C. Shekhar, Future Fuel: Could Biomass Be the New Petroleum?, Chemistry & Biology, vol.18, issue.10, pp.1199-1200, 2011.
DOI : 10.1016/j.chembiol.2011.10.010

W. Schwarz, The cellulosome and cellulose degradation by anaerobic bacteria, Applied Microbiology and Biotechnology, vol.56, issue.5-6, pp.634-649, 2001.
DOI : 10.1007/s002530100710

J. Edwards, D. Smith, J. Connolly, J. Mcdonald, and M. Cox, Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes, Genes, vol.1, issue.3, pp.371-384, 2010.
DOI : 10.3390/genes1030371

N. Mcneil, The contribution of the large intestine to energy supplies in man, Am J Clin Nutr, vol.39, pp.338-342, 1984.

M. Pauly and K. Keegstra, Cell-wall carbohydrates and their modification as a resource for biofuels, The Plant Journal, vol.173, issue.4, pp.559-568, 2008.
DOI : 10.1104/pp.127.1.324

E. Kaoutari, A. Armougom, F. Gordon, J. Raoult, D. Henrissat et al., The abundance and variety of carbohydrate-active enzymes in the human gut microbiota, Nature Reviews Microbiology, vol.6, issue.7, pp.497-504, 2013.
DOI : 10.1038/nrmicro3050

R. Deutschmann and R. Dekker, From plant biomass to bio-based chemicals: Latest developments in xylan research, Biotechnology Advances, vol.30, issue.6, pp.1627-1640, 2012.
DOI : 10.1016/j.biotechadv.2012.07.001

W. Bauer, K. Talmadge, K. Keegstra, and P. Albersheim, The Structure of Plant Cell Walls: II. The Hemicellulose of the Walls of Suspension-cultured Sycamore Cells, PLANT PHYSIOLOGY, vol.51, issue.1, pp.174-187, 1973.
DOI : 10.1104/pp.51.1.174

D. Burke, P. Kaufman, M. Mcneil, and P. Albersheim, The Structure of Plant Cell Walls: VI. A Survey of the Walls of Suspension-cultured Monocots, PLANT PHYSIOLOGY, vol.54, issue.1, pp.109-115, 1974.
DOI : 10.1104/pp.54.1.109

P. Capek, J. Alföldi, and D. Lisková, An acetylated galactoglucomannan from Picea abies L. Karst, Carbohydrate Research, vol.337, issue.11, pp.1033-1037, 2002.
DOI : 10.1016/S0008-6215(02)00090-3

M. Buckeridge, Seed Cell Wall Storage Polysaccharides: Models to Understand Cell Wall Biosynthesis and Degradation, PLANT PHYSIOLOGY, vol.154, issue.3, pp.1017-1023, 2010.
DOI : 10.1104/pp.110.158642

K. Caffall and D. Mohnen, The structure, function, and biosynthesis of plant cell wall pectic polysaccharides, Carbohydrate Research, vol.344, issue.14, pp.1879-1900, 2009.
DOI : 10.1016/j.carres.2009.05.021

B. Ridley, O. Neill, M. Mohnen, and D. , Pectins: structure, biosynthesis, and oligogalacturonide-related signaling, Phytochemistry, vol.57, issue.6, pp.929-96710, 2001.
DOI : 10.1016/S0031-9422(01)00113-3

D. Mohnen, Pectin structure and biosynthesis, Current Opinion in Plant Biology, vol.11, issue.3, pp.266-277, 2008.
DOI : 10.1016/j.pbi.2008.03.006

V. Lombard, G. Ramulu, H. Drula, E. Coutinho, P. Henrissat et al., The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Research, vol.42, issue.D1, pp.490-495, 2014.
DOI : 10.1093/nar/gkt1178

L. Lynd, P. Weimer, W. Van-zyl, and I. Pretorius, Microbial Cellulose Utilization: Fundamentals and Biotechnology, Microbiology and Molecular Biology Reviews, vol.66, issue.3, pp.506-577, 2002.
DOI : 10.1128/MMBR.66.3.506-577.2002

A. Tolonen, E. Petit, J. Blanchard, T. Warnick, and S. Leschine, CHAPTER 7. Technologies to Study Plant Biomass Fermentation Using the Model Bacterium Clostridium Phytofermentans, Biological conversion of biomass for fuels and chemicals, pp.114-139, 2013.
DOI : 10.1039/9781849734738-00114

T. Warnick, B. Methé, and S. Leschine, Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil., International Journal of Systematic and Evolutionary Microbiology, vol.52, issue.4, pp.1155-1160, 2002.
DOI : 10.1099/00207713-52-4-1155

R. Hatfield and P. Weimer, Degradation characteristics of isolated andin situ cell wall lucerne pectic polysaccharides by mixed ruminal microbes, Journal of the Science of Food and Agriculture, vol.47, issue.2, pp.185-196, 1995.
DOI : 10.1002/jsfa.2740690208

E. Martens, E. Lowe, H. Chiang, N. Pudlo, and M. Wu, Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts, PLoS Biology, vol.23, issue.12, 2011.
DOI : 10.1371/journal.pbio.1001221.s018

M. Muir, L. Williams, and T. Ferenci, Influence of transport energization on the growth yield of Escherichia coli, J Bacteriol, vol.163, pp.1237-1242, 1985.

Y. Zhang and L. Lynd, Cellulose utilization by Clostridium thermocellum: Bioenergetics and hydrolysis product assimilation, Proceedings of the National Academy of Sciences, vol.102, issue.20, pp.7321-7325, 2005.
DOI : 10.1073/pnas.0408734102

T. Nihira, H. Nakai, K. Chiku, and M. Kitaoka, Discovery of nigerose phosphorylase from Clostridium phytofermentans, Applied Microbiology and Biotechnology, vol.341, issue.4, pp.1513-1522, 2012.
DOI : 10.1007/s00253-011-3515-9

M. Nakajima, M. Nishimoto, and M. Kitaoka, Characterization of Three ??-Galactoside Phosphorylases from Clostridium phytofermentans: DISCOVERY OF D-GALACTOSYL-??1->4-L-RHAMNOSE PHOSPHORYLASE, Journal of Biological Chemistry, vol.284, issue.29, pp.19220-19227, 2009.
DOI : 10.1074/jbc.M109.007666

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, 2010.

A. Tolonen, T. Cerisy, H. El-sayyed, M. Boutard, and M. Salanoubat, Fungal lysis by a soil bacterium fermenting cellulose, Environmental Microbiology, vol.68, issue.8, 2014.
DOI : 10.1111/1462-2920.12495

A. Tolonen, A. Chilaka, and G. Church, Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367, Molecular Microbiology, vol.31, issue.Part 12, pp.1300-1313, 2009.
DOI : 10.1111/j.1365-2958.2009.06890.x

X. Zhang, N. Sathitsuksanoh, and Y. Zhang, Glycoside hydrolase family 9 processive endoglucanase from Clostridium phytofermentans: Heterologous expression, characterization, and synergy with family 48 cellobiohydrolase, Bioresource Technology, vol.101, issue.14, pp.5534-5538, 2010.
DOI : 10.1016/j.biortech.2010.01.152

X. Zhang, Z. Zhang, Z. Zhu, N. Sathitsuksanoh, and Y. Yang, The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity, Applied Microbiology and Biotechnology, vol.103, issue.2, pp.525-533, 2010.
DOI : 10.1007/s00253-009-2231-1

J. Knox, Revealing the structural and functional diversity of plant cell walls, Current Opinion in Plant Biology, vol.11, issue.3, pp.308-313, 2008.
DOI : 10.1016/j.pbi.2008.03.001

D. Abbott, S. Hrynuik, and A. Boraston, Identification and Characterization of a Novel Periplasmic Polygalacturonic Acid Binding Protein from Yersinia enterolitica, Journal of Molecular Biology, vol.367, issue.4, pp.1023-1033, 2007.
DOI : 10.1016/j.jmb.2007.01.030

H. Aspeborg, P. Coutinho, Y. Wang, H. Brumer, and B. Henrissat, Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5), BMC Evolutionary Biology, vol.12, issue.1, pp.186-196, 2012.
DOI : 10.1080/10635150390235520

H. Liao, X. Zhang, J. Rollin, and Y. Zhang, A minimal set of bacterial cellulases for consolidated bioprocessing of lignocellulose, Biotechnology Journal, vol.18, issue.72, pp.1409-1418, 2011.
DOI : 10.1002/biot.201100157

J. Benz, B. Chau, D. Zheng, S. Bauer, and N. Glass, reveals carbon source-specific cellular adaptations, Molecular Microbiology, vol.109, issue.2, pp.275-299, 2014.
DOI : 10.1111/mmi.12459

J. Nölling, G. Breton, M. Omelchenko, K. Makarova, and Q. Zeng, Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum, Journal of Bacteriology, vol.183, issue.16, pp.4823-4838, 2001.
DOI : 10.1128/JB.183.16.4823-4838.2001

A. Makishah, N. Mitchell, and W. , Dual Substrate Specificity of an N-Acetylglucosamine Phosphotransferase System in Clostridium beijerinckii, Applied and Environmental Microbiology, vol.79, issue.21, pp.6712-6718, 2013.
DOI : 10.1128/AEM.01866-13

M. Servinsky, J. Kiel, N. Dupuy, and C. Sund, Transcriptional analysis of differential carbohydrate utilization by Clostridium acetobutylicum, Microbiology, vol.156, issue.11, pp.3478-3491, 2010.
DOI : 10.1099/mic.0.037085-0

M. Chen, L. Chen, Y. Zou, M. Xue, and M. Liang, Wide sugar substrate specificity of galactokinase from Streptococcus pneumoniae TIGR4, Carbohydrate Research, vol.346, issue.15, pp.2421-2425, 2011.
DOI : 10.1016/j.carres.2011.08.014

M. Servinsky, K. Germane, S. Liu, J. Kiel, and A. Clark, Arabinose is metabolized via a phosphoketolase pathway in Clostridium acetobutylicum ATCC 824, Journal of Industrial Microbiology & Biotechnology, vol.194, issue.5, pp.1859-1867, 2012.
DOI : 10.1007/s10295-012-1186-x

T. Ng, A. Ben-bassat, and J. Zeikus, Ethanol Production by Thermophilic Bacteria: Fermentation of Cellulosic Substrates by Cocultures of Clostridium thermocellum and Clostridium thermohydrosulfuricum, Appl Environ Microbiol, vol.41, pp.1337-1343, 1981.

C. Xu, R. Huang, L. Teng, D. Wang, and C. Hemme, Structure and regulation of the cellulose degradome in Clostridium cellulolyticum, Biotechnology for Biofuels, vol.6, issue.1, pp.73-83, 2013.
DOI : 10.1002/pmic.200900375

A. Tolonen and W. Haas, Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling, Journal of Visualized Experiments, issue.89, pp.51416-51426, 2014.
DOI : 10.3791/51416

E. Johnson, A. Madia, and A. Demain, Chemically Defined Minimal Medium for Growth of the Anaerobic Cellulolytic Thermophile Clostridium thermocellum, Appl Environ Microbiol, vol.41, pp.1060-1062, 1981.

J. Hong, X. Ye, Y. Wang, and Y. Zhang, Bioseparation of recombinant cellulose-binding module-proteins by affinity adsorption on an ultra-high-capacity cellulosic adsorbent, Analytica Chimica Acta, vol.621, issue.2, pp.193-199, 2008.
DOI : 10.1016/j.aca.2008.05.041

A. Tolonen, W. Haas, A. Chilaka, J. Aach, and S. Gygi, Proteomewide systems analysis of a cellulosic biofuel-producing microbe, Mol Syst Biol, vol.7, 2011.

M. Deangelis, D. Wang, and T. Hawkins, Solid-phase reversible immobilization for the isolation of PCR products, Nucleic Acids Research, vol.23, issue.22, pp.4742-4743, 1995.
DOI : 10.1093/nar/23.22.4742

N. Rohland and D. Reich, Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture, Genome Research, vol.22, issue.5, pp.939-946, 2012.
DOI : 10.1101/gr.128124.111

B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, Ultrafast and memoryefficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, pp.10-1186, 2009.

L. Habegger, A. Sboner, T. Gianoulis, J. Rozowsky, and A. Agarwal, RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries, Bioinformatics, vol.27, issue.2, pp.281-283, 2011.
DOI : 10.1093/bioinformatics/btq643

A. Mandlik, J. Livny, W. Robins, J. Ritchie, and J. Mekalanos, RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression, Cell Host & Microbe, vol.10, issue.2, pp.165-174, 2011.
DOI : 10.1016/j.chom.2011.07.007

C. Aslanidis and P. De-jong, Ligation-independent cloning of PCR products (LIC-PCR), Nucleic Acids Research, vol.18, issue.20, pp.6069-6074, 1990.
DOI : 10.1093/nar/18.20.6069

T. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nature Methods, vol.6, issue.10, pp.785-786, 2011.
DOI : 10.1016/0005-2795(75)90109-9

G. Miller, Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar, Analytical Chemistry, vol.31, issue.3, pp.426-428, 1959.
DOI : 10.1021/ac60147a030

T. Watanabe, Y. Ito, T. Yamada, M. Hashimoto, and S. Sekine, The roles of the C-terminal domain and type III domains of chitinase A1 from Bacillus circulans WL-12 in chitin degradation., Journal of Bacteriology, vol.176, issue.15, pp.4465-4472, 1994.
DOI : 10.1128/jb.176.15.4465-4472.1994

E. Petit, W. Latouf, M. Coppi, T. Warnick, and D. Currie, Involvement of a Bacterial Microcompartment in the Metabolism of Fucose and Rhamnose by Clostridium phytofermentans, PLoS ONE, vol.53, issue.1, 2013.
DOI : 10.1371/journal.pone.0054337.s001

E. Zablackis, J. Huang, B. Mü-ller, A. Darvill, and P. Albersheim, Characterization of the Cell-Wall Polysaccharides of Arabidopsis thaliana Leaves, Plant Physiology, vol.107, issue.4, pp.1129-1138, 1995.
DOI : 10.1104/pp.107.4.1129

S. Prasad, A. Singh, and H. Joshi, Ethanol as an alternative fuel from agricultural, industrial and urban residues, Resources, Conservation and Recycling, vol.50, issue.1, pp.1-39, 2007.
DOI : 10.1016/j.resconrec.2006.05.007

P. Chow and S. Landhä-usser, A method for routine measurements of total sugar and starch content in woody plant tissues, Tree Physiology, vol.24, issue.10, pp.1129-1136, 2004.
DOI : 10.1093/treephys/24.10.1129

H. Scheller and P. Ulvskov, Hemicelluloses, Annual Review of Plant Biology, vol.61, issue.1, pp.263-289, 2010.
DOI : 10.1146/annurev-arplant-042809-112315

P. Dahal, D. Nevins, and K. Bradford, Relationship of Endo-[beta]-D-Mannanase Activity and Cell Wall Hydrolysis in Tomato Endosperm to Germination Rates, Plant Physiology, vol.113, issue.4, pp.1243-1252, 1997.
DOI : 10.1104/pp.113.4.1243

F. Pettolino, C. Walsh, G. Fincher, and A. Bacic, Determining the polysaccharide composition of plant cell walls, Nature Protocols, vol.55, issue.9, pp.1590-1607, 2012.
DOI : 10.1002/anie.197006101

O. Sørensen, S. , P. M. Bush, M. Skjøt, M. Mccann et al., Pectin engineering: Modification of potato pectin by in vivo expression of an endo-1,4-beta -D-galactanase, Proceedings of the National Academy of Sciences, vol.97, issue.13, pp.7639-7644, 2000.
DOI : 10.1073/pnas.130568297

J. Moore, E. Nguema-ona, C. L. Lindsey, G. Brandt, and W. , Response of the Leaf Cell Wall to Desiccation in the Resurrection Plant Myrothamnus flabellifolius, PLANT PHYSIOLOGY, vol.141, issue.2, pp.651-662, 2006.
DOI : 10.1104/pp.106.077701