R. Sender, S. Fuchs, and R. Milo, Revised estimates for the number of human and bacteria cells in the body, PLoS Biol, vol.14, p.1002533, 2016.

E. E. Hansen, C. A. Lozupone, F. E. Rey, M. Wu, J. L. Guruge et al., Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins, Proc Natl Acad Sci U S A, vol.108, pp.4599-606, 2011.

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.1228-1262, 2015.

L. Wegener-parfrey, W. A. Walters, and R. Knight, Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front. Microbiol [Internet, vol.2, 2011.

G. E. Flores, J. G. Caporaso, J. B. Henley, J. R. Rideout, D. Domogala et al., Temporal variability is a personalized feature of the human microbiome

, Genome Biol, vol.15, p.531, 2014.

K. Greenhalgh, K. M. Meyer, K. M. Aagaard, and P. Wilmes, The human gut microbiome in health: establishment and resilience of microbiota over a lifetime, Environ Microbiol, vol.18, pp.2103-2119, 2016.

I. Cho and M. J. Blaser, The human microbiome: at the interface of health and disease, Nat Rev Genet, vol.13, pp.260-70, 2012.

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, pp.1635-1643, 2005.

S. R. Gill, M. Pop, R. T. Deboy, P. B. Eckburg, P. J. Turnbaugh et al., Metagenomic analysis of the human distal gut microbiome, Science, vol.312, pp.1355-1364, 2006.

M. Rajili?-stojanovi? and W. M. De-vos, The first 1000 cultured species of the human gastrointestinal microbiota, FEMS Microbiol Rev, vol.38, pp.996-1047, 2014.

H. P. Browne, S. C. Forster, B. O. Anonye, N. Kumar, B. A. Neville et al., Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation, Nature, vol.533, pp.543-549, 2016.

M. Breitbart, I. Hewson, B. Felts, J. M. Mahaffy, J. Nulton et al., Metagenomic analyses of an uncultured viral community from human feces, J Bacteriol, vol.185, pp.6220-6223, 2003.

M. Breitbart, M. Haynes, S. Kelley, F. Angly, R. A. Edwards et al., Viral diversity and dynamics in an infant gut, Res Microbiol, vol.159, pp.367-73, 2008.

M. Arumugam, J. Raes, E. Pelletier, L. Paslier, D. Yamada et al., Enterotypes of the human gut microbiome, Nature, vol.473, pp.174-80, 2011.
URL : https://hal.archives-ouvertes.fr/cea-00903625

J. Qin, R. Li, J. Raes, M. Arumugam, K. S. Burgdorf et al., A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010.
URL : https://hal.archives-ouvertes.fr/cea-00908974

M. Kim, E. Park, S. W. Roh, and J. Bae, Diversity and Abundance of singlestranded DNA viruses in human feces, Appl Environ Microbiol, vol.77, pp.8062-70, 2011.

L. Hoyles, A. L. Mccartney, H. Neve, G. R. Gibson, J. D. Sanderson et al., Characterization of virus-like particles associated with the human faecal and caecal microbiota, Res Microbiol, vol.165, pp.803-815, 2014.

P. Lepage, J. Colombet, P. Marteau, T. Sime-ngando, J. Doré et al., Dysbiosis in inflammatory bowel disease: a role for bacteriophages?, Gut, vol.57, pp.424-429, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00526557

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

J. J. Barr, R. Auro, M. Furlan, K. L. Whiteson, M. L. Erb et al., Bacteriophage adhering to mucus provide a non-host-derived immunity, Proc Natl Acad Sci, vol.110, pp.10771-10777, 2013.

A. Reyes, M. Haynes, N. Hanson, F. E. Angly, A. C. Heath et al., Viruses in the fecal microbiota of monozygotic twins and their mothers, Nature, vol.466, pp.334-342, 2010.

S. Minot, R. Sinha, J. Chen, H. Li, S. A. Keilbaugh et al., The human gut virome: inter-individual variation and dynamic response to diet, Genome Res, vol.21, pp.1616-1641, 2011.

S. Minot, A. Bryson, C. Chehoud, G. D. Wu, J. D. Lewis et al., Rapid evolution of the human gut virome, Proc Natl Acad Sci U S A, vol.110, pp.12450-12455, 2013.

P. Manrique, B. Bolduc, S. T. Walk, J. Van-der-oost, W. M. De-vos et al., Healthy human gut phageome, Proc Natl Acad Sci, vol.113, pp.10400-10405, 2016.
DOI : 10.1073/pnas.1601060113

URL : http://www.pnas.org/content/113/37/10400.full.pdf

V. Pérez-brocal, R. García-lópez, J. F. Vázquez-castellanos, P. Nos, B. Beltrán et al., Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach, Clin. Transl. Gastroenterol, 2013.

J. M. Norman, S. A. Handley, M. T. Baldridge, L. Droit, C. Y. Liu et al., Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, vol.160, pp.447-60, 2015.

W. Wang, J. Jovel, B. Halloran, E. Wine, J. Patterson et al., Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria, Inflamm Bowel Dis, vol.21, pp.1419-1446, 2015.

A. Reyes, L. V. Blanton, S. Cao, G. Zhao, M. Manary et al., Gut DNA viromes of Malawian twins discordant for severe acute malnutrition, Proc Natl Acad Sci U S A, vol.112, pp.11941-11947, 2015.

C. L. Monaco, D. B. Gootenberg, G. Zhao, S. A. Handley, M. S. Ghebremichael et al., Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome, Cell Host Microbe, vol.19, pp.311-333, 2016.

J. Debelius, S. J. Song, Y. Vazquez-baeza, Z. Z. Xu, A. Gonzalez et al., Tiny microbes, enormous impacts: what matters in gut microbiome studies?, Genome Biol, vol.17, p.217, 2016.

S. Roux, M. Krupovic, D. Debroas, P. Forterre, and F. Enault, Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences, Open Biol, vol.3, p.130160, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00932219

N. Conceição-neto, M. Zeller, H. Lefrère, P. D. Bruyn, L. Beller et al., Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis, Sci Rep, vol.5, p.16532, 2015.

M. Kleiner, L. V. Hooper, and B. A. Duerkop, Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes, BMC Genomics, vol.16, p.7, 2015.

J. L. Castro-mejía, M. K. Muhammed, W. Kot, H. Neve, C. Franz et al., Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut, Microbiome, vol.3, p.64, 2015.

S. Roux, N. E. Solonenko, V. T. Dang, B. T. Poulos, S. M. Schwenck et al., Towards quantitative viromics for both double-stranded and singlestranded DNA viruses, PeerJ, vol.4, p.2777, 2016.
DOI : 10.7717/peerj.2777

URL : https://peerj.com/articles/2777.pdf

S. Cardona, A. Eck, M. Cassellas, M. Gallart, C. Alastrue et al., Storage conditions of intestinal microbiota matter in metagenomic analysis, BMC Microbiol, vol.12, p.158, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01190761

J. M. Choo, L. E. Leong, and G. B. Rogers, Sample storage conditions significantly influence faecal microbiome profiles, Sci Rep, vol.5, p.16350, 2015.

M. A. Gorzelak, S. K. Gill, N. Tasnim, Z. Ahmadi-vand, M. Jay et al., Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool, PLoS One, vol.10, p.134802, 2015.

F. Fouhy, J. Deane, M. C. Rea, Ó. O'sullivan, R. P. Ross et al., The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations, PLoS One, vol.10, p.119355, 2015.

M. J. Sergeant, C. Constantinidou, T. Cogan, C. W. Penn, and M. J. Pallen, High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature, PLoS One, vol.7, p.38094, 2012.

F. Stämmler, J. Gläsner, A. Hiergeist, E. Holler, D. Weber et al., Adjusting microbiome profiles for differences in microbial load by spike-in bacteria, Microbiome, vol.4, p.28, 2016.

A. Reyes, M. Wu, N. P. Mcnulty, F. L. Rohwer, and J. I. Gordon, Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut, Proc Natl Acad Sci U S A, vol.110, pp.20236-20277, 2013.

J. E. Hill, S. L. Penny, K. G. Crowell, S. H. Goh, and S. M. Hemmingsen, cpnDB: a chaperonin sequence database, Genome Res, vol.14, pp.1669-75, 2004.

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. R. Brister, D. Ako-adjei, Y. Bao, and O. Blinkova, NCBI viral genomes resource, Nucleic Acids Res, vol.43, pp.571-578, 2015.
DOI : 10.1093/nar/gku1207

URL : https://doi.org/10.1093/nar/gku1207

N. A. O'leary, M. W. Wright, J. R. Brister, S. Ciufo, D. Haddad et al., Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res, vol.44, pp.733-778, 2016.

G. Morilla, D. Janssen, S. García-andrés, E. Moriones, I. M. Cuadrado et al., Pepper (Capsicum annuum) is a dead-end host for tomato yellow leaf curl virus, Phytopathology, vol.95, pp.1089-97, 2005.

S. Kraberger, G. R. Argüello-astorga, L. G. Greenfield, C. Galilee, D. Law et al., Characterisation of a diverse range of circular replicationassociated protein encoding DNA viruses recovered from a sewage treatment oxidation pond, Infect Genet Evol, vol.31, pp.73-86, 2015.

S. Roux, M. Krupovic, A. Poulet, D. Debroas, and F. Enault, Evolution and diversity of the microviridae viral family through a collection of 81 new complete genomes assembled from virome reads, PLoS One, vol.7, p.40418, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00816089

J. Mahony, B. Martel, D. M. Tremblay, H. Neve, K. J. Heller et al., Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13, Appl Environ Microbiol, vol.79, pp.4401-4410, 2013.

B. E. Dutilh, N. Cassman, K. Mcnair, S. E. Sanchez, G. Silva et al., A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, Nat Commun, vol.5, p.5498, 2014.

T. Zhang, M. Breitbart, W. H. Lee, J. Run, C. L. Wei et al., RNA viral community in human feces: prevalence of plant pathogenic viruses, PLoS Biol, 2005.

T. F. Thingstad, G. Bratbak, and M. Heldal, Aquatic phage ecology, Bacteriophage Ecol. Popul. Growth Evol. Impact Bact, pp.251-280, 2008.

D. Kang, J. B. Adams, A. C. Gregory, T. Borody, L. Chittick et al., Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study, Microbiome, vol.5, p.10, 2017.

M. Ly, M. B. Jones, S. R. Abeles, T. M. Santiago-rodriguez, J. Gao et al., Transmission of viruses via our microbiomes, Microbiome, vol.4, p.64, 2016.

S. R. Modi, H. H. Lee, C. S. Spina, and J. J. Collins, Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome, Nature, vol.499, pp.219-241, 2013.

F. Enault, A. Briet, L. Bouteille, S. Roux, M. B. Sullivan et al., Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses, ISME J, vol.11, pp.237-284, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01557484

K. M. Wylie, K. A. Mihindukulasuriya, E. Sodergren, G. M. Weinstock, and G. A. Storch, Sequence analysis of the human virome in febrile and afebrile children, PLoS One, vol.7, p.27735, 2012.

J. Wagner, J. Maksimovic, G. Farries, W. H. Sim, R. F. Bishop et al., Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing, Inflamm Bowel Dis, vol.19, pp.1598-608, 2013.

S. R. Krishnamurthy, A. B. Janowski, G. Zhao, D. Barouch, and D. Wang, Hyperexpansion of RNA bacteriophage diversity, PLoS Biol, vol.14, p.1002409, 2016.

M. Krupovic and P. Forterre, Microviridae goes temperate: microvirus-related proviruses reside in the genomes of bacteroidetes, PLoS One, vol.6, p.19893, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00593769

K. Kim and J. Bae, Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses, Appl Environ Microbiol, vol.77, pp.7663-7671, 2011.

K. Cadwell, The virome in host health and disease, Immunity, vol.42, pp.805-818, 2015.

D. Bonito, P. , D. Libera, S. Petricca, S. Iaconelli et al., A large spectrum of alpha and beta papillomaviruses are detected in human stool samples, J Gen Virol, vol.96, pp.607-620, 2015.

K. Bibby and J. Peccia, Identification of viral pathogen diversity in sewage sludge by metagenome analysis, Environ Sci Technol, vol.47, pp.1945-51, 2013.

A. Hiergeist, U. Reischl, and A. Gessner, Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high intercenter variability, Int J Med Microbiol, vol.306, pp.334-376, 2016.

M. Krajden, J. M. Minor, O. Rifkin, and L. Comanor, Effect of multiple freeze-thaw cycles on hepatitis B virus DNA and hepatitis C virus RNA quantification as measured with branched-DNA technology, J Clin Microbiol, vol.37, pp.1683-1689, 1999.

J. Jovel, J. Patterson, W. Wang, N. Hotte, S. O'keefe et al., Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol, vol.7, 2016.

R. Poretsky, -. Rodriguez, . Lm, C. Luo, D. Tsementzi et al., Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics, PLoS ONE

B. J. Callahan, P. J. Mcmurdie, M. J. Rosen, A. W. Han, A. Johnson et al., DADA2: high-resolution sample inference from Illumina amplicon data, Nat Methods, vol.13, pp.581-584, 2016.

R. C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat Methods, vol.10, pp.996-1004, 2013.

P. D. Schloss, S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann et al., Introducing mothur: Open-Source, Platform-Independent, CommunitySupported Software for Describing and Comparing Microbial Communities, Appl Environ Microbiol, vol.75, pp.7537-7578, 2009.

G. Allard, F. J. Ryan, I. B. Jeffery, and M. J. Claesson, SPINGO: a rapid species-classifier for microbial amplicon sequences, BMC Bioinformatics, vol.16, p.324, 2015.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree: computing large minimum evolution trees with profiles instead of a distance matrix, Mol Biol Evol, vol.26, pp.1641-50, 2009.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet Journal, vol.17, pp.10-12, 2011.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2134, 2014.

S. Nurk, D. Meleshko, A. Korobeynikov, and P. A. Pevzner, metaSPAdes: a new versatile metagenomic assembler, Genome Res, vol.27, pp.824-858, 2017.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-366, 2012.

E. Kopylova, L. Noé, and H. Touzet, SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.28, pp.3211-3218, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00748990

C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer et al., The SILVA ribosomal RNA gene database project: improved data processing and webbased tools, Nucleic Acids Res, vol.41, pp.590-596, 2013.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

S. Weiss, Z. Z. Xu, S. Peddada, A. Amir, K. Bittinger et al., Normalization and microbial differential abundance strategies depend upon data characteristics, Microbiome, vol.5, p.27, 2017.
DOI : 10.1186/s40168-017-0237-y

URL : https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/s40168-017-0237-y

M. J. Anderson, A new method for non-parametric multivariate analysis of variance, Austral Ecol, vol.26, pp.32-46, 2001.