O. Hara, A. Shanahan, and F. , The gut flora as a forgotten organ, EMBO reports, vol.13, issue.7, pp.688-693, 2006.
DOI : 10.1097/00001574-200411000-00011

L. Hooper and J. Gordon, Commensal Host-Bacterial Relationships in the Gut, Science, vol.292, issue.5519, pp.1115-1118, 2001.
DOI : 10.1126/science.1058709

E. Zoetendal, M. Rajiliä-stojanoviä, and W. De-vos, High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota, Gut, vol.57, issue.11, pp.1605-1615, 2008.
DOI : 10.1136/gut.2007.133603

U. Steinhoff, Who controls the crowd? New findings and old questions about the intestinal microflora, Immunology Letters, vol.99, issue.1, pp.12-16, 2005.
DOI : 10.1016/j.imlet.2004.12.013

F. Guarner and J. Malagelada, Gut flora in health and disease. The Lancet, pp.512-519, 2003.

C. Sears, A dynamic partnership: Celebrating our gut flora, Anaerobe, vol.11, issue.5, pp.247-251, 2005.
DOI : 10.1016/j.anaerobe.2005.05.001

J. Qin, R. Li, J. Raes, M. Arumugam, K. Burgdorf et al., A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.13, issue.7285, pp.59-65, 2010.
DOI : 10.1038/nature08821

URL : https://hal.archives-ouvertes.fr/cea-00908974

R. Aebersold and M. Mann, Mass spectrometry-based proteomics, Nature, vol.1, issue.6928, pp.198-207, 2003.
DOI : 10.1016/S0960-9822(01)00632-7

C. Ansong, S. Purvine, J. Adkins, M. Lipton, and R. Smith, Proteogenomics: needs and roles to be filled by proteomics in genome annotation, Briefings in Functional Genomics and Proteomics, vol.7, issue.1, pp.50-62, 2008.
DOI : 10.1093/bfgp/eln010

C. Lacerda and K. Reardon, Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology, Briefings in Functional Genomics and Proteomics, vol.8, issue.1, pp.75-87, 2009.
DOI : 10.1093/bfgp/elp005

E. Marcotte, How do shotgun proteomics algorithms identify proteins? Nat Biotech, pp.755-757, 2007.
DOI : 10.1038/nbt0707-755

F. Shanahan, The host-microbe interface within the gut. Best Practice & Research Clinical Gastroenterology, pp.915-931, 2002.

B. Habermann, J. Oegema, S. Sunyaev, and A. Shevchenko, The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches, Molecular & Cellular Proteomics, vol.3, issue.3, pp.238-249, 2004.
DOI : 10.1074/mcp.M300073-MCP200

M. Wilkins, N. Verberkmoes, K. Williams, S. Callister, P. Mouser et al., Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation, Applied and Environmental Microbiology, vol.75, issue.20, pp.6591-6599, 2009.
DOI : 10.1128/AEM.01064-09

N. Verberkmoes, V. Denef, R. Hettich, and J. Banfield, Systems Biology: Functional analysis of natural microbial consortia using community proteomics, Nature Reviews Microbiology, vol.42, issue.3, pp.196-205, 2009.
DOI : 10.1038/nrmicro2080

S. Callister, M. Wilkins, C. Nicora, K. Williams, J. Banfield et al., Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles, Environmental Science & Technology, vol.44, issue.23, 2010.
DOI : 10.1021/es101029f

M. Rajili?-stojanovi?, H. Heilig, D. Molenaar, K. Kajander, A. Surakka et al., Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults, Environmental Microbiology, vol.57, issue.7, pp.1736-1751, 2009.
DOI : 10.1111/j.1462-2920.2009.01900.x

M. Derrien, M. Collado, K. Ben-amor, S. Salminen, and W. De-vos, The Mucin Degrader Akkermansia muciniphila Is an Abundant Resident of the Human Intestinal Tract, Applied and Environmental Microbiology, vol.74, issue.5, pp.1646-1648, 2008.
DOI : 10.1128/AEM.01226-07

J. Morgan, A. Darling, and J. Eisen, Metagenomic Sequencing of an In Vitro-Simulated Microbial Community, PLoS ONE, vol.5, issue.4, p.10209, 2010.
DOI : 10.1371/journal.pone.0010209.t003

J. Elias and S. Gygi, Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry, Nature Methods, vol.4, issue.3, pp.207-214, 2007.
DOI : 10.1038/nmeth1019

K. Mavromatis, M. Land, A. Lapidus, I. Grigoriev, P. Richardson et al., Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nature Methods, vol.22, issue.6, pp.495-500, 2007.
DOI : 10.1038/nmeth1043

K. Hoff, The effect of sequencing errors on metagenomic gene prediction, BMC Genomics, vol.10, issue.1, pp.520-520, 2009.
DOI : 10.1186/1471-2164-10-520

V. Gotea, V. Veeramachaneni, and W. Makalowski, Mastering seeds for genomic size nucleotide BLAST searches, Nucleic Acids Research, vol.31, issue.23, pp.6935-6941, 2003.
DOI : 10.1093/nar/gkg886

URL : http://doi.org/10.1093/nar/gkg886

R. Tatusov, D. Natale, I. Garkavtsev, T. Tatusova, U. Shankavaram et al., The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Research, vol.29, issue.1, pp.22-28, 2001.
DOI : 10.1093/nar/29.1.22

S. Hercberg, P. Galan, P. Preziosi, S. Bertrais, L. Mennen et al., The SU.VI.MAX Study, Archives of Internal Medicine, vol.164, issue.21, pp.2335-2342, 2004.
DOI : 10.1001/archinte.164.21.2335

URL : https://hal.archives-ouvertes.fr/hal-01346671

M. Kimie, F. Tsutomu, M. Masataka, and N. S. , One-step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing-thawing and two-dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles, ELECTROPHORESIS, vol.22, pp.2872-2880, 2001.

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

L. Geer, S. Markey, J. Kowalak, L. Wagner, M. Xu et al., Open Mass Spectrometry Search Algorithm, Journal of Proteome Research, vol.3, issue.5, pp.958-964, 2004.
DOI : 10.1021/pr0499491

URL : http://arxiv.org/abs/q-bio/0406002

B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=