3 C10H15O4N3 | 12 11 10 4 5 | |||
8 | N | 269.13940 | 12.3 | C14H22O5 (99.99%) | 5 | No hits | 251.12892 225.14969 | C14H19O4 C13H21O3 | 6 4 | |||
9 | N | 405.24944 | 19.3 | C20H38O8 (99.92%) | 3 | No hits | 359.24274 267.19690 | C19H35O6 C16H27O3 | 3 4 | |||
10 | N | 285.20719 | 21.5 | C16H30O4 (88.36%) | 3 | Hexadecanedioic acid/ethyl plakortide Z/ethyl didehydro-seco-plakortide Z | 267.19641 | C16H27O3 | 4 | 125.09721 141.12836 185.11803 223.20638 | C8H13O C9H17O C10H17O3 C15H27O | 3 2 3 3 |
Peak ID | ESI Mode | m/z | Rt (min) | Molecular Formula (Isotope Fit Score A0 to A3) | Hits | RDB | Fragment Ions MS2 | Molecular Formula | RDB | Fragment Ions MS3 | Molecular Formula | RDB |
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | P | 230.2481 | 17.3 | C14H31ON (99.77%) | Xestoaminol C | 1 | 212.23662 | C14H30N | 1 | |||
2 | P | 258.2793 | 19.4 | C16H35ON (99.95%) | No hits | 1 | 240.26793 | C16H34N | 1 | |||
3 | P | 597.5208 | 30.1 | C35H68O5N2 (99.01%) | No hits | 3 | 337.28409 355.29462 351.29974 369.31042 | C20H37O2N2 C20H39O3N2 C21H39O2N2 C21H41O3N2 | 4 3 4 3 | 319.27350
295.27368 | C20H35ON2 C18H35ON2 | 5
3 |
4 | N | 265.1476 | 17.6 | C12H26O4S (99.25%) | No hits | 1 | 96.9590 | [HSO4]− | 1 | |||
5 | N | 760.54162 | 17.6 | C42H75O5N5S (90.86%) | No hits | 9 | 531.30280 | C30H45O5NS | 9 | 96.9590 | [HSO4]− | |
6 | N | 279.1631 | 19.1 | C13H28O4S (98.04%) | No hits | 1 | 96.9590 | [HSO4]− | 1 | 96.9590 | ||
7 | N | 816.60400 | 19.1 | C46H83O5N5S (87.43%) | No hits | 9 | 279.16318 | C32H49O5NS C13H27O4S | 9 1 | 96.9590 | [HSO4]− | |
8 | N | 309.17358 | 19.7 | C14H30O5S (98.04%) | No hits | 1 | 96.9590 | [HSO4]− | 1 | |||
9 | N | 293.1790 | 21.6 | C14H30O4S (99.86%) | No hits | 1 | 96.9590 | [HSO4]− | 1 |
Rt (min) | m/z [M + H]+ | Molecular Formula | Isotope Fit Score A0 to A3 (%) | RDB | Predictions to Calculated RDB |
---|---|---|---|---|---|
19.23 | 462.1727 | C19H23O7N7 | 87.66 | 12 | Cyclic with Phe/Tyr |
21.43 | 499.1871 | C18H26O9N8 | 87.64 | 10 | Cyclic |
22.15 | 587.2399 | C22H34O11N8 | 82.51 | 10 | Linear |
28.14 | 569.4893 | C33H64O5N2 | 99.99 | 3 | Linear |
29.46 | 583.5048 | C34H66O5N2 | 99.95 | 3 | Linear |
33.77 | 1078.7151 | C59H95O11N7 | 99.86 | 16 | Cyclic with Trp |
35.30 | 1118.7461 | C62H99O11N7 | 98.83 | 17 | Cyclic with Trp/Arg |
35.64 | 1092.7308 | C60H97O11N7 C55H97O13N9 | 99.91 85.21 | 16 12 | Cyclic with Trp Cyclic |
36.80 | 1106.7460 | C61H99O11N7 C56H99O13N9 | 99.50 99.05 | 16 12 | Cyclic with Trp Cyclic |
37.55 | 849.6953 | C51H88O4N6 C56H88O2N4 | 99.92 58.43 | 11 15 | Cyclic with Trp/Arg Cyclic with Trp/Arg |
3.2. Bacterial Culture and Extraction
3.3. Mass Spectrometry
3.4. NMR Spectroscopy
3.5. Data Analysis Tools for Mass Spectrometry Data
3.6. Molecular Identification
3.7. Bioassay Screening
3.7.1. Anti-Infectives
3.7.2. Metabolic Disease and Inflammation
3.7.3. Cell-based Functional Assays
4. Conclusions
Supplementary Files
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Macintyre, L.; Zhang, T.; Viegelmann, C.; Martinez, I.J.; Cheng, C.; Dowdells, C.; Abdelmohsen, U.R.; Gernert, C.; Hentschel, U.; Edrada-Ebel, R. Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts. Mar. Drugs 2014, 12, 3416-3448. https://doi.org/10.3390/md12063416
Macintyre L, Zhang T, Viegelmann C, Martinez IJ, Cheng C, Dowdells C, Abdelmohsen UR, Gernert C, Hentschel U, Edrada-Ebel R. Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts. Marine Drugs. 2014; 12(6):3416-3448. https://doi.org/10.3390/md12063416
Chicago/Turabian StyleMacintyre, Lynsey, Tong Zhang, Christina Viegelmann, Ignacio Juarez Martinez, Cheng Cheng, Catherine Dowdells, Usama Ramadan Abdelmohsen, Christine Gernert, Ute Hentschel, and RuAngelie Edrada-Ebel. 2014. "Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts" Marine Drugs 12, no. 6: 3416-3448. https://doi.org/10.3390/md12063416
APA StyleMacintyre, L., Zhang, T., Viegelmann, C., Martinez, I. J., Cheng, C., Dowdells, C., Abdelmohsen, U. R., Gernert, C., Hentschel, U., & Edrada-Ebel, R. (2014). Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts. Marine Drugs, 12(6), 3416-3448. https://doi.org/10.3390/md12063416