E. G. Altmann and M. Gerlach, Statistical Laws in Linguistics, Creativity and Universality in Language, pp.7-26, 2016.
DOI : 10.1068/b4105c

URL : http://arxiv.org/pdf/1502.03296

A. Andreeva, D. Howorth, S. E. Brenner, T. J. Hubbard, C. Chothia et al., SCOP database in 2004: refinements integrate structure and sequence family data, Nucleic Acids Research, vol.32, issue.90001, pp.32226-229, 2004.
DOI : 10.1093/nar/gkh039

A. Angelini, A. Amato, G. Bianconi, B. Bassetti, and M. C. Lagomarsino, Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains, Physical Review E, vol.37, issue.2, p.81021919, 2010.
DOI : 10.1371/journal.pbio.0020055

F. E. Angly, D. Willner, A. Prieto-davó, R. A. Edwards, R. Schmieder et al., The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes, PLoS Computational Biology, vol.9, issue.12, p.1000593, 2009.
DOI : 10.1371/journal.pcbi.1000593.s010

S. K. Baek, S. Bernhardsson, and P. Minnhagen, Zipf's law unzipped, New Journal of Physics, vol.13, issue.4, p.43004, 2011.
DOI : 10.1088/1367-2630/13/4/043004

URL : http://iopscience.iop.org/article/10.1088/1367-2630/13/4/043004/pdf

A. Bairoch, The ENZYME database in 2000, Nucleic Acids Research, vol.28, issue.1, pp.304-305, 2000.
DOI : 10.1093/nar/28.1.304

A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich et al., The Pfam protein families database, Nucleic Acids Research, vol.32, issue.90001, pp.138-141, 2004.
DOI : 10.1093/nar/gkh121

URL : https://hal.archives-ouvertes.fr/hal-01294685

L. M. Bettencourt, J. Lobo, D. Helbing, C. Kühnert, and G. B. West, Growth, innovation, scaling, and the pace of life in cities, Proceedings of the national academy of sciences, pp.7301-7306, 2007.
DOI : 10.2307/2118405

P. Bork, C. Bowler, C. D. Vargas, G. Gorsky, E. Karsenti et al., Tara Oceans studies plankton at planetary scale, Science, vol.15, issue.10, pp.348873-873, 2015.
DOI : 10.1371/journal.pbio.1001177

URL : https://hal.archives-ouvertes.fr/hal-01258211

C. I. Branden, Introduction to protein structure Genomic repertoires of dna-binding transcription factors across the tree of life, Garland Science Nucleic acids research, issue.1121, pp.387364-7377, 1999.

O. X. Cordero and P. Hogeweg, Regulome size in Prokaryotes: universality and lineage-specific variations, Trends in Genetics, vol.25, issue.7, 2009.
DOI : 10.1016/j.tig.2009.05.001

B. Corominas-murtra, R. Hanel, and S. Thurner, Sample space reducing cascading processes produce the full spectrum of scaling exponents, Scientific Reports, vol.12, issue.2
DOI : 10.1103/PhysRevE.50.3502

B. Corominas-murtra, R. Hanel, and S. Thurner, Understanding scaling through history-dependent processes with collapsing sample space, Proceedings of the National Academy of Sciences, vol.1, issue.2, pp.5348-5353, 2015.
DOI : 10.1080/15427951.2004.10129088

URL : http://www.pnas.org/content/112/17/5348.full.pdf

M. C. Lagomarsino, A. Sellerio, P. Heijning, and B. Bassetti, Universal features in the genome-level evolution of protein domains, Genome Biology, vol.10, issue.1, p.12, 2009.
DOI : 10.1186/gb-2009-10-1-r12

C. Debes, M. Wang, G. Caetano-anolles, and F. Graeter, Evolutionary Optimization of Protein Folding, PLoS Computational Biology, vol.9, issue.1, p.1002861, 2013.
DOI : 10.1371/journal.pcbi.1002861.s012

M. R. Evans and T. Hanney, Nonequilibrium statistical mechanics of the zero-range process and related models, Journal of Physics A: Mathematical and General, vol.38, issue.19, p.195, 2005.
DOI : 10.1088/0305-4470/38/19/R01

R. D. Finn, A. Bateman, J. Clements, P. Coggill, R. Y. Eberhardt et al., Pfam: the protein families database, Nucleic Acids Research, issue.D1, pp.42-222, 2014.
DOI : 10.1002/047001153x.g306303

URL : https://hal.archives-ouvertes.fr/hal-01294685

R. D. Finn, J. Mistry, B. Schuster-böckler, S. Griths-jones, V. Hollich et al., Pfam: clans, web tools and services, Nucleic Acids Research, vol.34, issue.90001, pp.34-247, 2006.
DOI : 10.1093/nar/gkj149

URL : https://academic.oup.com/nar/article-pdf/34/suppl_1/D247/3926414/gkj149.pdf

R. D. Fleischmann, M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness et al., Whole-genome random sequencing and assembly of haemophilus influenzae rd. science, pp.496-512, 1995.

F. Font-clos and Á. Corral, Log-Log Convexity of Type-Token Growth in Zipf???s Systems, Physical Review Letters, vol.2, issue.23, p.238701, 2015.
DOI : 10.2478/s11600-013-0154-9

M. A. Fortuna, J. A. Bonachela, and S. A. Levin, Evolution of a modular software network, Proceedings of the National Academy of Sciences, pp.19985-19989, 2011.
DOI : 10.1016/j.jtbi.2007.03.017

C. M. Fraser, J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton et al., The minimal gene complement of mycoplasma genitalium. science, pp.397-403, 1995.

X. Gabaix, Zipf's Law for Cities: An Explanation, The Quarterly Journal of Economics, vol.114, issue.1, pp.739-767, 1999.
DOI : 10.1086/452537

URL : http://pages.stern.nyu.edu/%7Exgabaix/papers/zipf.pdf

S. J. Giovannoni, J. C. Thrash, and B. Temperton, Implications of streamlining theory for microbial ecology, The ISME Journal, vol.581, issue.8, p.1553, 2014.
DOI : 10.1016/j.febslet.2007.03.010

J. Gough, K. Karplus, R. Hughey, and C. Chothia, Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure, Journal of Molecular Biology, vol.313, issue.4, pp.903-919, 2001.
DOI : 10.1006/jmbi.2001.5080

L. Grassi, M. Caselle, M. J. Lercher, and M. C. Lagomarsino, Horizontal gene transfers as metagenomic gene duplications, Molecular BioSystems, vol.35, issue.3, pp.790-795, 2012.
DOI : 10.1093/nar/gkm204

URL : https://hal.archives-ouvertes.fr/hal-01528436

L. Grassi, J. Grilli, and M. C. Lagomarsino, Large-scale dynamics of horizontal transfers, Mobile Genetic Elements, vol.2, issue.3, pp.163-167, 2012.
DOI : 10.1186/1471-2164-12-32

URL : https://hal.archives-ouvertes.fr/hal-01588577

J. Grilli, B. Bassetti, S. Maslov, and M. C. Lagomarsino, Joint scaling laws in functional and evolutionary categories in prokaryotic genomes, Nucleic Acids Research, vol.31, issue.2, pp.530-540, 2012.
DOI : 10.1093/nar/gkq617

URL : https://hal.archives-ouvertes.fr/hal-01527307

J. Grilli, M. Romano, F. Bassetti, and M. C. Lagomarsino, Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers, Nucleic Acids Research, vol.6, issue.5, pp.6850-60, 2014.
DOI : 10.1016/j.mib.2003.09.008

URL : https://hal.archives-ouvertes.fr/hal-01332631

R. Hanel and S. Thurner, When do generalized entropies apply? How phase space volume determines entropy, EPL (Europhysics Letters), vol.96, issue.5, p.50003, 2011.
DOI : 10.1209/0295-5075/96/50003

URL : http://arxiv.org/pdf/1104.2064

D. Heckerman, D. M. Chickering, C. Meek, R. Rounthwaite, and C. Kadie, Dependency networks for inference, collaborative filtering, and data visualization, Journal of Machine Learning Research, vol.1, pp.49-75, 2000.

G. Herdan, Re: type-token mathematics, Information and Control, vol.4, issue.2-3, 1960.
DOI : 10.1016/S0019-9958(61)80016-8

URL : https://doi.org/10.1016/s0019-9958(61)80016-8

S. Hunter, M. Corbett, H. Denise, M. Fraser, A. Gonzalez-beltran et al., Ebi metagenomicsâ ? A ? Ta new resource for the analysis and archiving of metagenomic data, Nucleic acids research, issue.D1, pp.42-600, 2013.

M. Huynen and E. Van-nimwegen, The frequency distribution of gene family sizes in complete genomes, Molecular Biology and Evolution, vol.15, issue.5, pp.583-589, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025959

D. Johnston, Stretched exponential relaxation arising from a continuous sum of exponential decays, Physical Review B, vol.70, issue.18, p.184430, 2006.
DOI : 10.1016/j.jnoncrysol.2003.08.060

G. P. Karev, Y. I. Wolf, F. S. Berezovskaya, and E. V. Koonin, Gene family evolution: an indepth theoretical and simulation analysis of non-linear birth-death-innovation models, BMC Evolutionary Biology, vol.4, issue.1, p.32, 2004.
DOI : 10.1186/1471-2148-4-32

F. H. Karlsson, V. Tremaroli, I. Nookaew, G. Bergström, C. J. Behre et al., Gut metagenome in European women with normal, impaired and diabetic glucose control, Nature, vol.35, issue.7452, p.49899, 2013.
DOI : 10.1111/j.1574-6976.2010.00251.x

D. Y. Kenett, M. Tumminello, A. Madi, G. Gur-gershgoren, R. N. Mantegna et al., Dominating Clasp of the Financial Sector Revealed by Partial Correlation Analysis of the Stock Market, PLoS ONE, vol.59, issue.1, p.15032, 2010.
DOI : 10.1371/journal.pone.0015032.s002

K. T. Konstantinidis, J. Bra?, D. M. Karl, and E. F. Delong, Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre, Applied and Environmental Microbiology, vol.75, issue.16, pp.755345-5355, 2009.
DOI : 10.1128/AEM.00473-09

E. V. Koonin, Are There Laws of Genome Evolution?, PLoS Computational Biology, vol.205, issue.8, p.1002173, 2011.
DOI : 10.1371/journal.pcbi.1002173.g002

E. V. Koonin, The logic of chance: the nature and origin of biological evolution, 2011.

E. V. Koonin and Y. I. Wolf, Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucleic Acids Research, vol.52, issue.5, pp.6688-6719, 2008.
DOI : 10.1080/10635150390235520

E. V. Koonin, Y. I. Wolf, and G. P. Karev, The structure of the protein universe and genome evolution, Nature, vol.11, issue.6912, p.420218, 2002.
DOI : 10.1093/NAR/30.1.281

C. Kuo, N. A. Moran, and H. Ochman, The consequences of genetic drift for bacterial genome complexity, Genome Research, vol.19, issue.8, pp.1450-1454, 2009.
DOI : 10.1101/gr.091785.109

J. M. Leinaas and J. Myrheim, ?? ???????????? ?????????????????????????? ????????????, Il Nuovo Cimento B Series 11, vol.56, issue.1, pp.1-23, 1971.
DOI : 10.1017/CBO9780511666278

R. E. Ley, M. Hamady, C. Lozupone, P. Turnbaugh, R. R. Ramey et al., Evolution of Mammals and Their Gut Microbes, Science, vol.99, issue.12, pp.3201647-1651, 2008.
DOI : 10.1073/pnas.102164299

A. E. Lobkovsky, Y. I. Wolf, and E. V. Koonin, Gene Frequency Distributions Reject a Neutral Model of Genome Evolution, Genome Biology and Evolution, vol.8, issue.1, pp.233-242, 2013.
DOI : 10.1186/1471-2164-8-121

N. J. Loman, C. Constantinidou, M. Christner, H. Rohde, J. Z. Chan et al., A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4, JAMA, vol.309, issue.14, pp.3091502-1510, 2013.
DOI : 10.1001/jama.2013.3231

R. Louf and M. Barthelemy, Modeling the polycentric transition of cities. Physical review letters, p.198702, 2013.

C. Lozupone and R. Knight, UniFrac: a New Phylogenetic Method for Comparing Microbial Communities, Applied and Environmental Microbiology, vol.71, issue.12, pp.8228-8235, 2005.
DOI : 10.1128/AEM.71.12.8228-8235.2005

URL : http://aem.asm.org/content/71/12/8228.full.pdf

M. , M. Babu, and S. Teichmann, Evolution of transcription factors and the gene regulatory network in escherichia coli, Nucleic Acids Res, vol.31, pp.1234-1244, 2003.

M. A. Mahowald, F. E. Rey, H. Seedorf, P. J. Turnbaugh, R. S. Fulton et al., Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla, Proceedings of the National Academy of Sciences, pp.5859-5864, 2009.
DOI : 10.1093/bioinformatics/bth137

S. Maslov, S. Krishna, T. Y. Pang, and K. Sneppen, Toolbox model of evolution of prokaryotic metabolic networks and their regulation, Proceedings of the National Academy of Sciences, vol.61, issue.4, pp.9743-9748, 2009.
DOI : 10.1007/s00239-005-0027-1

B. A. Methé, K. E. Nelson, M. Pop, H. H. Creasy, M. G. Giglio et al., A framework for human microbiome research, Nature, vol.26, issue.7402, p.486215, 2012.
DOI : 10.1093/bioinformatics/btq461

N. Molina and E. Van-nimwegen, The evolution of domain-content in bacterial genomes, Biology Direct, vol.3, issue.1, p.51, 2008.
DOI : 10.1186/1745-6150-3-51

N. Molina and E. Van-nimwegen, Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in genetics : TIG, pp.243-250, 2009.
DOI : 10.1016/j.tig.2009.04.004

S. Nayfach and K. S. Pollard, Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome, Genome Biology, vol.57, issue.1, p.51, 2015.
DOI : 10.1093/bioinformatics/bts429

S. Nayfach and K. S. Pollard, Toward Accurate and Quantitative Comparative Metagenomics, Cell, vol.166, issue.5, pp.1103-1116, 2016.
DOI : 10.1016/j.cell.2016.08.007

URL : https://cloudfront.escholarship.org/dist/prd/content/qt9v4543tn/qt9v4543tn.pdf

A. Ndhlovu, P. M. Durand, and S. Hazelhurst, EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A, Database, vol.2015, p.65, 2015.
DOI : 10.1371/journal.pone.0009490

C. A. Orengo, A. Michie, S. Jones, D. T. Jones, M. Swindells et al., CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-1109, 1997.
DOI : 10.1016/S0969-2126(97)00260-8

C. A. Orengo and J. M. Thornton, PROTEIN FAMILIES AND THEIR EVOLUTION???A STRUCTURAL PERSPECTIVE, Annual Review of Biochemistry, vol.74, issue.1, pp.867-900, 2005.
DOI : 10.1146/annurev.biochem.74.082803.133029

T. Y. Pang and S. Maslov, A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology, PLoS Computational Biology, vol.4, issue.5, p.1001137, 2011.
DOI : 10.1371/journal.pcbi.1001137.s001

J. Peterson, S. Garges, M. Giovanni, P. Mcinnes, L. Wang et al., The nih human microbiome project, Genome research, vol.19, issue.12, pp.2317-2323, 2009.

D. M. Powers, Applications and explanations of Zipf's law, Proceedings of the Joint Conferences on New Methods in Language Processing and Computational Natural Language Learning, NeMLaP3/CoNLL '98, pp.151-160, 1998.
DOI : 10.3115/1603899.1603924

T. Prakash and T. D. Taylor, Functional assignment of metagenomic data: challenges and applications, Briefings in Bioinformatics, vol.77, issue.10, pp.711-727, 2012.
DOI : 10.1128/AEM.02758-10

J. Qian, N. M. Luscombe, and M. Gerstein, Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model, Journal of Molecular Biology, vol.313, issue.4, pp.673-681, 2001.
DOI : 10.1006/jmbi.2001.5079

J. Raes, J. O. Korbel, M. J. Lercher, C. V. Mering, and P. Bork, Prediction of e?ective genome size in metagenomic samples, Genome Biology, vol.8, issue.1, p.10, 2007.
DOI : 10.1186/gb-2007-8-1-r10

J. A. Ranea, D. W. Buchan, J. M. Thornton, and C. A. Orengo, Evolution of Protein Superfamilies and Bacterial Genome Size, Journal of Molecular Biology, vol.336, issue.4, pp.871-887, 2004.
DOI : 10.1016/j.jmb.2003.12.044

J. A. Ranea, A. Grant, J. M. Thornton, and C. A. Orengo, Microeconomic principles explain an optimal genome size in bacteria, Trends in Genetics, vol.21, issue.1, pp.21-25, 2005.
DOI : 10.1016/j.tig.2004.11.014

R. F. Schwabe and C. Jobin, The microbiome and cancer, Nature Reviews Cancer, vol.109, issue.11, pp.800-812, 2013.
DOI : 10.1073/pnas.1207230109

S. Schwartz, I. Friedberg, I. V. Ivanov, L. A. Davidson, J. S. Goldsby et al., A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response, Genome Biology, vol.13, issue.4, p.32, 2012.
DOI : 10.1186/gb-2012-13-4-r32

B. Snel, P. Bork, and M. A. Huynen, Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content, Genome Research, vol.12, issue.1, pp.17-25, 2002.
DOI : 10.1101/gr.176501

D. Sornette, Critical phenomena in natural sciences: chaos, fractals, selforganization and disorder: concepts and tools, 2006.
DOI : 10.1007/978-3-662-04174-1

S. Suweis, J. Grilli, J. R. Banavar, S. Allesina, and A. Maritan, E?ect of localization on the stability of mutualistic ecological networks, Nature communications, vol.6, 2015.

T. Thomas, J. Gilbert, and F. Meyer, Metagenomics-a guide from sampling to data analysis. Microbial informatics and experimentation, p.3, 2012.
DOI : 10.1186/2042-5783-2-3

URL : http://microbialinformaticsj.biomedcentral.com/track/pdf/10.1186/2042-5783-2-3?site=microbialinformaticsj.biomedcentral.com

F. Tria, V. Loreto, V. D. Servedio, and S. H. Strogatz, The dynamics of correlated novelties Scientific reports, p.5890, 2014.

P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan et al., A core gut microbiome in obese and lean twins, Nature, vol.8, issue.7228, p.457480, 2009.
DOI : 10.4319/lo.1997.42.3.0487

F. Turroni, C. Peano, D. A. Pass, E. Foroni, M. Severgnini et al., Diversity of Bifidobacteria within the Infant Gut Microbiota, PLoS ONE, vol.105, issue.444, p.36957, 2012.
DOI : 10.1371/journal.pone.0036957.s004

E. Van-nimwegen, Scaling laws in the functional content of genomes, Trends in Genetics, vol.19, issue.9, pp.479-484, 2003.
DOI : 10.1016/S0168-9525(03)00203-8

T. V?trovsk-`-v?trovsk-`-y and P. Baldrian, The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses, PLoS ONE, vol.7, issue.2, p.57923, 2013.
DOI : 10.1371/journal.pone.0057923.s006

C. Vogel and C. Chothia, Protein Family Expansions and Biological Complexity, PLoS Computational Biology, vol.19, issue.5, p.48, 2006.
DOI : 10.1371/journal.pcbi.0020048.st002

URL : https://doi.org/10.1371/journal.pcbi.0020048

J. Walter and R. Ley, The human gut microbiome: ecology and recent evolutionary changes. Annual review of microbiology, pp.411-429, 2011.
DOI : 10.1146/annurev-micro-090110-102830

J. C. Wooley, A. Godzik, and I. Friedberg, A Primer on Metagenomics, PLoS Computational Biology, vol.14, issue.2, p.1000667, 2010.
DOI : 10.1371/journal.pcbi.1000667.t002

URL : https://doi.org/10.1371/journal.pcbi.1000667

G. K. Zipf, the psycho-biology of language: An introduction to dynamic philology, 1935.