J. L. Jansen, J. Nienhuis, and E. W. Triplett, Molecular microbial diversity of an agricultural soil in Wisconsin, Appl. Environ. Microbiol, vol.62, pp.1935-1943, 1996.

I. Brook, The role of anaerobic bacteria in bacteremia, Anaerobe, vol.16, issue.3, pp.183-189, 2010.
DOI : 10.1016/j.anaerobe.2009.12.001

D. H. Buckley and T. M. Schmidt, Diversity and dynamics of microbial communities in soils from agro-ecosystems, Environmental Microbiology, vol.10, issue.6, pp.441-452, 2003.
DOI : 10.1073/pnas.95.12.6578

B. L. Cantarel, P. M. Coutinho, C. Rancurel, T. Bernard, V. Lombard et al., The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic Acids Research, vol.37, issue.Database, pp.233-238, 2009.
DOI : 10.1093/nar/gkn663

N. C. Carpita and D. M. Gibeaut, Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth, The Plant Journal, vol.99, issue.1, pp.1-30, 1993.
DOI : 10.1016/S0008-6215(00)90807-3

E. J. Carroll and R. E. Hungate, The magnitude of the microbial fermentation in the bovine rumen, Appl. Microbiol, vol.2, pp.205-214, 1954.

O. Beja, L. Aravind, E. V. Koonin, M. T. Suzuki, A. Hadd et al., Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea, Science, vol.289, issue.5486, pp.1902-1906, 2000.
DOI : 10.1126/science.289.5486.1902

I. A. Beleneva and N. V. Zhukova, Bacterial communities of some brown and red algae from Peter the Great Bay, the Sea of Japan, Microbiology, vol.75, issue.3, pp.410-419, 2006.
DOI : 10.1134/S0026261706030180

Y. Benno, K. Suzuki, K. Narisawa, W. R. Bruce, and T. Mitsuoka, Comparison of the Fecal Microflora in Rural Japanese and Urban Canadians, Microbiology and Immunology, vol.20, issue.6, pp.521-532, 1986.
DOI : 10.1111/j.1348-0421.1986.tb02978.x

J. O. Berg, L. Lindqvist, and C. E. Nord, Purification of glycoside hydrolases from Bacteroides fragilis, 1980.

. Bergey-'s, Bergey's Manual of Systematic Bacteriology, 2011.

J. Bernardet and Y. Nakagawa, An Introduction to the Family Flavobacteriaceae, Prokaryotes, vol.7, pp.455-480, 2006.
DOI : 10.1007/0-387-30747-8_16

E. M. Bik, P. B. Eckburg, S. R. Gill, K. E. Nelson, E. A. Purdom et al., Molecular analysis of the bacterial microbiota in the human stomach, Proc. Natl. Acad. Sci. U.S.A. 103, pp.732-737, 2006.
DOI : 10.1073/pnas.0506655103

F. Azam and F. Malfatti, Microbial structuring of marine ecosystems, Nature Reviews Microbiology, vol.16, issue.10, pp.782-791, 2007.
DOI : 10.1038/nrmicro1747

F. Backhed, R. E. Ley, J. L. Sonnenburg, D. A. Peterson, G. et al., Host-Bacterial Mutualism in the Human Intestine, Science, vol.307, issue.5717, 1915.
DOI : 10.1126/science.1104816

E. S. Balakirev, V. A. Pavlyuchkov, and F. J. Ayala, DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius, Proceedings of the National Academy of Sciences, vol.105, issue.42, pp.16218-16223, 2008.
DOI : 10.1073/pnas.0807860105

. Zobellia-galactanovorans-gen, nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of, Int. J. Syst. Evol. Microbiol, vol.51, pp.985-997

T. Barbeyron, S. L-'haridon, G. Michel, and M. Czjzek, Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.58, issue.9, pp.2107-2113, 2008.
DOI : 10.1099/ijs.0.65674-0

URL : https://hal.archives-ouvertes.fr/hal-00562492

M. Bauer, M. Kube, H. Teeling, M. Richter, T. Lombardot et al., Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter, Environmental Microbiology, vol.18, issue.12, pp.2201-2213, 2006.
DOI : 10.1016/j.tim.2003.11.007

G. D. Abrams, Impact of the Intestinal Microflora on Intestinal Structure and Function, Human Intestinal Microflora in Health and Disease, pp.292-310, 1983.
DOI : 10.1016/B978-0-12-341280-5.50019-7

A. L. Alldredge, J. J. Cole, C. , and D. A. , Production of heterotrophic bacteria inhabiting macroscopic organic aggregates (marine snow) from surface waters1, Limnology and Oceanography, vol.31, issue.1, pp.68-78, 1986.
DOI : 10.4319/lo.1986.31.1.0068

R. I. Amann, W. Ludwig, and K. H. Schleifer, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev, vol.59, pp.143-169, 1995.

K. L. Anderson and A. A. Salyers, Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes., Journal of Bacteriology, vol.171, issue.6, pp.3192-3198, 1989.
DOI : 10.1128/jb.171.6.3192-3198.1989

K. L. Anderson and A. A. Salyers, Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron., Journal of Bacteriology, vol.171, issue.6, pp.3199-3204, 1989.
DOI : 10.1128/jb.171.6.3199-3204.1989

A. F. Andersson, M. Lindberg, H. Jakobsson, F. Backhed, P. Nyren et al., Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing, PLoS ONE, vol.11, issue.7, 2008.
DOI : 10.1371/journal.pone.0002836.s003

B. Austin, A. , and D. A. , Bacterial Fish Pathogens: Disease of Farmed and Wild Fish, 2007.

D. Greiner, M. , and D. , Selected characteristics of pathogenic and nonpathogenic strains of Bacteroides gingivalis, J. Clin. Microbiol, vol.25, pp.738-740, 1987.

C. Han, S. Spring, A. Lapidus, T. G. Del-rio, H. Tice et al., Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T), Standards in Genomic Sciences, vol.1, issue.1, pp.54-62, 2009.
DOI : 10.4056/sigs.22138

J. H. Hehemann, G. Correc, T. Barbeyron, W. Helbert, M. Czjzek et al., Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota, Nature, vol.5, issue.7290, pp.908-912, 2010.
DOI : 10.1038/nature08937

B. Henrissat, A classification of glycosyl hydrolases based on amino acid sequence similarities, Biochemical Journal, vol.280, issue.2, pp.309-316, 1991.
DOI : 10.1042/bj2800309

URL : https://hal.archives-ouvertes.fr/hal-00310263

M. A. Hildebrandt, C. Hoffmann, S. A. Sherrill-mix, S. A. Keilbaugh, M. Hamady et al., High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity, Gastroenterology, vol.137, issue.5, pp.1716-1724, 2009.
DOI : 10.1053/j.gastro.2009.08.042

Y. Hongoh, V. K. Sharma, T. Prakash, S. Noda1, H. Toh et al., Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis Within Protist Cells in Termite Gut, Science, vol.322, issue.5904, pp.1108-1109, 2008.
DOI : 10.1126/science.1165578

C. J. Hugo, P. J. Jooste, P. Segers, M. Vancanneyt, and K. Kersters, A Polyphasic Taxonomic Study of Chryseobacterium Strains Isolated from Dairy Sources, Systematic and Applied Microbiology, vol.22, issue.4, pp.586-595, 1999.
DOI : 10.1016/S0723-2020(99)80012-5

H. F. Jenkinson, L. , and R. J. , Oral microbial communities in sickness and in health, Trends in Microbiology, vol.13, issue.12, pp.589-595, 2005.
DOI : 10.1016/j.tim.2005.09.006

P. J. Jooste, H. , and C. J. , The taxonomy, ecology and cultivation of bacterial genera belonging to the family Flavobacteriaceae, International Journal of Food Microbiology, vol.53, issue.2-3, pp.81-94, 1999.
DOI : 10.1016/S0168-1605(99)00162-2

E. M. Julies, B. M. Fuchs, C. Arnosti, and V. Brüchert, Organic carbon degradation in anoxic Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces, Appl. Environ. Microbiol, vol.68, pp.2214-2228, 2010.

S. Fukuda, H. Saito, S. Nakaji, M. Yamada, N. Ebine et al., Pattern of dietary fiber intake among the Japanese general population, European Journal of Clinical Nutrition, vol.26, issue.1, pp.99-103, 2007.
DOI : 10.1038/sj.ejcn.1602505

F. C. Gibson, A. Genco, and C. , The Genus Porphyromonas, Prokaryotes, vol.7, pp.428-454, 2006.
DOI : 10.1007/0-387-30747-8_15

T. M. Gihring, M. Humphrys, H. J. Mills, M. Huettel, and J. E. Kostka, Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands, Limnology and Oceanography, vol.54, issue.4, pp.1073-1083, 2009.
DOI : 10.4319/lo.2009.54.4.1073

F. O. Glöckner, B. M. Fuchs, and R. Amann, Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization, Appl. Environ. Microbiol, vol.65, pp.3721-3726, 1999.

M. J. Goldberg, J. W. Smith, N. , and R. L. , Comparison of the Fecal Microflora of Seventh-Day Adventists with Individuals Consuming a General Diet, Annals of Surgery, vol.186, issue.1, pp.97-100, 1977.
DOI : 10.1097/00000658-197707000-00013

L. Gomez-consarnau, J. M. Gonzalez, M. Coll-llado, P. Gourdon, T. Pascher et al., Light stimulates growth of proteorhodopsin-containing marine Flavobacteria, Nature, vol.38, issue.7124, pp.210-213, 2007.
DOI : 10.1111/j.1462-2920.2004.00676.x

P. R. Gomez-pereira, B. M. Fuchs, C. Alonso, M. J. Oliver, J. E. Van-beusekom et al., Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean, The ISME Journal, vol.9, issue.4, pp.472-487, 2010.
DOI : 10.1038/ismej.2009.142

J. M. Gonzalez, B. Fernandez-gomez, A. Fernandez-guerra, L. Gomez-consarnau, O. Sanchez et al., Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp, MED152 (Flavobacteria). Proc. Natl. Acad. Sci. U.S.A. 105, pp.8724-8729, 2008.

A. J. Gooday, Biological responses to seasonally varying fluxes of organic matter to the ocean floor: a review, 2002.

L. E. Graham, M. E. Cook, and J. S. Busse, The origin of plants: Body plan changes contributing to a major evolutionary radiation, Proc. Natl. Acad, 2000.
DOI : 10.1073/pnas.97.9.4535

E. F. Delong, D. G. Franks, A. , and A. L. , Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages, Limnology and Oceanography, vol.38, issue.5, pp.924-934, 1993.
DOI : 10.4319/lo.1993.38.5.0924

R. Dubos, R. W. Schaedler, R. Costello, and P. Hoet, INDIGENOUS, NORMAL, AND AUTOCHTHONOUS FLORA OF THE GASTROINTESTINAL TRACT, Journal of Experimental Medicine, vol.122, issue.1, p.67, 1965.
DOI : 10.1084/jem.122.1.67

E. Duchaud, M. Boussaha, V. Loux, J. F. Bernardet, C. Michel et al., Complete genome sequence of the fish pathogen Flavobacterium psychrophilum, Nature Biotechnology, vol.34, issue.7, pp.763-769, 2007.
DOI : 10.1038/nbt1313

B. I. Duerden, Virulence Factors in Anaerobes, Clinical Infectious Diseases, vol.18, issue.Supplement 4, pp.253-259, 1994.
DOI : 10.1093/clinids/18.Supplement_4.S253

P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen et al., Diversity of the Human Intestinal Microbial Flora, Science, vol.308, issue.5728, pp.1635-1638, 2005.
DOI : 10.1126/science.1110591

J. L. Edwards, D. L. Smith, J. Connolly, J. E. Mcdonald, M. J. Cox et al., 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

L. B. Fandino, L. Riemann, G. F. Steward, R. A. Long, and F. Azam, Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing, Aquatic Microbial Ecology, vol.23, pp.119-130, 2001.
DOI : 10.3354/ame023119

R. P. Ferraris, Dietary and developmental regulation of intestinal sugar transport, Biochemical Journal, vol.360, issue.2, pp.265-276, 2001.
DOI : 10.1042/bj3600265

R. M. Figge, M. Schubert, H. Brinkmann, C. , and R. , Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer, Molecular Biology and Evolution, vol.16, issue.4, pp.429-440, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026125

H. M. Fletcher, H. A. Schenkein, R. M. Morgan, K. A. Bailey, C. R. Berry et al., Virulence of a Porphyromonas gingivalis W83 mutant defective in the prtH gene, Infect. Immun, vol.63, pp.1521-1528, 1995.

W. C. Chin, M. V. Orellana, and P. Verdugo, Spontaneous assembly of marine dissolved organic matter into polymer gels, Nature, vol.391, pp.568-572, 1998.

M. J. Church, Resource Control of Bacterial Dynamics in the Sea, Microbial Ecology of the Oceans, 2nd Edn, pp.335-382, 2008.
DOI : 10.1002/9780470281840.ch10

K. D. Clements and S. Bullivant, An unusual symbiont from the gut of surgeonfishes may be the largest known prokaryote., Journal of Bacteriology, vol.173, issue.17, pp.5359-5362, 1991.
DOI : 10.1128/jb.173.17.5359-5362.1991

M. T. Cottrell and D. L. Kirchman, Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization, Applied and Environmental Microbiology, vol.66, issue.12, pp.5116-5122, 2000.
DOI : 10.1128/AEM.66.12.5116-5122.2000

B. C. Crump, E. V. Armbrust, and J. A. Baross, Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean, Appl. Environ. Microbiol, vol.65, pp.3192-3204, 1999.

B. C. Crump and E. W. Koch, Attached Bacterial Populations Shared by Four Species of Aquatic Angiosperms, Applied and Environmental Microbiology, vol.74, issue.19, pp.5948-5957, 2008.
DOI : 10.1128/AEM.00952-08

G. J. Davies, T. M. Gloster, and B. Henrissat, Recent structural insights into the expanding world of carbohydrate-active enzymes, Current Opinion in Structural Biology, vol.15, issue.6, pp.637-645, 2005.
DOI : 10.1016/j.sbi.2005.10.008

H. S. Davis, A new bacterial disease of fresh-water fishes, Bulletin of the U.S. Bureau of Fisheries, pp.261-280, 1922.
DOI : 10.5962/bhl.title.49773

D. Filippo, C. Cavalieri, D. , D. Paola, M. Ramazzotti et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc. Natl, 2010.
DOI : 10.1073/pnas.1005963107

D. 'elia, J. N. Salyers, and A. A. , Effect of regulatory protein levels on utilization of starch by Bacteroides thetaiotaomicron., Journal of Bacteriology, vol.178, issue.24, pp.7180-7186, 1996.
DOI : 10.1128/jb.178.24.7180-7186.1996

D. Rio, T. G. Abt, B. Spring, S. Lapidus, A. Nolan et al., Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T), Stand. Genomic Sci, vol.2, pp.87-95, 2010.

E. F. Delong and O. Beja, The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times, PLoS Biol, 2010.

. Thomas, Linking environmental and gut Bacteroidetes Frontiers in Microbiology | Cellular and Infection Microbiology, p.12, 2011.

E. C. Martens, N. M. Koropatkin, T. J. Smith, G. , and J. I. , Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm, Journal of Biological Chemistry, vol.284, issue.37, pp.24673-24677, 2009.
DOI : 10.1074/jbc.R109.022848

I. Martinez, J. Kim, P. R. Duffy, V. L. Schlegel, and J. Walter, Resistant Starches Types 2 and 4 Have Differential Effects on the Composition of the Fecal Microbiota in Human Subjects, PLoS ONE, vol.97, issue.11, 2010.
DOI : 10.1371/journal.pone.0015046.s007

M. Martinez-alonso, J. Escolano, E. Montesinos, and N. Gaju, Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis, Int. Microbiol, vol.13, pp.123-134, 2010.

H. Matsui, Y. Kato, T. Chikaraishi, M. Moritani, T. Ban-tokuda et al., Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species, Anaerobe, vol.16, issue.2, pp.83-93, 2010.
DOI : 10.1016/j.anaerobe.2009.07.005

K. Mavrommatis, S. Gronow, E. Saunders, M. Land, A. Lapidus et al., Complete genome sequence of Capnocytophaga ochracea type strain, 2009.

S. K. Mazmanian, Capsular polysaccharides of symbiotic bacteria modulate immune responses during experimental colitis, J. Pediatr. Gastroenterol. Nutr, vol.46, pp.11-12, 2008.

S. K. Mazmanian, J. L. Round, and D. L. Kasper, A microbial symbiosis factor prevents intestinal inflammatory disease, Nature, vol.6, issue.7195, pp.620-625, 2008.
DOI : 10.1038/nature07008

M. J. Mcbride, G. Xie, E. C. Martens, A. Lapidus, B. Henrissat et al., Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis, Applied and Environmental Microbiology, vol.75, issue.21, pp.6864-6875, 2009.
DOI : 10.1128/AEM.01495-09

J. P. Mccutcheon, N. A. Moran, and K. , Functional convergence in reduced genomes of bacterial symbiand Moller Cultureindependent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited, Appl. Environ. Microbiol, vol.68, pp.673-690, 2002.

R. E. Ley, D. A. Peterson, G. , and J. I. , Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine, Cell, vol.124, issue.4, pp.837-848, 2006.
DOI : 10.1016/j.cell.2006.02.017

R. E. Ley, P. J. Turnbaugh, S. Klein, G. , and J. I. , Microbial ecology: Human gut microbes associated with obesity, Nature, vol.308, issue.7122, pp.1022-1023, 2006.
DOI : 10.1038/4441022a

C. H. Liao, W. , and J. M. , Properties of Cytophaga johnsonae strains causing spoilage of fresh produce at food markets, Appl. Environ. Microbiol, vol.52, pp.1261-1265, 1986.

E. Llobet-brossa, R. Rossello-mora, and R. Amann, Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization, Appl. Environ. Microbiol, vol.64, pp.2691-2696, 1998.

W. J. Loesche, Bacterial Mediators in Periodontal Disease, Clinical Infectious Diseases, vol.16, issue.Supplement 4, pp.203-210, 1993.
DOI : 10.1093/clinids/16.Supplement_4.S203

M. J. Lopez-sanchez, A. Neef, J. Peretó, R. Patiño-navarrete, M. Pignatelli et al., Evolutionary Convergence and Nitrogen Metabolism in Blattabacterium strain Bge, Primary Endosymbiont of the Cockroach Blattella germanica, PLoS Genetics, vol.15, issue.11, 2009.
DOI : 10.1371/journal.pgen.1000721.s005

C. A. Lozupone, M. Hamady, B. L. Cantarel, P. M. Coutinho, B. Henrissat et al., The convergence of carbohydrate active gene repertoires in human gut microbes, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.15076-15081, 2008.
DOI : 10.1073/pnas.0807339105

J. Lu, S. Domingo, J. W. Hill, S. Edge, and T. A. , Microbial Diversity and Host-Specific Sequences of Canada Goose Feces, Applied and Environmental Microbiology, vol.75, issue.18, pp.5919-5926, 2009.
DOI : 10.1128/AEM.00462-09

H. Mammeri, S. Bellais, and P. Nordmann, Chromosome-Encoded ??-Lactamases TUS-1 and MUS-1 from Myroides odoratus and Myroides odoratimimus (Formerly Flavobacterium odoratum), New Members of the Lineage of Molecular Subclass B1 Metalloenzymes, Antimicrobial Agents and Chemotherapy, vol.46, issue.11, pp.3561-3567, 2002.
DOI : 10.1128/AAC.46.11.3561-3567.2002

J. Manrique and H. H. Jensen, Spanish Household Demand for Seafood, Journal of Agricultural Economics, vol.21, issue.3, pp.23-37, 2001.
DOI : 10.1111/j.1477-9552.2001.tb00936.x

J. R. Marchesi, Prokaryotic and Eukaryotic Diversity of the Human Gut, Adv. Appl. Microbiol, vol.72, pp.43-62, 2010.
DOI : 10.1016/S0065-2164(10)72002-5

E. C. Martens, H. C. Chiang, G. , and J. I. , Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacteciated alpha-amylase from a prominent human gut symbiont targets complex starch molecules, Structure, vol.18, pp.200-215, 2008.

T. Kuwahara, A. Yamashita, H. Hirakawa, H. Nakayama, H. Toh et al., Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation, Proc. Natl, 2004.
DOI : 10.1073/pnas.0404172101

K. Lail, J. Sikorski, E. Saunders, A. Lapidus, T. G. Del-rio et al., Complete genome sequence of Spirosoma linguale type strain (1T), Standards in Genomic Sciences, vol.2, issue.2, 2010.
DOI : 10.4056/sigs.741334

R. A. Laine, to development of single-method saccharide sequencing or synthesis systems, Glycobiology, vol.4, issue.6, pp.759-767, 1994.
DOI : 10.1093/glycob/4.6.759

E. Lang, A. Lapidus, O. Chertkov, T. Brettin, J. C. Detter et al., Complete genome sequence of Dyadobacter fermentans type strain (NS114T), Standards in Genomic Sciences, vol.1, issue.2, pp.133-140, 2009.
DOI : 10.4056/sigs.19262

D. B. Largo, K. Fukami, and T. Nishijima, Occasional pathogenic bacteria promoting ice-ice disease in the carrageenan-producing red algae Kappaphycus alvarezii and Eucheuma denticulatum (Solieriaceae, Gigartinales, Rhodophyta), Journal of Applied Phycology, vol.55, issue.6, pp.545-554, 1995.
DOI : 10.1007/BF00003941

C. L. Lauber, M. Hamady, R. Knight, and N. Fierer, Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale, Applied and Environmental Microbiology, vol.75, issue.15, pp.5111-5120, 2009.
DOI : 10.1128/AEM.00335-09

E. R. Leadbetter, The Genus Capnocytophaga, Prokaryotes, vol.7, pp.709-711, 2006.
DOI : 10.1007/0-387-30747-8_28

M. Lee, S. G. Woo, J. Park, and S. A. Yoo, Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.60, issue.11, pp.2577-2582, 2010.
DOI : 10.1099/ijs.0.019653-0

J. Leng, L. Xie, R. Zhu, S. Yang, X. Gou et al., Dominant bacterial communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grunniens) and Yunnan Yellow Cattle (Bos taurs) revealed by denaturing gradient gel electrophoresis, Molecular Biology Reports, vol.229, issue.8, 2010.
DOI : 10.1007/s11033-010-0627-8

T. D. Leser, J. Z. Amenuvor, T. K. Jensen, R. H. Lindecrona, and M. Boye, organic-rich shelf sediments: biogeochemical rates and microbial abundance, Geomicrobiol. J, vol.27, pp.303-314

B. J. Keijser, E. Zaura, S. M. Huse, J. M. Van-der-vossen, F. H. Schuren et al., Pyrosequencing analysis of the Oral Microflora of healthy adults, Journal of Dental Research, vol.87, issue.11, 2008.
DOI : 10.1177/154405910808701104

. Flavobacterium-daejeonense-sp, nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea, Int. J. Syst. Evol. Microbiol, vol.56, pp.1645-1649

H. Kim, A. J. Miller, J. Mcgowan, and M. L. Carter, Coastal phytoplankton blooms in the Southern California Bight, Progress in Oceanography, vol.82, issue.2, pp.137-147, 2009.
DOI : 10.1016/j.pocean.2009.05.002

K. K. Kim, M. K. Kim, J. H. Lim, H. Y. Park, L. et al., Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov., INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.55, issue.3, pp.1287-1293, 2005.
DOI : 10.1099/ijs.0.63541-0

Y. S. Kim and J. A. Milner, Dietary modulation of colon cancer risk, J. Nutr, vol.137, pp.2576-2579, 2007.

E. O. King, Studies on a Group of Previously Unclassified Bacteria Associated with Meningitis in Infants, American Journal of Clinical Pathology, vol.31, issue.3, pp.241-247, 1959.
DOI : 10.1093/ajcp/31.3.241

D. L. Kirchman, The ecology of Cytophaga???Flavobacteria in aquatic environments, FEMS Microbiology Ecology, vol.39, issue.2, pp.91-100, 2002.
DOI : 10.1016/S0168-6496(01)00206-9

D. L. Kirchman, New light on an important microbe in the ocean, Proceedings of the National Academy of Sciences, vol.105, issue.25, pp.8487-8488, 2008.
DOI : 10.1073/pnas.0804196105

M. Kitamura, M. Okuyama, F. Tanzawa, H. Mori, Y. Kitago et al., Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron, Journal of Biological Chemistry, vol.283, issue.52, pp.36328-36337, 2008.
DOI : 10.1074/jbc.M806115200

B. A. Knapp, J. Seeber, A. Rief, E. Meyer, and H. Insam, Bacterial community composition of the gut microbiota of Cylindroiulus fulviceps (diplopoda) as revealed by molecular fingerprinting and cloning, Folia Microbiologica, vol.7, issue.5, pp.489-496, 2010.
DOI : 10.1007/s12223-010-0081-y

N. M. Koropatkin, E. C. Martens, J. I. Gordon, and T. J. Smith, Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices, Structure, vol.16, issue.7, pp.1105-1115, 2008.
DOI : 10.1016/j.str.2008.03.017

. Thomas, Linking environmental and gut Bacteroidetes www.frontiersin Article 93 | 13 protein-glycosaminoglycan interactions, Chem. Biol, vol.2, issue.12, pp.267-277, 2011.

J. Rath, K. Y. Wu, G. J. Herndl, and E. F. Delong, High phylogenetic diversity in a marine-snow-associated bacterial assemblage, Aquatic Microbial Ecology, vol.14, pp.261-269, 1998.
DOI : 10.3354/ame014261

H. Ratner, Topics in Clinical Microbiology Flavobacterium Meningosepticum, Infection Control, vol.1, issue.05, pp.237-239, 1984.
DOI : 10.1097/00007611-198106000-00034

E. Rebuffet, A. Groisillier, A. Thompson, A. Jeudy, T. Barbeyron et al., Discovery and structural characterization of a novel glycosidase family of marine origin, Environmental Microbiology, vol.67, issue.5, pp.1253-1270, 2011.
DOI : 10.1111/j.1462-2920.2011.02426.x

A. R. Reeves, G. R. Wang, and A. A. Salyers, Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron., Journal of Bacteriology, vol.179, issue.3, pp.643-649, 1997.
DOI : 10.1128/jb.179.3.643-649.1997

H. Reichenbach, The order cytophagales, Prokaryotes, vol.7, pp.549-590, 2006.

L. Riemann, G. F. Steward, and F. Azam, Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom, Applied and Environmental Microbiology, vol.66, issue.2, pp.578-587, 2000.
DOI : 10.1128/AEM.66.2.578-587.2000

S. P. Riepe, J. Goldstein, A. , and D. H. , Effect of Secreted Bacteroides Proteases on Human Intestinal Brush Border Hydrolases, Journal of Clinical Investigation, vol.66, issue.2, pp.314-322, 1980.
DOI : 10.1172/JCI109859

F. Rohwer, V. Seguritan, F. Azam, and N. Knowlton, Diversity and distribution of coral-associated bacteria, Marine Ecology Progress Series, vol.243, pp.1-10, 2002.
DOI : 10.3354/meps243001

G. A. Rook and L. R. Brunet, Microbes, immunoregulation, and the gut, Gut, vol.54, issue.3, pp.317-320, 2005.
DOI : 10.1136/gut.2004.053785

W. Rudek and R. U. Haque, Extracellular enzymes of the genus Bacteroides, J. Clin. Microbiol, vol.4, pp.458-460, 1976.

Z. L. Sabree, S. Kambhampati, and N. A. Moran, Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endosymbiont, Proceedings of the National Academy of Sciences, vol.106, issue.46, pp.19521-19526, 2009.
DOI : 10.1073/pnas.0907504106

S. Salaun, N. Kervarec, P. Potin, D. Haras, M. Piotto et al., Whole-cell spectroscopy is a convenient tool to assist molecular identification of cultivatable marine bacteria and to investigate their adaptive metabolism, Talanta, vol.80, issue.5, pp.1758-1770, 2010.
DOI : 10.1016/j.talanta.2009.10.020

A. A. Salyers, J. R. Vercellotti, S. E. West, and T. D. Wilkins, Fermentation of mucin and plant polysaccharides by strains of Bacteroides, 1977.

A. Pena, H. Teeling, J. Huerta-cepas, F. Santos, P. Yarza et al., Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains, The ISME Journal, vol.52, issue.7, pp.882-895, 2010.
DOI : 10.1111/j.1574-6976.2008.00144.x

J. Pinhassi, F. Azam, J. Hemphälä, R. A. Long, J. Martinez et al., Coupling between bacterioplankton species composition, population dynamics, and organic matter degradation, Aquatic Microbial Ecology, vol.17, 1999.
DOI : 10.3354/ame017013

T. Pommier, B. Canback, L. Riemann, K. H. Bostrom, K. Simu et al., Global patterns of diversity and community structure in marine bacterioplankton, Molecular Ecology, vol.49, issue.46, pp.867-880, 2007.
DOI : 10.1111/j.1365-294X.2006.03189.x

P. B. Pope, S. E. Denman, M. Jones, S. G. Tringe, K. Barry et al., Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores, Proc. Natl. Acad. Sci. U.S.A. 107, pp.14793-14798, 2010.
DOI : 10.1073/pnas.1005297107

Z. A. Popper, G. Michel, C. Hervé, S. C. Domozych, W. G. Willats et al., Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants, Annual Review of Plant Biology, vol.62, issue.1, pp.567-590, 2011.
DOI : 10.1146/annurev-arplant-042110-103809

URL : https://hal.archives-ouvertes.fr/hal-01117618

J. Purushe, D. E. Fouts, M. Morrison, B. A. White, R. I. Mackie et al., Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche, Microbial Ecology, vol.64, issue.2, pp.721-729, 2010.
DOI : 10.1007/s00248-010-9692-8

Q. L. Qin, X. Y. Zhang, X. M. Wang, G. M. Liu, X. L. Chen et al., The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation, BMC Genomics, vol.11, issue.1, pp.10-1186, 2010.
DOI : 10.1186/1471-2164-11-247

R. Raman, V. Sasisekharan, and R. Sasisekharan, Structural insights into biological roles of, 2005.

K. Neill, S. Heesch, N. , and W. , Diseases, Pathogens and Parasites of Undaria pinnatifida, 2008.

K. E. Nelson, R. D. Fleischmann, R. T. Deboy, I. T. Paulsen, D. E. Fouts et al., Complete genome sequence of the oral pathogenic Bacterium Porphyromonas gingivalis strain W83, 2003.

K. J. Niklas, The Cell Walls that Bind the Tree of Life, BioScience, vol.54, issue.9, pp.831-841, 2004.
DOI : 10.1641/0006-3568(2004)054[0831:TCWTBT]2.0.CO;2

K. Nisizawa, H. Noda, R. Kikuchi, and T. Watanabe, The main seaweed foods in Japan, Hydrobiologia, vol.151152, pp.5-29, 1987.

M. Nolan, B. J. Tindall, H. Pomrenke, A. Lapidus, A. Copeland et al., Complete genome sequence of Rhodothermus marinus type strain (R-10T), Standards in Genomic Sciences, vol.1, issue.3, pp.283-290, 2009.
DOI : 10.4056/sigs.46736

H. M. Oh, S. J. Giovannoni, K. Lee, S. Ferriera, J. Johnson et al., Complete Genome Sequence of Robiginitalea biformata HTCC2501, Journal of Bacteriology, vol.191, issue.22, pp.7144-7145, 2009.
DOI : 10.1128/JB.01191-09

H. M. Oh, I. Kang, S. Ferriera, S. J. Giovannoni, and J. C. Cho, Complete genome sequence of, 2010.

H. M. Oh, I. Kang, S. J. Yang, Y. Jang, K. L. Vergin et al., Complete Genome Sequence of Strain HTCC2170, a Novel Member of the Genus Maribacter in the Family Flavobacteriaceae, Journal of Bacteriology, vol.193, issue.1, pp.303-304, 2011.
DOI : 10.1128/JB.01207-10

T. A. Pankratov, I. S. Kulichevskaya, W. Liesack, and S. N. Dedysh, Isolation of aerobic, gliding, xylanolytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicola Kampfer et al. 2006, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.56, issue.12, pp.2761-2764, 2006.
DOI : 10.1099/ijs.0.64451-0

Z. Pei, E. J. Bini, L. Yang, M. Zhou, F. Francois et al., Bacterial biota in the human distal esophagus, Proceedings of the National Academy of Sciences, vol.101, issue.12, pp.4250-4255, 2004.
DOI : 10.1073/pnas.0306398101

G. Michel, T. Tonon, D. Scornet, J. M. Cock, and B. Kloareg, The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes, New Phytologist, vol.9, issue.1, pp.82-97, 2010.
DOI : 10.1111/j.1469-8137.2010.03374.x

G. Michel, T. Tonon, D. Scornet, J. M. Cock, and B. Kloareg, Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes, New Phytologist, vol.7, issue.1, pp.67-81, 2010.
DOI : 10.1111/j.1469-8137.2010.03345.x

I. S. Middelbos, B. M. Vester-boler, A. Qu, B. A. White, K. S. Swanson et al., Phylogenetic Characterization of Fecal Microbial Communities of Dogs Fed Diets with or without Supplemental Dietary Fiber Using 454 Pyrosequencing, PLoS ONE, vol.5, issue.3, 2010.
DOI : 10.1371/journal.pone.0009768.s004

E. F. Mongodin, K. E. Nelson, S. Daugherty, R. T. Deboy, J. Wister et al., The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea, Proc. Natl. Acad. Sci. U.S.A. 102, pp.18147-18152, 2005.
DOI : 10.1073/pnas.0509073102

W. E. Moore and L. V. Holdeman, Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies, Am, 1974.

T. Nagata, Organic matterbacteria interactions in seawater, Microbial Ecology in the Oceans, 2nd Edn, pp.207-242, 2008.

M. Naito, H. Hirakawa, A. Yamashita, N. Ohara, M. Shoji et al., Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis, DNA Research, vol.15, issue.4, pp.215-225, 2008.
DOI : 10.1093/dnares/dsn013

I. Nasidze, J. Li, D. Quinque, K. Tang, and M. Stoneking, Global diversity in the human salivary microbiome, Genome Research, vol.19, issue.4, pp.636-643, 2009.
DOI : 10.1101/gr.084616.108

I. Nasidze, D. Quinque, J. Li, M. Li, K. Tang et al., Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches, Analytical Biochemistry, vol.391, issue.1, pp.64-68, 2009.
DOI : 10.1016/j.ab.2009.04.034

. Thomas, Linking environmental and gut Bacteroidetes Frontiers in Microbiology | Cellular and Infection Microbiology, 2011.

. Ornithobacterium-rhinotracheale-gen, nov., sp. nov. isolated from the avian respiratory tract, Int. J. Syst. Bacteriol, vol.44, pp.24-37

P. Vandamme, M. Vancanneyt, P. Segers, M. Ryll, B. Köhler et al., Coenonia anatina gen. nov., sp. nov., a novel bacterium associated with respiratory disease in ducks and geese, International Journal of Systematic Bacteriology, vol.49, issue.2, pp.867-874, 1999.
DOI : 10.1099/00207713-49-2-867

L. Wen, R. E. Ley, P. Y. Volchkov, P. B. Stranges, L. Avanesyan et al., Innate immunity and intestinal microbiota in the development of Type 1 diabetes, Nature, vol.7, issue.7216, pp.1109-1113, 2008.
DOI : 10.1038/nature07336

H. M. Wexler, Bacteroides: the Good, the Bad, and the Nitty-Gritty, Clinical Microbiology Reviews, vol.20, issue.4, 2007.
DOI : 10.1128/CMR.00008-07

W. B. Whitman, D. C. Coleman, and W. J. Wiebe, Prokaryotes: The unseen majority, Proceedings of the National Academy of Sciences, vol.95, issue.12, pp.6578-6583, 1998.
DOI : 10.1073/pnas.95.12.6578

C. R. Woese, Bacterial evolution, Microbiol. Rev, vol.51, pp.221-271, 1987.

C. R. Woese, D. Yang, L. Mandelco, and K. O. Stetter, The Flexibacter-Flavobacter Connection, Systematic and Applied Microbiology, vol.13, issue.2, pp.161-165, 1990.
DOI : 10.1016/S0723-2020(11)80163-3

B. S. Wostmann, C. Larkin, A. Moriarty, and E. Bruckner-kardoss, Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats, Lab. Anim. Sci, vol.33, pp.46-50, 1983.

T. Woyke, G. Xie, A. Copeland, J. M. Gonzalez, C. Han et al., Assembling the Marine Metagenome, One Cell at a Time, PLoS ONE, vol.5, issue.4, 2009.
DOI : 10.1371/journal.pone.0005299.s014

J. Xu, M. A. Mahowald, R. E. Ley, C. A. Lozupone, M. Hamady et al., Isolation of a bacterium that causes anaaki disease of the red algae Porphyra yezoensis, J, 1995.

L. Suomalainen, M. Tiirola, and E. T. Valtonen, Chondroitin AC lyase activity is related to virulence of fish pathogenic Flavobacterium columnare, Journal of Fish Diseases, vol.17, issue.12, pp.701-770, 2006.
DOI : 10.1007/s00203-005-0009-0

K. Tajima, R. I. Aminov, T. Nagamine, K. Ogata, M. Nakamura et al., Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries, FEMS Microbiology Ecology, vol.29, issue.2, pp.159-169, 1999.
DOI : 10.1111/j.1574-6941.1999.tb00607.x

A. C. Tanner, M. A. Listgarten, J. L. Ebersole, and M. N. Strzempko, Bacteroides forsythus sp. nov., a Slow-Growing, Fusiform Bacteroides sp. from the Human Oral Cavity, International Journal of Systematic Bacteriology, vol.36, issue.2, pp.213-221, 1986.
DOI : 10.1099/00207713-36-2-213

C. M. Thomas and K. M. Nielsen, Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria, Nature Reviews Microbiology, vol.84, issue.9, pp.711-721, 2005.
DOI : 10.1016/S0168-6445(98)00009-6

P. J. Turnbaugh, B. Henrissat, G. , and J. I. , Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes, Acta Crystallographica Section F Structural Biology and Crystallization Communications, vol.66, issue.10, pp.1261-1264, 2010.
DOI : 10.1107/S1744309110029088

P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-liggett, R. Knight et al., The Human Microbiome Project, Nature, vol.112, issue.7164, pp.804-810, 2007.
DOI : 10.1038/nature06244

P. J. Turnbaugh, V. K. Ridaura, J. J. Faith, F. E. Rey, R. Knight et al., The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice, Science Translational Medicine, vol.1, issue.6, pp.6-14, 2009.
DOI : 10.1126/scitranslmed.3000322

F. R. Uyenco, E. J. Zwart, G. Van-agterveld, M. P. Gons, H. J. Ebert et al., Microbiological studies of diseased Eucheuma sp. and other seaweeds Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses, National Seaweeds Symposium, Manilla, Philippines. van Hannen, pp.795-801, 1977.

P. Vandamme, P. Segers, M. Vancanneyt, K. Van-hove, R. Mutters et al., populations at a shallow submarine hydrothermal vent near Milos Island (Greece), Appl. Environ. Microbiol, vol.66, pp.3102-3109

S. Silvi, C. J. Rumney, A. Cresci, R. , and I. R. , Resistant starch modifies gut microflora and microbial metabolism in human flora-associated rats inoculated with faeces from Italian and UK donors, Journal of Applied Microbiology, vol.12, issue.3, pp.521-530, 1999.
DOI : 10.1016/0300-483X(85)90058-7

K. Simek, J. Armengol, M. Comerma, J. C. Garcia, P. Kojecka et al., Changes in the epilimnetic bacterial community composition, production, and protistinduced mortality along the longitudinal axis of a highly eutrophic reservoir, Microb. Ecol, vol.42, pp.359-371, 2001.

M. Simon, F. O. Glockner, and R. Amann, Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean, Aquatic Microbial Ecology, vol.18, pp.275-284, 1999.
DOI : 10.3354/ame018275

C. J. Smith and M. P. Bryant, Introduction to metabolic activities of intestinal bacteria, Am. J. Clin. Nutr, vol.32, pp.149-157, 1979.

C. J. Smith, E. R. Rocha, and B. J. Paster, The medically important Bacteroides spp, pp.381-427, 2006.

. Kordia-algicida-gen, nov., sp. nov., an algicidal bacterium isolated from red tide, Int. J. Syst. Evol. Microbiol, vol.54, pp.675-680

E. D. Sonnenburg, H. Zheng, P. Joglekar, S. K. Higginbottom, S. J. Firbank et al., Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations, Cell, vol.141, issue.7, pp.1241-1252, 2010.
DOI : 10.1016/j.cell.2010.05.005

J. L. Sonnenburg, Microbiology: Genetic pot luck, Nature, vol.27, issue.7290, pp.837-838, 2010.
DOI : 10.1038/464837a

E. A. Stahl and J. G. Bishop, Plant???pathogen arms races at the molecular level, Current Opinion in Plant Biology, vol.3, issue.4, pp.299-304, 2000.
DOI : 10.1016/S1369-5266(00)00083-2

T. Staufenberger, V. Thiel, J. Wiese, and J. F. Imhoff, Phylogenetic analysis of bacteria associated with Laminaria saccharina, FEMS Microbiology Ecology, vol.64, issue.1, pp.65-77, 2008.
DOI : 10.1111/j.1574-6941.2008.00445.x

K. Sugahara and H. Kitagawa, Heparin and Heparan Sulfate Biosynthesis, IUBMB Life (International Union of Biochemistry and Molecular Biology: Life), vol.54, issue.4, pp.163-175, 2002.
DOI : 10.1080/15216540214928

D. C. Savage, R. Dubos, and R. W. Schaedler, THE GASTROINTESTINAL EPITHELIUM AND ITS AUTOCHTHONOUS BACTERIAL FLORA, Journal of Experimental Medicine, vol.127, issue.1, pp.67-76, 1968.
DOI : 10.1084/jem.127.1.67

D. Schmitt-wagner, M. W. Friedrich, B. Wagner, and A. Brune, Phylogenetic Diversity, Abundance, and Axial Distribution of Bacteria in the Intestinal Tract of Two Soil-Feeding Termites (Cubitermes spp.), Applied and Environmental Microbiology, vol.69, issue.10, pp.6007-6017, 2003.
DOI : 10.1128/AEM.69.10.6007-6017.2003

S. Schmitz-esser, P. Tischler, R. Arnold, J. Montanaro, M. Wagner et al., The Genome of the Amoeba Symbiont "Candidatus Amoebophilus asiaticus" Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria, Journal of Bacteriology, vol.192, issue.4, pp.1045-1057, 2010.
DOI : 10.1128/JB.01379-09

A. J. Scupham, T. G. Patton, E. Bent, and D. O. Bayles, Comparison of the Cecal Microbiota of Domestic and Wild Turkeys, Microbial Ecology, vol.57, issue.Suppl 2, pp.322-331, 2008.
DOI : 10.1007/s00248-007-9349-4

P. Segers, W. Mannheim, M. Vancanneyt, K. De-brandt, K. H. Hinz et al., Riemerella anatipestifer gen. nov., comb. nov., the Causative Agent of Septicemia Anserum Exsudativa, and Its Phylogenetic Affiliation within the Flavobacterium-Cytophaga rRNA Homology Group, International Journal of Systematic Bacteriology, vol.43, issue.4, pp.768-776, 1993.
DOI : 10.1099/00207713-43-4-768

A. Sghir, G. Gramet, A. Suau, V. Rochet, P. Pochart et al., Quantification of Bacterial Groups within Human Fecal Flora by Oligonucleotide Probe Hybridization, Applied and Environmental Microbiology, vol.66, issue.5, pp.2263-2266, 2000.
DOI : 10.1128/AEM.66.5.2263-2266.2000

H. N. Shah, C. , and D. M. , NOTES: Prevotella, a New Genus To Include Bacteroides melaninogenicus and Related Species Formerly Classified in the Genus Bacteroides, International Journal of Systematic Bacteriology, vol.40, issue.2, pp.205-208, 1990.
DOI : 10.1099/00207713-40-2-205

J. A. Shipman, J. E. Berleman, and A. A. Salyers, Characterization of Four Outer Membrane Proteins Involved in Binding Starch to the Cell Surface of Bacteroides thetaiotaomicron, Journal of Bacteriology, vol.182, issue.19, pp.5365-5372, 2000.
DOI : 10.1128/JB.182.19.5365-5372.2000

J. A. Shipman, K. H. Cho, H. A. Siegel, and A. A. Salyers, Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron, J. Bacteriol, vol.181, pp.7206-7211, 1999.

N. B. Shoemaker, H. Vlamakis, K. Hayes, and A. A. Salyers, Evidence for Extensive Resistance Gene Transfer among Bacteroides spp. and among Bacteroides and Other Genera in the Human Colon, Applied and Environmental Microbiology, vol.67, issue.2, pp.561-568, 2001.
DOI : 10.1128/AEM.67.2.561-568.2001

S. M. Sievert, J. Kuever, and G. Muyzer, Identification of 16S ribosomal DNA-defined bacterial, 2000.

. Thomas, Article 93 | 15 Environmental and gut Bacteroidetes: the food connection. Front. Microbio. 2:93. doi: 10.3389/fmicb.2011.00093 This article was submitted to Frontiers in Cellular and Infection Microbiology, a specialty of Frontiers in Microbiology and Michel. This is an openaccess article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with, 2011.

Y. Zhu, M. D. Suits, A. J. Thompson, S. Chavan, Z. Dinev et al., Mechanistic insights into a Ca2+-dependent family of ??-mannosidases in a human gut symbiont, Nature Chemical Biology, vol.60, issue.2, pp.125-132, 2010.
DOI : 10.1038/nchembio.278

G. Zwart, B. C. Crump, M. P. Kamst-van-agterveld, F. Hagen, S. K. Han et al., Typical freshwater bacteria: an analysis of available 16S Evolution of symbiotic bacteria in the distal human intestine, PLoS Biol, 2002.

J. P. Zhou, Y. Huang, and M. Mo, Phylogenetic analysis on the soil bacteria distributed in karst forest, Brazilian Journal of Microbiology, vol.40, issue.4, 2009.
DOI : 10.1590/S1517-83822009000400013

X. Y. Zhu, T. Zhong, Y. Pandya, and R. D. Joerger, 16S rRNA-based analysis of microbiota from the cecum Thomas et al. Linking environmental and gut Bacteroidetes, 2002.