J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman, Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products, Chem. Biol, vol.5, pp.245-249, 1998.

P. Hugenholtz, B. M. Goebel, and N. R. Pace, Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J. Bacteriol, vol.180, pp.4765-4774, 1998.

J. Qin, R. Li, J. Raes, M. Arumugam, K. S. Burgdorf et al., A human gut microbial gene catalog established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010.

J. C. Venter, K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch et al., Environmental genome shotgun sequencing of the Sargasso Sea, Science, vol.304, pp.66-74, 2004.

N. R. Pace, A molecular view of microbial diversity and the biosphere, Science, vol.276, pp.734-740, 1997.

F. Partensky, W. R. Hess, and D. Vaulot, Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol, Mol. Biol. Rev, vol.63, pp.106-127, 1999.

A. L. Kau, P. P. Ahern, N. W. Griffin, A. L. Goodman, and J. I. Gordon, Human nutrition, the gut microbiome and the immune system, Nature, vol.474, pp.327-336, 2011.

J. F. Cryan and T. G. Dinan, Mind-altering microorganisms: The impact of the gut microbiota on brain and behaviour, Nat. Rev. Neurosci, vol.13, pp.701-712, 2012.

L. Philippot, J. M. Raaijmakers, P. Lemanceau, and W. H. Van-der-putten, Going back to the roots: The microbial ecology of the rhizosphere, Nat. Rev. Microbiol, vol.11, pp.789-799, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651785

J. Yang, J. W. Kloepper, and C. Ryu, Rhizosphere bacteria help plants tolerate abiotic stress, Trends Plant Sci, vol.14, pp.1-4, 2009.

L. A. Hug, B. J. Baker, K. Anantharaman, C. T. Brown, A. J. Probst et al., A new view of the tree of life, vol.1, p.16048, 2016.

S. Guermazi, P. Daegelen, C. Dauga, D. Rivière, T. Bouchez et al., Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach, Environ. Microbiol, vol.10, pp.2111-2123, 2008.
URL : https://hal.archives-ouvertes.fr/cea-00306560

P. Bork, C. Bowler, C. Vargas, G. Gorsky, E. Karsenti et al., Tara Oceans studies plankton at planetary scale, vol.348, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01258211

H. B. Nielsen, M. Almeida, A. S. Juncker, S. Rasmussen, J. Li et al., Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes, Nat. Biotechnol, vol.32, pp.822-828, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01195477

A. Schlüter, L. Krause, R. Szczepanowski, A. Goesmann, and A. Pühler, Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant, J. Biotechnol, vol.136, pp.65-76, 2008.

V. Sentchilo, A. P. Mayer, L. Guy, R. Miyazaki, S. G. Tringe et al., Community-wide plasmid gene mobilization and selection, ISME J, vol.7, pp.1173-1186, 2013.

L. A. Ogilvie and B. V. Jones, The human gut virome: A multifaceted majority, Front. Microbiol, vol.6, p.918, 2015.

E. S. Lim, Y. Zhou, G. Zhao, I. K. Bauer, L. Droit et al., Early life dynamics of the human gut virome and bacterial microbiome in infants, Nat. Med, vol.21, pp.1228-1234, 2015.

M. Breitbart, P. Salamon, B. Andresen, J. M. Mahaffy, A. M. Segall et al., Genomic analysis of uncultured marine viral communities, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.14250-14255, 2002.

D. M. Kristensen, A. R. Mushegian, V. V. Dolja, and E. V. Koonin, New dimensions of the virus world discovered through metagenomics, Trends Microbiol, vol.18, pp.11-19, 2010.

J. Flot, H. Marie-nelly, and R. Koszul, Contact genomics: Scaffolding and phasing (meta) genomes using chromosome 3D physical signatures, FEBS Lett, pp.2966-2974, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01419996

C. Canchaya, G. Fournous, S. Chibani-chennoufi, M. L. Dillmann, and H. Brüssow, Phage as agents of lateral gene transfer, Curr. Opin. Microbiol, vol.6, pp.417-424, 2003.

A. Stern, E. Mick, I. Tirosh, O. Sagy, and R. Sorek, CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome, Genome Res, vol.22, 1985.

C. A. Suttle, Viruses in the sea, Nature, vol.437, pp.356-361, 2005.

K. D. Seed, M. Yen, B. J. Shapiro, I. J. Hilaire, R. C. Charles et al., Evolutionary consequences of intra-patient phage predation on microbial populations, vol.3, p.3497, 2014.

B. M. Davis and M. K. Waldor, Filamentous phages linked to virulence of Vibrio cholerae, Curr. Opin. Microbiol, vol.6, pp.35-42, 2003.

S. L. Welkos and R. K. Holmes, Regulation of toxinogenesis in Corynebacterium diphtheriae. I. Mutations in bacteriophage b that alter the effects of iron on toxin production, J. Virol, vol.37, pp.936-945, 1981.

B. E. Dutilh, N. Cassman, K. Mcnair, S. E. Sanchez, G. G. Silva et al., A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, Nat. Commun, vol.5, p.4498, 2014.

R. A. Edwards, K. Mcnair, K. Faust, J. Raes, and B. E. Dutilh, Computational approaches to predict bacteriophage-host relationships, FEMS Microbiol. Rev, vol.40, pp.258-272, 2015.

H. Marie-nelly, M. Marbouty, A. Cournac, J. Flot, G. Liti et al., High-quality genome (re)assembly using chromosomal contact data, Nat. Commun, vol.5, p.5695, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01138788

N. Kaplan and J. Dekker, High-throughput genome scaffolding from in vivo DNA interaction frequency, Nat. Biotechnol, vol.31, pp.1143-1147, 2013.

C. W. Beitel, L. Froenicke, J. M. Lang, I. F. Korf, R. W. Michelmore et al., Strain-and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products, PeerJ, vol.2, p.415, 2014.

J. N. Burton, I. Liachko, M. J. Dunham, and J. Shendure, Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps, G3, vol.4, pp.1339-1346, 2014.

M. Marbouty, A. Cournac, J. Flot, H. Marie-nelly, J. Mozziconacci et al., Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms, vol.3, p.3318, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01316684

M. Marbouty and R. Koszul, Metagenome analysis exploiting high-throughput chromosome conformation capture (3C) data, Trends Genet, vol.31, pp.673-682, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01419974

J. Dekker, K. Rippe, M. Dekker, and N. Kleckner, Capturing chromosome conformation, Science, vol.295, pp.1306-1311, 2002.

V. V. Mesyanzhinov, J. Robben, B. Grymonprez, V. A. Kostyuchenko, M. V. Bourkaltseva et al., The genome of bacteriophage ?KZ of Pseudomonas aeruginosa, J. Mol. Biol, vol.317, pp.1-19, 2002.

A. Cornelissen, S. C. Hardies, O. V. Shaburova, V. N. Krylov, W. Mattheus et al., Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse fKZ-related phages, J. Virol, vol.86, pp.1844-1852, 2012.

A. S. Waller, T. Yamada, D. M. Kristensen, J. R. Kultima, S. Sunagawa et al., Classification and quantification of bacteriophage taxa in human gut metagenomes, ISME J, vol.8, pp.1391-1402, 2014.

Y. Peng, H. C. Leung, S. M. Yiu, and F. Y. Chin, IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, vol.28, pp.1420-1428, 2012.

W. Zhu, A. Lomsadze, and M. Borodovsky, Ab initio gene identification in metagenomic sequences, Nucleic Acids Res, vol.38, p.132, 2010.

F. Meyer, D. Paarmann, M. Souza, R. Olson, E. M. Glass et al., The metagenomics RAST server-A public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, vol.9, p.386, 2008.

L. Xiao, Q. Feng, S. Liang, S. B. Sonne, Z. Xia et al., A catalog of the mouse gut metagenome, Nat. Biotechnol, vol.33, pp.1103-1108, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02639961

D. E. Wood and S. L. Salzberg, Kraken: Ultrafast metagenomic sequence classification using exact alignments, Genome Biol, vol.15, p.46, 2014.

S. Roux, F. Enault, B. L. Hurwitz, and M. B. Sullivan, VirSorter: Mining viral signal from microbial genomic data, PeerJ, vol.3, p.985, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01557667

J. Guglielmini, B. Néron, S. S. Abby, M. P. Garcillán-barcia, F. Cruz et al., Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res, vol.42, pp.5715-5727, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01374962

V. D. Blondel, J. Guillaume, R. Lambiotte, and E. Lefebvre, Fast unfolding of communities in large networks, J. Stat. Mech. Theory Exp, p.10008, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01146070

M. Albertsen, P. Hugenholtz, A. Skarshewski, K. L. Nielsen, G. W. Tyson et al., Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes, Nat. Biotechnol, vol.31, pp.533-538, 2013.

D. H. Parks, M. Imelfort, C. T. Skennerton, P. Hugenholtz, and G. W. Tyson, CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res, vol.25, pp.1043-1055, 2015.

J. Guglielmini, L. Quintais, M. P. Garcillán-barcia, F. Cruz, and E. P. Rocha, The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation, PLOS Genet, vol.7, p.1002222, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00647077

J. M. Lang, A. E. Darling, and J. A. Eisen, Phylogeny of bacterial and archaeal genomes using conserved genes: Supertrees and supermatrices, PLOS ONE, vol.8, p.62510, 2013.

M. A. Umbarger, E. Toro, M. A. Wright, G. J. Porreca, D. Baù et al., The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation, Mol. Cell, vol.44, pp.252-264, 2011.

M. Marbouty, A. L. Gall, D. I. Cattoni, A. Cournac, A. Koh et al., Condensin-and replication-mediated bacterial chromosome folding and origin condensation revealed by Hi-C and super-resolution imaging, Mol. Cell, vol.59, pp.588-602, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01419993

M. Val, M. Marbouty, F. De-lemos, S. P. Martins, H. Kennedy et al., A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae, Sci. Adv, vol.2, p.1501914, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01309592

X. Wang, T. B. Le, B. R. Lajoie, J. Dekker, M. T. Laub et al., Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis, Genes Dev, vol.29, pp.1661-1675, 2015.

D. Arndt, J. R. Grant, A. Marcu, T. Sajed, A. Pon et al., PHASTER: A better, faster version of the PHAST phage search tool, Nucleic Acids Res, vol.44, pp.16-21, 2016.

D. M. Kristensen, X. Cai, and A. Mushegian, Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts, J. Bacteriol, vol.193, pp.1806-1814, 2011.

D. M. Kristensen, A. S. Waller, T. Yamada, P. Bork, A. R. Mushegian et al., Orthologous gene clusters and taxon signature genes for viruses of prokaryotes, J. Bacteriol, vol.195, pp.941-950, 2013.

S. Akhter, R. K. Aziz, and R. A. Edwards, PhiSpy: A novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies, Nucleic Acids Res, vol.40, p.126, 2012.

C. O. Flores, J. R. Meyer, S. Valverde, L. Farr, and J. S. Weitz, Statistical structure of host-phage interactions, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.288-297, 2011.

N. A. Bokulich, S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon et al., Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing, Nat. Methods, vol.10, pp.57-59, 2013.

S. R. Eddy, A new generation of homology search tools based on probabilistic inference, Genome Inform, vol.23, pp.205-211, 2009.

K. Rippe, Making contacts on a nucleic acid polymer, Trends Biochem. Sci, vol.26, pp.733-740, 2001.

R. Overbeek, R. Olson, G. D. Pusch, G. J. Olsen, J. J. Davis et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Res, vol.42, pp.206-214, 2014.

M. Marbouty, L. Baudry, A. Cournac, and R. Koszul, , p.1602105


, This article cites 64 articles, 16 of which you can access for free