Host-centric proteomics of stool: A novel strategy focused on intestinal responses to the gut microbiota

Molecular and Cellular Proteomics

Volumn 12, Issue 11, 2013, Pages 3310-3318

  Lichtman, Joshua S ^a   Marcobal, Angela ^a   Sonnenburg, Justin L ^a   Elias, Joshua E ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; FEASIBILITY STUDY; FECES ANALYSIS; GNOTOBIOTICS; HOST RANGE; HUMAN; IMMUNE RESPONSE; INTESTINE FLORA; MALE; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MOUSE; NONHUMAN; NORMAL HUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN METHYLATION; PROTEIN SECRETION; PROTEOMICS;

ANIMALS; CHROMATOGRAPHY, LIQUID; FECES; GERM-FREE LIFE; HUMANS; INTESTINES; MICE; MICROBIOTA; MODELS, ANIMAL; PROTEOME; PROTEOMICS; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY;

EID: 84887096280     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.029967     Document Type: Article

References (34)

1. Bä ckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., and Gordon, J. I. (2005) Host-bacterial mutualism in the human intestine. Science 307, 1915-20. (Pubitemid 40404694)
2. Round, J. L., and Mazmanian, S. K. (2006) The gut microbiota shapes intestinal immune responses during health and disease. Nature Rev. 9, 313-23.
3. Sanderson, S., Boardman, W., Ciofi, C., and Gibson, R. (2006) Human gut microbes associated with obesity. Nature 444, 1022-1023.
4. Maslowski, K. M., and Mackay, C. R. (2011) Diet, gut microbiota and immune responses. Nat. Immunol. 12, 5-9.
5. Reid, G., Younes, J. A., Van der Mei, H. C., Gloor, G. B., Knight, R., and Busscher, H. J. (2011) Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat. Rev. Microbiol. 9, 27-38.
6. Gill, S. R., Pop, M., Deboy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., and Nelson, K. E. (2006) Metagenomic analysis of the human distal gut micro biome. Science 312, 1355-9. (Pubitemid 43839542)
7. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E. and Relman, D. A. (2005) Diversity of the human intestinal microbial flora. Science 308, 1635-8. (Pubitemid 40807514)
8. Stappenbeck, T. S., Hooper, L. V., Manchester, J. K., Wong, M. H., and Gordon, J. I. (2002) Laser capture microdissection of mouse intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations. Methods Enzymol. 356, 167-96. (Pubitemid 35217233)
9. Verberkmoes, N. C., Russell, A. L., Shah, M., Godzik, A., Rosenquist, M., Halfvarson, J., Lefsrud, M. G., Apajalahti, J., Tysk, C., Hettich, R. L., and Jansson, J. K. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179-89.
10. Erickson, A. R., Cantarel, B. L., Lamendella, R., Darzi, Y., Mongodin, E. F., Pan, C., Shah, M., Halfvarson, J., Tysk, C., Henrissat, B., Raes, J., Verberkmoes, N. C., Fraser, C. M., Hettich, R. L., and Jansson, J. K. (2012) Integrated metagenomics/metaproteomics reveals human hostmicrobiota signatures of Crohn's disease. PloS one 7, e49138.
11. Sonnenburg, E. D., Zheng, H., Joglekar, P., Higginbottom, S. K., Firbank, S. J., Bolam, D. N., and Sonnenburg, J. L. (2010) Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241-52.
12. Kashyap, P., Marcobal, A., and Ursell, L. (2013) Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology doi:10.1053/j.gastro.2013.01.047.
13. Consortium, T. U. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40, D71-5.
14. Markowitz, V. M., Chen, I.-M. a, Chu, K., Szeto, E., Palaniappan, K., Jacob, B., Ratner, A., Liolios, K., Pagani, I., Huntemann, M., Mavromatis, K., Ivanova, N. N., and Kyrpides, N. C. (2012) IMG/M-HMP: A metagenome comparative analysis system for the Human Microbiome Project. PloS one 7, e40151.
15. Elias, J., and Gygi, S. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214. (Pubitemid 46358868)
16. Pappin, D. J. C., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567. (Pubitemid 30007252)
17. Vizcaíno, J. A., Cô té, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Pé rez-Riverol, Y., Reisinger, F., Ríos, D., Wang, R., and Hermjakob, H. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-9.
18. Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research 37, 1-13.
19. Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44-57.
20. Apajalahti, J. H., Sä rkilahti, L. K., Mä ki, B. R., Heikkinen, J. P., Nurminen, P. H., and Holben, W. E. (1998) Effective recovery of bacterial DNA and percent-guanine-plus-cytosine-based analysis of community structure in the gastrointestinal tract of broiler chickens. Appl. Environ. Micro biol. 64, 4084-8. (Pubitemid 28463022)
21. Resing, K. A., Meyer-Arendt, K., Mendoza, A. M., Aveline-Wolf, L. D., Jonscher, K. R., Pierce, K. G., Old, W. M., Cheung, H. T., Russell, S., Wattawa, J. L., Goehle, G. R., Knight, R. D., and Ahn, N. G. (2004) Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 76, 3556-68. (Pubitemid 38868816)
22. Glajch, J. L., Kirkland, J. J., and Kohler, J. (1987) Effect of column degradation on the reversed-phase high-performance separation of peptides and proteins. J. Chromatography. A 384, 81-90. (Pubitemid 17227468)
23. Elias, J., Haas, W., Faherty, B., and Gygi, S. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2, 667-675. (Pubitemid 41223093)
24. Olsen, J. V., Ong, S. E., and Mann, M. (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 3, 608-14. (Pubitemid 38878520)
25. Hapfelmeier, S., Lawson, M. A. E., Slack, E., Kirundi, J. K., Stoel, M., Heikenwalder, M., Cahenzli, J., Velykoredko, Y., Balmer, M. L., Endt, K., Geuking, M. B., Curtiss, R., McCoy, K. D., and Macpherson, A. J. (2010) Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science 328, 1705-9.
26. Thompson, C. L., Hofer, M. J., Campbell, I. L., and Holmes, A. J. (2010) Community dynamics in the mouse gut microbiota: A possible role for IRF9-regulated genes in community homeostasis. PloS one 5, e10335.
27. Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., and Knight, R. (2009) Bacterial community variation in human body habitats across space and time. Science 326, 1694-7.
28. Rawls, J. F., Samuel, B. S., and Gordon, J. I. (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut micro biota. Proc. Natl. Acad. Sci. U. S. A. 101, 4596-601. (Pubitemid 38437456)
29. Turnbaugh, P., and Ridaura, V. (2009) The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci. Translational Med. 1, 1-19.
30. Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., and Gordon, J. I. (2009) The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci. Translational Med. 1, 6ra14.
31. Agerberth, B., Charo, J., Werr, J., Olsson, B., Idali, F., Lindbom, L., Kiessling, R., Jö rnvall, H., Wigzell, H., and Gudmundsson, G. H. (2000) The human antimicrobial and chemotactic peptides LL-37 and alphadefensins are expressed by specific lymphocyte and monocyte populations. Blood 96, 3086-93.
32. Thompson, A., Schä fer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A. K. A., and Hamon, C. (2003) Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-904. (Pubitemid 36438013)
33. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-69.
34. Mahowald, M. a, Rey, F. E., Seedorf, H., Turnbaugh, P. J., Fulton, R. S., Wollam, A., Shah, N., Wang, C., Magrini, V., Wilson, R. K., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Crock, L. W., Russell, A., Verberkmoes, N. C., Hettich, R. L., and Gordon, J. I. (2009) Characterizing a model human gut micro biota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. U. S. A. 106, 5859-64.