Biofuels from microbes, Applied Microbiology and Biotechnology, vol.71, issue.1, pp.23-35, 2007. ,
DOI : 10.1007/s00253-007-1163-x
New generation biomass processing: Consolidated bioprocessing Biomass Recalcitrance: Deconstructing the Plant Cell Wall for Bioenergy, pp.480-494, 2008. ,
Consolidated bioprocessing of cellulosic biomass: an update, Current Opinion in Biotechnology, vol.16, issue.5, pp.577-583, 2005. ,
DOI : 10.1016/j.copbio.2005.08.009
Butanol fermentation research: upstream and downstream manipulations, The Chemical Record, vol.17, issue.5, pp.305-314, 2004. ,
DOI : 10.1002/tcr.20023
Cellulase, Clostridia, and Ethanol, Microbiology and Molecular Biology Reviews, vol.69, issue.1, pp.124-154, 2005. ,
DOI : 10.1128/MMBR.69.1.124-154.2005
: model organism of mesophilic cellulolytic clostridia, FEMS Microbiology Reviews, vol.29, issue.4, pp.741-764, 2005. ,
DOI : 10.1016/j.femsre.2004.11.003
Unravelling Carbon Metabolism in Anaerobic Cellulolytic Bacteria, Biotechnology Progress, vol.54, issue.Pt 1, pp.1229-1238, 2006. ,
DOI : 10.1002/bp060016e
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
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
Heterologous Production, Assembly, and Secretion of a Minicellulosome by Clostridium acetobutylicum ATCC 824, Applied and Environmental Microbiology, vol.71, issue.3, pp.1215-1222, 2005. ,
DOI : 10.1128/AEM.71.3.1215-1222.2005
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
Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences, Applied and Environmental Microbiology, vol.75, issue.24, pp.7718-7724, 2009. ,
DOI : 10.1128/AEM.01959-09
Consolidated bioprocessing (CBP) of AFEX???-pretreated corn stover for ethanol production using Clostridium phytofermentans at a high solids loading, Biotechnology and Bioengineering, vol.102, issue.20, pp.1929-1936, 2012. ,
DOI : 10.1002/bit.24458
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
Proteome-wide systems analysis of a cellulosic biofuel-producing microbe, Molecular Systems Biology, vol.170, issue.1, p.21245846, 2011. ,
DOI : 10.1186/1471-2105-9-173
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
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
Engineering of Clostridium phytofermentans Endoglucanase Cel5A for Improved Thermostability, Applied and Environmental Microbiology, vol.76, issue.14, pp.4914-4917, 2010. ,
DOI : 10.1128/AEM.00958-10
Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality, Biotechnology for Biofuels, vol.5, issue.1, p.22316115, 2012. ,
DOI : 10.1016/j.ab.2004.12.001
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
3-O-??-d-Glucopyranosyl-l-rhamnose phosphorylase from Clostridium phytofermentans, Carbohydrate Research, vol.350, pp.94-97, 2012. ,
DOI : 10.1016/j.carres.2011.12.019
Functional Expression of a Bacterial Xylose Isomerase in Saccharomyces cerevisiae, Applied and Environmental Microbiology, vol.75, issue.8, pp.2304-2311, 2009. ,
DOI : 10.1128/AEM.02522-08
Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering, Biotechnology for Biofuels, vol.6, issue.1, pp.89-99, 2013. ,
DOI : 10.1186/1754-6834-2-8
Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture, Biotechnology for Biofuels, vol.6, issue.1, p.23628342, 2013. ,
DOI : 10.1186/1754-6834-6-59
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, issue.5223, pp.496-512, 1995. ,
DOI : 10.1126/science.7542800
II. Error Probabilities, Genome Research, vol.8, issue.3, pp.186-194, 1998. ,
DOI : 10.1101/gr.8.3.186
Assembling Genomic DNA Sequences with PHRAP, Curr Protoc Bioinforma, vol.147, 2007. ,
DOI : 10.1002/0471250953.bi1104s17
A Graphical Tool for Sequence???Finishing, Genome Research, vol.8, issue.3, pp.195-202, 1998. ,
DOI : 10.1101/gr.8.3.195
CRITICA: coding region identification tool invoking comparative analysis, Molecular Biology and Evolution, vol.16, issue.4, pp.512-524, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026133
URL : http://mbe.oxfordjournals.org/cgi/content/short/16/4/512
Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics, vol.23, issue.6, pp.673-679, 2007. ,
DOI : 10.1093/bioinformatics/btm009
KEGG for integration and interpretation of largescale molecular data sets, Nucleic Acids Res, vol.40, p.22080510, 2012. ,
KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Research, vol.38, issue.Database, pp.355-360, 2010. ,
DOI : 10.1093/nar/gkp896
KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000. ,
DOI : 10.1093/nar/28.1.27
InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Research, vol.40, issue.D1, pp.306-312, 2012. ,
DOI : 10.1093/nar/gkr948
URL : https://hal.archives-ouvertes.fr/hal-00697960
The Pfam Protein Families Database, Nucleic Acids Research, vol.30, issue.1, pp.276-280, 2002. ,
DOI : 10.1093/nar/30.1.276
URL : https://hal.archives-ouvertes.fr/hal-01294685
TIGRFAMs: a protein family resource for the functional identification of proteins, Nucleic Acids Research, vol.29, issue.1, pp.41-43, 2001. ,
DOI : 10.1093/nar/29.1.41
SMART: identification and annotation of domains from signalling and extracellular protein sequences, Nucleic Acids Research, vol.27, issue.1, pp.229-232, 1999. ,
DOI : 10.1093/nar/27.1.229
PROSITE, a protein domain database for functional characterization and annotation, Nucleic Acids Research, vol.38, issue.Database, pp.161-166, 2010. ,
DOI : 10.1093/nar/gkp885
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012, Database, vol.2012, issue.0, p.19, 2012. ,
DOI : 10.1093/database/bas019
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons, Nucleic Acids Research, vol.28, issue.1, pp.267-269, 2000. ,
DOI : 10.1093/nar/28.1.267
URL : https://hal.archives-ouvertes.fr/hal-00427044
The Clusters of Orthologous Groups (COGs) Database: Phylogenetic classification of proteins from complete genomes, 2002. ,
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels, Nucleic Acids Research, vol.35, issue.Database, pp.274-279, 2007. ,
DOI : 10.1093/nar/gkl925
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, vol.25, issue.24, pp.4876-4882, 1997. ,
DOI : 10.1093/nar/25.24.4876
PHYLIP?Phylogeny Inference Package (Version 3.2), Cladistics, vol.5, pp.164-166, 1989. ,
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses, Nucleic Acids Research, vol.33, issue.Web Server, pp.451-454, 2005. ,
DOI : 10.1093/nar/gki487
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-9021275, 1996. ,
DOI : 10.1093/bioinformatics/12.6.543
URL : https://hal.archives-ouvertes.fr/hal-00435028
Chapter IV A Roll Tube Method for Cultivation of Strict Anaerobes, Methods Microbiol, vol.3, p.117, 1969. ,
DOI : 10.1016/S0580-9517(08)70503-8
Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, vol.4, issue.2, pp.249-264, 2003. ,
DOI : 10.1093/biostatistics/4.2.249
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla, Proceedings of the National Academy of Sciences, vol.106, issue.14, pp.5859-5864, 2009. ,
DOI : 10.1073/pnas.0901529106
Regulation of endospore formation in Bacillus subtilis, Nature Reviews Microbiology, vol.178, issue.2, pp.117-126, 2003. ,
DOI : 10.1046/j.1365-2958.2000.01731.x
Compartmentalization of Gene Expression during Bacillus subtilis Spore Formation, Microbiology and Molecular Biology Reviews, vol.68, issue.2, pp.234-262, 2004. ,
DOI : 10.1128/MMBR.68.2.234-262.2004
Where asymmetry in gene expression originates, Molecular Microbiology, vol.25, issue.3, pp.611-620, 2005. ,
DOI : 10.1111/j.1365-2958.2005.04687.x
Bacterial Microcompartments, Annual Review of Microbiology, vol.64, issue.1, pp.391-408, 2010. ,
DOI : 10.1146/annurev.micro.112408.134211
Involvement of a Bacterial Microcompartment in the Metabolism of Fucose and Rhamnose by Clostridium phytofermentans, PLoS ONE, vol.53, issue.1, p.23382892, 2013. ,
DOI : 10.1371/journal.pone.0054337.s001
Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis, Nature Reviews Microbiology, vol.307, issue.2, pp.121-131, 2008. ,
DOI : 10.1038/nrmicro1817
A Multitask ATPase Serving Different ABC-Type Sugar Importers in Bacillus subtilis, Journal of Bacteriology, vol.192, issue.20, pp.5312-5318, 2010. ,
DOI : 10.1128/JB.00832-10
Arac/XylS family of transcriptional regulators, Microbiol Mol Biol Rev, vol.61, pp.393-410, 1997. ,
A family of bacterial regulators homologous to Gal and Lac repressors, J Biol Chem, vol.267, pp.15869-15874, 1992. ,
NADP+ Reduction with Reduced Ferredoxin and NADP+ Reduction with NADH Are Coupled via an Electron-Bifurcating Enzyme Complex in Clostridium kluyveri, Journal of Bacteriology, vol.192, issue.19, pp.5115-5123, 2010. ,
DOI : 10.1128/JB.00612-10
Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase, Proceedings of the National Academy of Sciences, vol.107, issue.42, pp.18138-18142, 2010. ,
DOI : 10.1073/pnas.1010318107
Energy conservation in chemotrophic anaerobic bacteria, Bacteriol . Rev, vol.41, pp.100-180, 1977. ,
Hydrogenase, Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, vol.594, issue.2-3, pp.105-176, 1980. ,
DOI : 10.1016/0304-4173(80)90007-5
Characterization of the cellulolytic and hydrogen-producing activities of six mesophilic Clostridium species, Journal of Applied Microbiology, vol.180, issue.Pt. 8, pp.2258-2266, 2007. ,
DOI : 10.1111/j.1365-2672.2007.03477.x
The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations, International Journal of Systematic Bacteriology, vol.44, issue.4, pp.812-826, 1994. ,
DOI : 10.1099/00207713-44-4-812