Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome (original) (raw)

References

  1. Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337–341 (2011)
    Article CAS ADS Google Scholar
  2. Brandl, K. et al. Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits. Nature 455, 804–807 (2008)
    Article CAS ADS Google Scholar
  3. Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241–244 (2011)
    Article CAS ADS Google Scholar
  4. Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006)
    Article ADS Google Scholar
  5. Faith, J. J., McNulty, N. P., Rey, F. E. & Gordon, J. I. Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science 333, 101–104 (2011)
    Article CAS ADS Google Scholar
  6. Dethlefsen, L., Huse, S., Sogin, M. L. & Relman, D. A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, e280 (2008)
    Article Google Scholar
  7. Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108 (Suppl. 1). 4554–4561 (2011)
    Article CAS ADS Google Scholar
  8. Antunes, L. C. et al. Effect of antibiotic treatment on the intestinal metabolome. Antimicrob. Agents Chemother. 55, 1494–1503 (2011)
    Article CAS Google Scholar
  9. Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334–338 (2010)
    Article CAS ADS Google Scholar
  10. Oliver, K. M., Degnan, P. H., Hunter, M. S. & Moran, N. A. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325, 992–994 (2009)
    Article CAS ADS Google Scholar
  11. Chen, J. & Novick, R. P. Phage-mediated intergeneric transfer of toxin genes. Science 323, 139–141 (2009)
    Article CAS ADS Google Scholar
  12. Lindell, D., Jaffe, J. D., Johnson, Z. I., Church, G. M. & Chisholm, S. W. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438, 86–89 (2005)
    Article CAS ADS Google Scholar
  13. Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L. & Rohwer, F. Laboratory procedures to generate viral metagenomes. Nature Protocols 4, 470–483 (2009)
    Article CAS Google Scholar
  14. Breitbart, M. et al. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185, 6220–6223 (2003)
    Article CAS Google Scholar
  15. Dinsdale, E. A. et al. Functional metagenomic profiling of nine biomes. Nature 452, 629–632 (2008)
    Article CAS ADS Google Scholar
  16. Walsh, C. Molecular mechanisms that confer antibacterial drug resistance. Nature 406, 775–781 (2000)
    Article CAS Google Scholar
  17. Hanaki, H. et al. Activated cell-wall synthesis is associated with vancomycin resistance in methicillin-resistant Staphylococcus aureus clinical strains Mu3 and Mu50. J. Antimicrob. Chemother. 42, 199–209 (1998)
    Article CAS Google Scholar
  18. Foti, J. J., Devadoss, B., Winkler, J. A., Collins, J. J. & Walker, G. C. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science 336, 315–319 (2012)
    Article CAS ADS Google Scholar
  19. Kohanski, M. A., Dwyer, D. J. & Collins, J. J. How antibiotics kill bacteria: from targets to networks. Nature Rev. Microbiol. 8, 423–435 (2010)
    Article CAS Google Scholar
  20. Hanage, W. P., Fraser, C., Tang, J., Connor, T. R. & Corander, J. Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324, 1454–1457 (2009)
    Article CAS ADS Google Scholar
  21. Chang, D. E. et al. Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl Acad. Sci. USA 101, 7427–7432 (2004)
    Article CAS ADS Google Scholar
  22. Xu, J. & Gordon, J. I. Honor thy symbionts. Proc. Natl Acad. Sci. USA 100, 10452–10459 (2003)
    Article CAS ADS Google Scholar
  23. Stern, A., Mick, E., Tirosh, I., Sagy, O. & Sorek, R. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res. 22, 1984–1994 (2012)
    Article Google Scholar
  24. Zimmer, M., Scherer, S. & Loessner, M. J. Genomic analysis of Clostridium perfringens bacteriophage ϕ3626, which integrates into guaA and possibly affects sporulation. J. Bacteriol. 184, 4359–4368 (2002)
    Article CAS Google Scholar
  25. Dorscht, J. et al. Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J. Bacteriol. 191, 7206–7215 (2009)
    Article CAS Google Scholar
  26. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012)
    Article CAS ADS Google Scholar
  27. Liu, B. & Pop, M. ARDB—Antibiotic Resistance Genes Database. Nucleic Acids Res. 37, D443–D447 (2009)
    Article CAS Google Scholar
  28. Gomez-Alvarez, V., Teal, T. K. & Schmidt, T. M. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3, 1314–1317 (2009)
    Article Google Scholar
  29. Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000)
    Article CAS Google Scholar
  30. Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233–D238 (2009)
    Article CAS Google Scholar
  31. Goodman, A. L. et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108, 6252–6257 (2011)
    Article CAS ADS Google Scholar

Download references