J. F. Cryan and T. G. Dinan, Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour, Nature Reviews Neuroscience, vol.109, issue.10, pp.701-712, 2012.
DOI : 10.1038/nrn3346

I. Hanski, Environmental biodiversity, human microbiota, and allergy are interrelated, Proc. Natl. Acad. Sci, pp.8334-8339, 2012.
DOI : 10.1128/AEM.00062-07
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361383

A. L. Kau, Human nutrition, the gut microbiome and the immune system, Nature, vol.455, issue.7351, pp.327-336, 2011.
DOI : 10.1038/nature10213
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298082

R. Joice, Determining Microbial Products and Identifying Molecular Targets in the Human Microbiome, Cell Metabolism, vol.20, issue.5, pp.731-741, 2014.
DOI : 10.1016/j.cmet.2014.10.003

O. Manor, Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome, Cell Metabolism, vol.20, issue.5, pp.742-752, 2014.
DOI : 10.1016/j.cmet.2014.07.021

T. J. Sharpton, An introduction to the analysis of shotgun metagenomic data, Frontiers in Plant Science, vol.38, issue.e132, p.7, 2014.
DOI : 10.1093/nar/gkq275

M. S. Rappé and S. J. Giovannoni, The Uncultured Microbial Majority, Annual Review of Microbiology, vol.57, issue.1, pp.369-394, 2003.
DOI : 10.1146/annurev.micro.57.030502.090759

E. A. Franzosa, Sequencing and beyond: integrating molecular 'omics' for microbial community profiling, Nature Reviews Microbiology, vol.7, issue.6, pp.360-372, 2015.
DOI : 10.1038/nrmicro3451
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4800835

M. S. Rappé, Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina, Limnology and Oceanography, vol.42, issue.5, pp.811-826, 1997.
DOI : 10.4319/lo.1997.42.5.0811

N. A. Hasan, Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing. PLoS ONE 9, e97699 11 Mangrola, A. et al. Deciphering the microbiota of Tuwa hot spring, India using shotgun metagenomic sequencing approach, Genomics Data, 2014.

J. C. Venter, Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science, vol.304, issue.5667, pp.66-74, 2004.
DOI : 10.1126/science.1093857

J. T. Simpson and M. J. Pop, The Theory and Practice of Genome Sequence Assembly Real-time DNA sequencing from single polymerase molecules, Annu. Rev. Genomics Hum. Genet. Science, vol.16, issue.323, pp.133-138, 2009.

E. B. Fichot and R. S. Norman, Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform, Microbiome, vol.1, issue.1, 2013.
DOI : 10.1186/gb-2011-12-2-r18
URL : http://doi.org/10.1186/2049-2618-1-10

L. J. Steinbock and A. Radenovic, The emergence of nanopores in next-generation sequencing, Nanotechnology, vol.26, issue.7, p.74003, 2015.
DOI : 10.1088/0957-4484/26/7/074003

C. Rinke, Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.45, issue.7459, pp.431-437, 2013.
DOI : 10.1093/bib/bbs031

D. R. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801

Y. Peng, IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, vol.28, issue.11, pp.1420-1428, 2012.
DOI : 10.1093/bioinformatics/bts174

. Afiahayati, MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning, DNA Research, vol.22, issue.1, pp.69-77, 2015.
DOI : 10.1093/dnares/dsu041

I. Saeed, Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition, Nucleic Acids Research, vol.40, issue.5, p.34, 2012.
DOI : 10.1093/nar/gkr1204

R. Carr, Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution, PLoS Computational Biology, vol.40, issue.10, p.1003292, 2013.
DOI : 10.1371/journal.pcbi.1003292.s018

L. A. Hug, Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling, Microbiome, vol.1, issue.1, p.22, 2013.
DOI : 10.1128/AEM.06510-11

M. Albertsen, Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes, Nature Biotechnology, vol.5, issue.6, pp.533-538, 2013.
DOI : 10.1093/nar/gkr201

J. Flot, Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures, FEBS Letters, vol.111, issue.20PartA, 2015.
DOI : 10.1016/j.febslet.2015.04.034
URL : https://hal.archives-ouvertes.fr/pasteur-01419996

J. Dekker, Capturing Chromosome Conformation, Science, vol.295, issue.5558, pp.1306-1311, 2002.
DOI : 10.1126/science.1067799

J. Dekker, Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Nature Reviews Genetics, vol.8, issue.6, pp.390-403, 2013.
DOI : 10.1186/gb-2012-13-8-418

E. Lieberman-aiden, Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome, Science, vol.27, issue.2, pp.289-293, 2009.
DOI : 10.1038/nbt.1523

J. N. Burton, Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nature Biotechnology, vol.39, issue.12, pp.1119-1125, 2013.
DOI : 10.1006/jmbi.1990.9999

N. Kaplan and J. Dekker, High-throughput genome scaffolding from in vivo DNA interaction frequency, Nature Biotechnology, vol.12, issue.12, p.31, 2013.
DOI : 10.1090/S0025-5718-1980-0572855-7
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880131

H. Marie-nelly, High-quality genome (re)assembly using chromosomal contact data Strain-and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products, Nat. Commun. PeerJ, vol.5, issue.2, p.415, 2014.

J. N. Burton, Species-Level Deconvolution of Metagenome Assemblies with Hi-C???Based Contact Probability Maps, G3: Genes|Genomes|Genetics, vol.4, issue.7, pp.1339-1346, 2014.
DOI : 10.1534/g3.114.011825

M. Marbouty, Author response, eLife, vol.18, p.3318, 2014.
DOI : 10.7554/eLife.03318.030

E. Pelletier, "Candidatus Cloacamonas Acidaminovorans": Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division, Journal of Bacteriology, vol.190, issue.7, pp.2572-2579, 2008.
DOI : 10.1128/JB.01248-07

L. Weng, Two Applications of Clustering Techniques to Twitter: Community Detection and Issue Extraction. Discrete Dyn Complex brain networks: graph theoretical analysis of structural and functional systems, Virality Prediction and Community Structure in Social Networks. Sci. Rep. Nat. Soc. Nat. Rev. Neurosci, vol.3, issue.10, pp.186-198, 2009.

V. D. Blondel, Fast unfolding of communities in large networks A Generalized and Adaptive Method for Community Detection. ArXiv14062518 Phys Using MCL to extract clusters from networks, J. Stat. Mech. Theory Exp Methods Mol. Biol. Clifton NJ, vol.804, pp.281-295, 2008.

A. Lancichinetti, S. Fortunato, and W. Liu, Community detection algorithms: a comparative analysis Detecting Communities Based on Overlapping community detection in networks with positive and negative links, ) Uncovering the overlapping community structure of complex networks in nature and society, pp.814-818, 2005.

W. Wang, Fuzzy overlapping community detection based on local random walk and multidimensional scaling, Physica A: Statistical Mechanics and its Applications, vol.392, issue.24, pp.6578-6586, 2013.
DOI : 10.1016/j.physa.2013.08.028

A. Cournac, Normalization of a chromosomal contact map, BMC Genomics, vol.13, issue.1, p.436, 2012.
DOI : 10.1186/gb-2009-10-3-r25
URL : https://hal.archives-ouvertes.fr/pasteur-00769663

E. Yaffe and A. Tanay, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nature Genetics, vol.464, issue.11, pp.1059-1065, 2011.
DOI : 10.1038/nature06008

W. Ma, Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes, Nature Methods, vol.503, issue.1, pp.71-78, 2015.
DOI : 10.1038/nbt.1621

R. A. Edwards and F. Rohwer, Opinion: Viral metagenomics, Nature Reviews Microbiology, vol.51, issue.6, pp.504-510, 2005.
DOI : 10.1073/pnas.93.12.5854

M. Muniesa, Potential impact of environmental bacteriophages in spreading antibiotic resistance genes, Future Microbiology, vol.8, issue.6, pp.739-751, 2013.
DOI : 10.2217/fmb.13.32

A. Stern, CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome, Genome Research, vol.22, issue.10, 1985.
DOI : 10.1101/gr.138297.112

L. A. Ogilvie, Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences, Nature Communications, vol.47, p.2420, 2013.
DOI : 10.1016/S0166-0934(00)00182-8

R. V. Thurber, Laboratory procedures to generate viral metagenomes, Nature Protocols, vol.7, issue.4, pp.470-483, 2009.
DOI : 10.1593/neo.05754

M. Marbouty, Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging, Molecular Cell, vol.59, issue.4, pp.588-602, 2015.
DOI : 10.1016/j.molcel.2015.07.020
URL : https://hal.archives-ouvertes.fr/pasteur-01419993

M. Guidi, Spatial reorganization of telomeres in long-lived quiescent cells, Genome Biology, vol.294, issue.1, 2015.
DOI : 10.1186/s13059-015-0766-2
URL : https://hal.archives-ouvertes.fr/hal-01206018

M. L. Metzker, Sequencing technologies ??? the next generation, Nature Reviews Genetics, vol.37, issue.1, pp.31-46, 2010.
DOI : 10.1038/nrg2626

J. R. Dixon, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.148, issue.7398, pp.376-380, 2012.
DOI : 10.1038/nature11082

T. B. Le, High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome, Science, vol.110, issue.5, pp.731-734, 2013.
DOI : 10.1073/pnas.1220824110

S. Bennett, Solexa Ltd, Pharmacogenomics, vol.5, issue.4, pp.433-438, 2004.
DOI : 10.1517/14622416.5.4.433

M. Margulies, Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, pp.376-380, 2005.
DOI : 10.1016/0888-7543(88)90007-9
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464427

J. M. Rothberg, An integrated semiconductor device enabling non-optical genome sequencing, Nature, vol.32, issue.7, pp.348-352, 2011.
DOI : 10.1038/nature10242

M. Bastian, Gephi: An Open Source Software for Exploring and Manipulating Networks ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software, Third International AAAI Conference on Weblogs and Social Media 64 Jacomy, p.98679, 2009.

R. A. Jarvis and E. A. Patrick, Clustering Using a Similarity Measure Based on Shared Near Neighbors, IEEE Transactions on Computers, vol.22, issue.11, pp.1025-1034, 1973.
DOI : 10.1109/T-C.1973.223640

M. B. Eisen, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. 95, pp.14863-14868, 1998.
DOI : 10.1016/0092-8674(81)90326-3
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24541