Human commensals producing a novel antibiotic impair pathogen colonization (original) (raw)

References

  1. Arias, C. A. & Murray, B. E. Antibiotic-resistant bugs in the 21st century—a clinical super-challenge. N. Engl. J. Med. 360, 439–443 (2009)
    CAS PubMed Google Scholar
  2. Laxminarayan, R. et al. Antibiotic resistance—the need for global solutions. Lancet Infect. Dis. 13, 1057–1098 (2013)
    PubMed Google Scholar
  3. DeLeo, F. R., Otto, M., Kreiswirth, B. N. & Chambers, H. F. Community-associated meticillin-resistant Staphylococcus aureus. Lancet 375, 1557–1568 (2010)
    PubMed PubMed Central Google Scholar
  4. Arias, C. A. & Murray, B. E. The rise of the Enterococcus: beyond vancomycin resistance. Nat. Rev. Microbiol. 10, 266–278 (2012)
    Article CAS PubMed PubMed Central Google Scholar
  5. Boucher, H. W. et al. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin. Infect. Dis. 48, 1–12 (2009)
    PubMed Google Scholar
  6. WHO. Antimicrobial resistance: global report on surveillance 2014. http://www.who.int/drugresistance/documents/surveillancereport/en/ (2014)
  7. Cooper, M. A. & Shlaes, D. Fix the antibiotics pipeline. Nature 472, 32 (2011)
    ADS CAS PubMed Google Scholar
  8. Bierbaum, G. & Sahl, H. G. The search for new anti-infective drugs: untapped resources and strategies. Int. J. Med. Microbiol. 304, 1–2 (2014)
    PubMed Google Scholar
  9. Ling, L. L. et al. A new antibiotic kills pathogens without detectable resistance. Nature 517, 455–459 (2015)
    ADS CAS PubMed PubMed Central Google Scholar
  10. Laureti, L. et al. Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens. Proc. Natl Acad. Sci. USA 108, 6258–6263 (2011)
    ADS CAS PubMed PubMed Central Google Scholar
  11. Hosaka, T. et al. Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12. Nat. Biotechnol. 27, 462–464 (2009)
    CAS PubMed Google Scholar
  12. Lincke, T., Behnken, S., Ishida, K., Roth, M. & Hertweck, C. Closthioamide: an unprecedented polythioamide antibiotic from the strictly anaerobic bacterium Clostridium cellulolyticum. Angew. Chem. Int. Ed. Engl. 49, 2011–2013 (2010)
    CAS PubMed Google Scholar
  13. Schroeder, B. O. et al. Reduction of disulphide bonds unmasks potent antimicrobial activity of human β-defensin 1. Nature 469, 419–423 (2011)
    ADS CAS PubMed Google Scholar
  14. Zasloff, M. Inducing endogenous antimicrobial peptides to battle infections. Proc. Natl Acad. Sci. USA 103, 8913–8914 (2006)
    ADS CAS PubMed PubMed Central Google Scholar
  15. Bush, K. et al. Tackling antibiotic resistance. Nat. Rev. Microbiol. 9, 894–896 (2011)
    CAS PubMed PubMed Central Google Scholar
  16. Marshall, B. M. & Levy, S. B. Food animals and antimicrobials: impacts on human health. Clin. Microbiol. Rev. 24, 718–733 (2011)
    CAS PubMed PubMed Central Google Scholar
  17. Penders, J., Stobberingh, E. E., Savelkoul, P. H. & Wolffs, P. F. The human microbiome as a reservoir of antimicrobial resistance. Front. Microbiol. 4, 87 (2013)
    PubMed PubMed Central Google Scholar
  18. Davis, M. F., Price, L. B., Liu, C. M. & Silbergeld, E. K. An ecological perspective on U.S. industrial poultry production: the role of anthropogenic ecosystems on the emergence of drug-resistant bacteria from agricultural environments. Curr. Opin. Microbiol. 14, 244–250 (2011)
    PubMed Google Scholar
  19. Bode, L. G. et al. Preventing surgical-site infections in nasal carriers of Staphylococcus aureus. N. Engl. J. Med. 362, 9–17 (2010)
    CAS PubMed Google Scholar
  20. Wertheim, H. F. et al. The role of nasal carriage in Staphylococcus aureus infections. Lancet Infect. Dis. 5, 751–762 (2005)
    PubMed Google Scholar
  21. Thomas, C. M., Hothersall, J., Willis, C. L. & Simpson, T. J. Resistance to and synthesis of the antibiotic mupirocin. Nat. Rev. Microbiol. 8, 281–289 (2010)
    CAS PubMed Google Scholar
  22. van der Meer, J. W. & Vandenbroucke-Grauls, C. M. Resistance to selective decontamination: the jury is still out. Lancet Infect. Dis. 13, 282–283 (2013)
    PubMed Google Scholar
  23. Schloss, P. D. Microbiology: An integrated view of the skin microbiome. Nature 514, 44–45 (2014)
    ADS CAS PubMed Google Scholar
  24. Laufer, A. S. et al. Microbial communities of the upper respiratory tract and otitis media in children. MBio 2, e00245–e10 (2011)
    PubMed PubMed Central Google Scholar
  25. Krismer, B. et al. Nutrient limitation governs Staphylococcus aureus metabolism and niche adaptation in the human nose. PLoS Pathog. 10, e1003862 (2014)
    PubMed PubMed Central Google Scholar
  26. Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15–25 (2010)
    CAS PubMed PubMed Central Google Scholar
  27. Dobson, A., Cotter, P. D., Ross, R. P. & Hill, C. Bacteriocin production: a probiotic trait? Appl. Environ. Microbiol. 78, 1–6 (2012)
    CAS PubMed PubMed Central Google Scholar
  28. Kommineni, S. et al. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract. Nature 526, 719–722 (2015)
    ADS CAS PubMed PubMed Central Google Scholar
  29. Challinor, V. L. & Bode, H. B. Bioactive natural products from novel microbial sources. Ann. NY Acad. Sci. 1354, 82–97 (2015)
    ADS PubMed Google Scholar
  30. Donia, M. S. et al. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell 158, 1402–1414 (2014)
    CAS PubMed PubMed Central Google Scholar
  31. Heilbronner, S. et al. Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors. FEMS Microbiol. Lett. 322, 60–67 (2011)
    CAS PubMed Google Scholar
  32. Sidda, J. D. et al. Discovery of a family of gamma-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster. Chem. Sci.) 5, 86–89 (2014)
    CAS Google Scholar
  33. Rutledge, P. J. & Challis, G. L. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat. Rev. Microbiol. 13, 509–523 (2015)
    CAS PubMed Google Scholar
  34. Sasaki, O., Igarashi, Y., Saito, N. & Furumai, T. Watasemycins A and B, new antibiotics produced by Streptomyces sp. TP-A0597. J Antibiot. (Tokyo) 55, 249–255 (2002)
    CAS Google Scholar
  35. Miller, D. A., Luo, L., Hillson, N., Keating, T. A. & Walsh, C. T. Yersiniabactin synthetase: a four-protein assembly line producing the nonribosomal peptide/polyketide hybrid siderophore of Yersinia pestis. Chem. Biol. 9, 333–344 (2002)
    CAS PubMed Google Scholar
  36. Weber, T. et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, W237–W243 (2015)
    CAS PubMed PubMed Central Google Scholar
  37. Walsh, C. T. Insights into the chemical logic and enzymatic machinery of NRPS assembly lines. Nat. Prod. Rep. 33, 127–135 (2015)
    Google Scholar
  38. Mootz, H. D., Schwarzer, D. & Marahiel, M. A. Ways of assembling complex natural products on modular nonribosomal peptide synthetases. ChemBioChem 3, 490–504 (2002)
    CAS PubMed Google Scholar
  39. Hobbs, J. K., Miller, K., O’Neill, A. J. & Chopra, I. Consequences of daptomycin-mediated membrane damage in Staphylococcus aureus. J. Antimicrob. Chemother. 62, 1003–1008 (2008)
    CAS PubMed Google Scholar
  40. Tacconelli, E. & Kern, W. V. New antibiotics for skin and skin-structure infections. Lancet Infect. Dis. 14, 659–661 (2014)
    PubMed Google Scholar
  41. Zervos, M. J. et al. Epidemiology and outcomes of complicated skin and soft tissue infections in hospitalized patients. J. Clin. Microbiol. 50, 238–245 (2012)
    PubMed PubMed Central Google Scholar
  42. Weidenmaier, C., Goerke, C. & Wolz, C. Staphylococcus aureus determinants for nasal colonization. Trends Microbiol. 20, 243–250 (2012)
    CAS PubMed Google Scholar
  43. Baur, S. et al. A nasal epithelial receptor for Staphylococcus aureus WTA governs adhesion to epithelial cells and modulates nasal colonization. PLoS Pathog. 10, e1004089 (2014)
    PubMed PubMed Central Google Scholar
  44. Andersen, P. S. et al. Influence of host genetics and environment on nasal carriage of Staphylococcus aureus in Danish middle-aged and elderly twins. J. Infect. Dis. 206, 1178–1184 (2012)
    PubMed PubMed Central Google Scholar
  45. Bieber, L. & Kahlmeter, G. Staphylococcus lugdunensis in several niches of the normal skin flora. Clin. Microbiol. Infect. 16, 385–388 (2010)
    CAS PubMed Google Scholar
  46. Iwase, T. et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature 465, 346–349 (2010)
    ADS CAS PubMed Google Scholar
  47. Sanders, M. E. Impact of probiotics on colonizing microbiota of the gut. J. Clin. Gastroenterol. 45 (Suppl), S115–S119 (2011)
    PubMed Google Scholar
  48. Becker, K., Heilmann, C. & Peters, G. Coagulase-negative staphylococci. Clin. Microbiol. Rev. 27, 870–926 (2014)
    CAS PubMed PubMed Central Google Scholar
  49. Clemente, J. C., Ursell, L. K., Parfrey, L. W. & Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258–1270 (2012)
    CAS PubMed PubMed Central Google Scholar
  50. Ho, P. L. et al. Novel selective medium for isolation of Staphylococcus lugdunensis from wound specimens. J. Clin. Microbiol. 52, 2633–2636 (2014)
    PubMed PubMed Central Google Scholar
  51. Geiger, T. et al. The stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression. PLoS Pathog. 8, e1003016 (2012)
    CAS PubMed PubMed Central Google Scholar
  52. Winstel, V., Kühner, P., Krismer, B., Peschel, A. & Rohde, H. Transfer of plasmid DNA to clinical coagulase-negative staphylococcal pathogens by using a unique bacteriophage. Appl. Environ. Microbiol. 81, 2481–2488 (2015)
    CAS PubMed PubMed Central Google Scholar
  53. Wenzel, M. et al. Small cationic antimicrobial peptides delocalize peripheral membrane proteins. Proc. Natl Acad. Sci. USA 111, E1409–E1418 (2014)
    CAS PubMed PubMed Central Google Scholar
  54. Bandow, J. E., Brötz, H., Leichert, L. I., Labischinski, H. & Hecker, M. Proteomic approach to understanding antibiotic action. Antimicrob. Agents Chemother. 47, 948–955 (2003)
    CAS PubMed PubMed Central Google Scholar
  55. Hutter, B. et al. Prediction of mechanisms of action of antibacterial compounds by gene expression profiling. Antimicrob. Agents Chemother. 48, 2838–2844 (2004)
    CAS PubMed PubMed Central Google Scholar
  56. Sass, P. et al. Antibiotic acyldepsipeptides activate ClpP peptidase to degrade the cell division protein FtsZ. Proc. Natl Acad. Sci. USA 108, 17474–17479 (2011)
    ADS CAS PubMed PubMed Central Google Scholar
  57. Wang, R. et al. Identification of novel cytolytic peptides as key virulence determinants for community-associated MRSA. Nat. Med. 13, 1510–1514 (2007)
    CAS PubMed Google Scholar
  58. Bara, R. et al. Atropisomeric dihydroanthracenones as inhibitors of multiresistant Staphylococcus aureus. J. Med. Chem. 56, 3257–3272 (2013)
    CAS PubMed Google Scholar
  59. Wanke, I. et al. Staphylococcus aureus skin colonization is promoted by barrier disruption and leads to local inflammation. Exp. Dermatol. 22, 153–155 (2013)
    CAS PubMed Google Scholar

Download references

Acknowledgements

We thank V. Winstel for technical assistance and A. Bobic, S. Heilbronner, W. Hoffmann, A. Jorge, D. Kretschmer, A. Kulik, M. Nega, E. Stegmann, V. Winstel, T. Weber, and W. Wohlleben for assistance and helpful discussions. Thanks to Bruker Daltonics for selected initial high-resolution mass spectrometry analysis and to T. Paululat for NMR experiments. This work was financed by German Research Council grants GRK1708 to S.G. and A.P.; TRR156, Schi510/8-1, and PE805/5-1 to B.S. and A.P.; TRR34 to C.W. and A.P; and SFB766 to C.W., H.B.-O., S.G., and A.P.; and by the German Center for Infection Research (DZIF) to C.W., A.P., B.K., M.W., and H.B.-O.

Author information

Author notes

  1. Daniela Janek
    Present address: †Present address: Boehringer Ingelheim, 88400 Biberach, Germany.,
  2. Alexander Zipperer and Martin C. Konnerth: These authors contributed equally to this work.

Authors and Affiliations

  1. Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, 72076, Germany
    Alexander Zipperer, Claudia Laux, Daniela Janek, Christoph Slavetinsky, Andreas Peschel & Bernhard Krismer
  2. German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, 72076, Germany
    Alexander Zipperer, Claudia Laux, Daniela Janek, Christopher Weidenmaier, Christoph Slavetinsky, Matthias Willmann, Heike Brötz-Oesterhelt, Andreas Peschel & Bernhard Krismer
  3. Institute of Organic Chemistry, University of Tübingen, Tübingen, 72076, Germany
    Martin C. Konnerth, Nadine A. Schilling & Stephanie Grond
  4. Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, 72076, Germany
    Anne Berscheid & Heike Brötz-Oesterhelt
  5. Interfaculty Institute of Microbiology and Infection Medicine, Medical Microbiology, University of Tübingen, Tübingen, 72076, Germany
    Christopher Weidenmaier, Matthias Marschal & Matthias Willmann
  6. Department of Dermatology, Division of Dermatooncology, University of Tübingen, Tübingen, 72076, Germany
    Marc Burian & Birgit Schittek
  7. Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, 72076, Germany
    Nadine A. Schilling & Hubert Kalbacher

Authors

  1. Alexander Zipperer
    You can also search for this author inPubMed Google Scholar
  2. Martin C. Konnerth
    You can also search for this author inPubMed Google Scholar
  3. Claudia Laux
    You can also search for this author inPubMed Google Scholar
  4. Anne Berscheid
    You can also search for this author inPubMed Google Scholar
  5. Daniela Janek
    You can also search for this author inPubMed Google Scholar
  6. Christopher Weidenmaier
    You can also search for this author inPubMed Google Scholar
  7. Marc Burian
    You can also search for this author inPubMed Google Scholar
  8. Nadine A. Schilling
    You can also search for this author inPubMed Google Scholar
  9. Christoph Slavetinsky
    You can also search for this author inPubMed Google Scholar
  10. Matthias Marschal
    You can also search for this author inPubMed Google Scholar
  11. Matthias Willmann
    You can also search for this author inPubMed Google Scholar
  12. Hubert Kalbacher
    You can also search for this author inPubMed Google Scholar
  13. Birgit Schittek
    You can also search for this author inPubMed Google Scholar
  14. Heike Brötz-Oesterhelt
    You can also search for this author inPubMed Google Scholar
  15. Stephanie Grond
    You can also search for this author inPubMed Google Scholar
  16. Andreas Peschel
    You can also search for this author inPubMed Google Scholar
  17. Bernhard Krismer
    You can also search for this author inPubMed Google Scholar

Contributions

A.Z. isolated lugdunin, designed experiments and investigated the biological activities of lugdunin. M.C.K. purified lugdunin, designed experiments and determined the structure of lugdunin. D.J. identified IVK28 and performed transposon mutagenesis. A.B. designed and performed precursor incorporation studies. C.L. designed the human colonization study and analysed data. M.B., A.Z., C.S. and C.W. performed animal experiments, and M.W. and C.W. analysed data and performed statistical analysis. M.M. provided patient samples and supported MALDI-TOF analysis. N.A.S. and H.K. established total chemical synthesis of lugdunin. B.K. isolated lugdunin, analysed operon structure and performed bioinformatic analyses, A.Z., M.C.K., B.S., H.B.-O., S.G., A.P. and B.K. designed the study, analysed results, and wrote the paper.

Corresponding author

Correspondence toAndreas Peschel.

Ethics declarations

Competing interests

Tuebingen University has filed a provisional patent application that covers the compound lugdunin and derivatives thereof, as well as the application of lugdunin- producing bacteria for the prevention of bacterial infections (European patent application number EP 15 160 285.1).

Additional information

Reviewer Information Nature thanks G. Challis, M. Gilmore and K. Lewis for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Figure 1 Gene cluster of lugdunin and generation of S. lugdunensis IVK28-Xyl.

a, The lugdunin genes are located on a 30-kbp operon. lugA–D encode the four NRPS, which are preceded by the putative regulator gene lugR. Encoded upstream are putative ABC transporter genes (lugE_–_H) and genes for proteins with no described function (lugI and lugJ). A type-II thioesterase, that functions as a repair enzyme for stalled PCP domains, is encoded between lugC and lugD. The 4’-phosphopantetheinyl transferase LugZ converts inactive PCPs (apo-PCP) into the active holo-form by attachment of the 4’-phosphopantetheine cofactor. Encoded downstream is a putative monooxygenase (lugM). The transposon insertion site of Tn917, generating the lugdunin-deficient mutant IVK28 M1, is indicated by a red arrow. b, The xylose-inducible lugdunin producer strain S. lugdunensis IVK28-xyl was generated by replacement of the regulator gene lugR by the xylAB promoter along with the xylR gene encoding a xylose-sensitive repressor. The erythromycin resistance cassette ermB was integrated for selection purposes.

Extended Data Figure 2 Structure elucidation by multistage tandem and electrospray ionization high-resolution mass spectrometry.

a, A single-stage high-resolution MS/MS experiment revealed a superposition of fragment ions typically found for cyclic peptides. Quasi molecular ion selected for fragmentation is marked with a blue rhombus (m/z = 783.45). For sequence annotation, fragment ions were searched for b-ions of high intensity. One fragmentation route is annotated exemplarily by highlighting respective a-, b- and c-ion series signals. Thia, thiazoldine. b, Data generated by multistage tandem mass spectrometry show that lugdunin mainly fragmented along four routes (blue digits; (I), (II), (III), (IV)). Initial protonation occurs at the secondary amine of thiazolidine (blue H atom). Proton transfer to nearby peptide bonds initiated ring cleavage with subsequent fragmentation. Initial loss of ammonia for fragmentation route (I) can be explained by a precedent six-membered transition state. Intensities are in arbitrary units. Blue rhombuses label the position of initial ring cleavage. Fragmentation route molecules are shown in linearized form.

Extended Data Figure 3 NMR spectra of the natural product lugdunin.

The two diastereomeric and interconvertible forms of lugdunin (see imine intermediate, Extended Data Fig. 4d) show distinctive sets of NMR signals with consistent patterns, which were assigned by two-dimensional NMR methods (COSY, HMBC, HSQC-DEPT, ROESY and TOCSY) and corroborated the thiazolidine heterocycle as a special feature of lugdunin. Chemical shifts (δ) are shown in p.p.m. a, 1H NMR spectrum (600 MHz) of lugdunin in DMSO-d6 at 308 K. b, 13C NMR spectrum (150 MHz) of lugdunin in DMSO-d6 at 308 K. Atom numbering refers to full spectral assignment shown in Extended Data Table 1. c, Expansion of HMBC spectrum (heteronuclear multiple bond correlation) shows distinct correlations between the amino acid α-proton and the carbonyl C-atom of the respective amino acid. d, Expansion of ROESY spectrum (rotation frame nuclear Overhauser effect spectroscopy) shows short-ranged correlations through space between α-protons and amino acid amide protons. e, Taken together, HMBC (green arrows) and ROESY (double headed blue arrows) correlations allowed for a full sequential walk along the peptide backbone, which readily confirmed the amino acid sequence of both lugdunin diastereomers (the sequential walk is exemplarily shown for one diastereomer).

Extended Data Figure 4 The thiazolidine moiety of lugdunin and its formation by peptide cyclisation.

a, Blue rhombus marks the b2-ion from fragmentation route I (Extended Data Fig. 2). The ion was selected from an in-source collision-induced decay (isCID) experiment and was further fragmented in order to find thiazolidine-specific fragment ions. High-resolution MS data are shown with annotated sum formulas and respective deviations from calculated masses (errors in p.p.m.). Shown fragment ions reveal the b1-ion at m/z = 170.0635 Da. Intensity is shown in arbitrary units. b, Photometric detection of thiazolidines at 670 nm. A positive colour reaction with 3-methyl-2-benzothiazolone hydrazone hydrochloride (Sawicki reagent) gives rise to detectable absorbance at 670 nm. Thiazolidine-4-carboxylic acid (thiazolidine) was chosen as positive control, whereas 2-methyl-2-thiazoline (thiazoline) and DMSO acted as negative controls. c, Observable colours for the thiazolidine detection reaction. Thiazolidine-4-carboxlic acid (blue), lugdunin (green) and negative controls (yellow). d, The terminal reductase of LugC is proposed to initiate cleavage of the thioester-bound peptide chain with the aid of an NAD(P)H cofactor. The mature heptapeptide is liberated reductively from the NRPS multienzyme complex and cyclises via the N-terminal amine (l-Cys) and C-terminal aldehyde (l-Val) to form a macrocyclic imine/Schiff base. Subsequent nucleophilic attack of the cysteine thiol group generates the five-membered thiazolidine heterocycle. Nucleophilic attack by the l-cysteine sulfhydryl group may occur either at the re or si face of the imine thus leading to a diastereomeric mixture of two structural populations (depicted with wavy bond). LugC is shown as truncated gene, as indicated by the two lines (||).

Extended Data Figure 5 Lugdunin activity against eukaryotic cells.

a, b, Human neutrophil granulocytes (a) or erythrocytes (b) were incubated with high concentrations of lugdunin. Their lysis was monitored by the release of the enzyme lactate dehydrogenase (a) or haemoglobin (b), respectively. Cells without lugdunin were used as negative control. Incubation of cells in 2% Triton X-100 was used as positive control for high lysis. The data represent three independent experiments ± s.d. c, Promyelocytic leukaemia (HL60) cells were incubated with high concentrations of lugdunin. In order to determine the 50% inhibitory concentration of lugdunin, the metabolic activity of HL60 cells was measured by the conversion of resazurin into the highly fluorescent resorufin. The apoptosis-inducing staurosporine was used as positive control. IC50 values were calculated from the means of three independent experiments.

Source data

Extended Data Figure 6 Time course of incorporation of tritium-labelled metabolic precursors into lugdunin-treated B. subtilis.

B. subtilis 168 (trpC2) is a widely used model organism for mode of action investigations and was also used for orienting studies on the mechanism of lugdunin. Susceptibility of B. subtilis and S. aureus to lugdunin is similar (Table 1), with an MIC for B. subtilis of 4 μg ml−1 in the Belitzky minimal medium used in this assay. a–d, Incorporation of thymidine into DNA (a), uridine into RNA (b), leucine into protein (c) or _N_-acetylglucosamine into peptidoglycan (d) ceased within minutes during lugdunin treatment. The experiment was repeated on three days with three independent bacterial cultures. One representative experiment is shown. At a concentration of half the MIC (1/2 MIC), incorporation of precursors into all pathways ceased reproducibly. At 1/8 MIC, incorporation continued repeatedly in parallel with the untreated control. At 1/4 MIC, the depicted experiment shows protein and peptidoglycan syntheses slightly more impaired than DNA and RNA syntheses, whereas the opposite occurred in another experiment. In summary, all four metabolic pathways seem to be equally impaired by lugdunin.

Source data

Extended Data Figure 7 Nasal colonization rates by S. aureus and S. lugdunensis in cotton rats.

a–c, Different inocula of S. aureus Newman (a), S. lugdunensis IVK 28 wild type (b) and S. lugdunensis IVK 28 Δ_lugD_ (c) were instilled intranasally to determine their efficiency to colonize the noses of cotton rats (5 or 6 animals per group). c.f.u. of each strain were determined per nose after 5 days and plotted as individual dots. Lines represent the median of each group.

Source data

Extended Data Table 1 NMR spectral assignment of lugdunin diastereomers

Full size table

Extended Data Table 2 Primers used in this study

Full size table

Supplementary information

PowerPoint slides

Source data

Rights and permissions

About this article

Cite this article

Zipperer, A., Konnerth, M., Laux, C. et al. Human commensals producing a novel antibiotic impair pathogen colonization.Nature 535, 511–516 (2016). https://doi.org/10.1038/nature18634

Download citation