S. Greenblum, P. J. Turnbaugh, and E. Borenstein, Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease, Proceedings of the National Academy of Sciences, vol.109, pp.594-599, 2012.

H. Consortium, Structure, function and diversity of the healthy human microbiome, Nature, vol.486, pp.207-214, 2012.

E. O. Petrof, G. B. Gloor, S. J. Vanner, S. J. Weese, and D. Carter, Stool substitute transplant therapy for the eradication of Clostridium difficile infection, RePOOPulating'the gut. Microbiome, vol.1, pp.1-12, 2013.

L. A. David, C. F. Maurice, R. N. Carmody, D. B. Gootenberg, and J. E. Button, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 2013.

J. K. Goodrich, J. L. Waters, A. C. Poole, J. L. Sutter, and O. Koren, Human genetics shape the gut microbiome, Cell, vol.159, p.25417156, 2014.

D. Knights, K. G. Lassen, and R. J. Xavier, Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome, Gut, vol.62, pp.1505-1510, 2013.

A. Spor, O. Koren, and R. Ley, Unravelling the effects of the environment and host genotype on the gut microbiome, Nature Reviews Microbiology, vol.9, pp.279-290, 2011.

R. Blekhman, J. K. Goodrich, K. Huang, Q. Sun, and R. Bukowski, Host genetic variation impacts microbiome composition across human body sites, Genome Biology, vol.16, pp.1-12, 2014.

M. G. Dominguez-bello, E. K. Costello, M. Contreras, M. Magris, and G. Hidalgo, Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns, Proceedings of the National Academy of Sciences, vol.107, pp.11971-11975, 2010.

P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-liggett, and R. Knight, The Human Microbiome Project, Nature, vol.449, p.17943116, 2007.

I. Cho and M. J. Blaser, The human microbiome: at the interface of health and disease, Nature Reviews Genetics, vol.13, pp.260-270, 2012.

T. Bersaglieri, P. C. Sabeti, N. Patterson, T. Vanderploeg, and S. F. Schaffner, Genetic signatures of strong recent positive selection at the lactase gene, The American Journal of Human Genetics, vol.74, p.15114531, 2004.

G. H. Perry, N. J. Dominy, K. G. Claw, A. S. Lee, and H. Fiegler, Diet and the evolution of human amylase gene copy number variation, Nature genetics, vol.39, p.17828263, 2007.

D. P. Kwiatkowski, How malaria has affected the human genome and what human genetics can teach us about malaria, The American Journal of Human Genetics, vol.77, p.16001361, 2005.

C. De-filippo, D. Cavalieri, D. Paola, M. Ramazzotti, M. Poullet et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proceedings of the National Academy of Sciences, vol.107, pp.14691-14696, 2010.

T. Yatsunenko, F. E. Rey, M. J. Manary, I. Trehan, and M. G. Dominguez-bello, Human gut microbiome viewed across age and geography, Nature, vol.486, p.222, 2012.

A. Lin, E. M. Bik, E. K. Costello, L. Dethlefsen, and R. Haque, Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States, Plos One, vol.8, p.53838, 2013.

S. L. Schnorr, M. Candela, S. Rampelli, M. Centanni, and C. Consolandi, Gut microbiome of the Hadza hunter-gatherers, Nature communications, vol.5, 2014.

S. Rampelli, S. L. Schnorr, C. Consolandi, S. Turroni, and M. Severgnini, Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota, Current Biology, 2015.

A. J. Obregon-tito, R. Y. Tito, J. Metcalf, K. Sankaranarayanan, and J. C. Clemente, Subsistence strategies in traditional societies distinguish gut microbiomes, Nat Commun, vol.6, 2015.

J. Nakayama, K. Watanabe, J. Jiang, K. Matsuda, and S. Chao, Diversity in gut bacterial community of school-age children in Asia, 2015.

E. D. Sonnenburg and J. L. Sonnenburg, Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates, Cell metabolism, vol.20, p.25156449, 2014.

J. C. Clemente, E. C. Pehrsson, M. J. Blaser, K. Sandhu, and Z. Gao, The microbiome of uncontacted Amerindians, Science Advances, vol.1, 2015.

J. Zhang, Z. Guo, A. Lim, Y. Zheng, and E. Y. Koh, Mongolians core gut microbiota and its correlation with seasonal dietary changes, 2014.

L. Dethlefsen and D. Relman, Microbes and health sackler colloquium: incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proc Natl Acad Sci, vol.108, pp.4516-4522, 2010.

I. Martínez, J. C. Stegen, M. X. Maldonado-gómez, A. M. Eren, and P. M. Siba, The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes, Cell reports, vol.11, pp.527-538, 2015.

X. C. Morgan, T. L. Tickle, H. Sokol, D. Gevers, and K. L. Devaney, Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, Genome Biol, vol.13, p.79, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00736429

A. D. Kostic, D. Gevers, H. Siljander, T. Vatanen, and T. Hyötyläinen, The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes, Cell Host & Microbe, vol.17, pp.260-273, 2015.

D. E. Elliott, R. W. Summers, and J. V. Weinstock, Helminths as governors of immune-mediated inflammation, International journal for parasitology, vol.37, p.17313951, 2007.

W. H. Organization, Prevention and control of intestinal parasitic infections: report of a WHO Expert Committee, 1986.

G. L. Kay, A. Millard, M. J. Sergeant, N. Midzi, and R. Gwisai, Differences in the faecal microbiome in Schistosoma haematobium infected children vs. uninfected children, PLoS Negl Trop Dis, vol.9, p.3861, 2015.

M. Fumagalli, U. Pozzoli, R. Cagliani, G. P. Comi, and S. Riva, Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions, The Journal of experimental medicine, vol.206, pp.1395-1408, 2009.

E. K. Costello, K. Stagaman, L. Dethlefsen, B. Bohannan, and D. A. Relman, The Application of Ecological Theory Toward an Understanding of the Human Microbiome, Science, vol.336, p.22674335, 2012.

C. G. Buffie and E. G. Pamer, Microbiota-mediated colonization resistance against intestinal pathogens, Nature Reviews Immunology, vol.13, pp.790-801, 2013.

K. S. Hayes, A. J. Bancroft, M. Goldrick, C. Portsmouth, and I. S. Roberts, Exploitation of the Intestinal Microflora by the Parasitic Nematode Trichuris muris, Science, vol.328, p.20538949, 2010.

H. Okada, C. Kuhn, H. Feillet, and J. F. Bach, The 'hygiene hypothesis' for autoimmune and allergic diseases: an update, Clinical & Experimental Immunology, vol.160, pp.1-9, 2010.

R. M. Maizels, H. J. Mcsorley, and D. J. Smyth, Helminths in the hygiene hypothesis: sooner or later?, Clinical & Experimental Immunology, vol.177, pp.38-46, 2014.

G. J. Koppert, E. Dounias, A. Froment, and P. Pasquet, Food consumption in three forest populations of the southern coastal area of Cameroon: Yassa-Mvae-Bakola, Man and the Biosphere Series, vol.13, pp.295-295, 1993.

P. Verdu, F. Austerlitz, A. Estoup, R. Vitalis, and M. Georges, Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa, Current Biology, vol.19, pp.312-318, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00397221

E. Patin, G. Laval, L. B. Barreiro, A. Salas, and O. Semino, Inferring the demographic history of African farmers and Pygmy hunter-gatherers using a multilocus resequencing data set, PLoS Genetics, vol.5, p.1000448, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00397240

J. Diamond and P. Bellwood, Farmers and their languages: the first expansions, Science, vol.300, p.12714734, 2003.

A. Froment and S. H. Ambrose, Analyses tissulaires isotopiques et reconstruction du régime alimentaire en milieu tropical: implications pour l'archéologie. Bulletins et Mémoires de la Société d'Anthropologie de, vol.7, pp.79-98, 1995.

C. Lozupone, M. E. Lladser, D. Knights, J. Stombaugh, and R. Knight, UniFrac: an effective distance metric for microbial community comparison, The ISME journal, vol.5, p.20827291, 2011.

D. Karagiannis-voules, P. Biedermann, U. F. Ekpo, A. Garba, and E. Langer, Spatial and temporal distribution of soil-transmitted helminth infection in sub-Saharan Africa: a systematic review and geostatistical meta-analysis, The Lancet Infectious Diseases, vol.15, pp.74-84, 2015.

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B (Methodological, pp.289-300, 1995.

O. Geissinger, D. P. Herlemann, E. Mörschel, U. G. Maier, and A. Brune, The ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum, Applied and Environmental Microbiology, vol.75, pp.2831-2840, 2009.

N. J. Evans, J. M. Brown, R. D. Murray, B. Getty, and R. J. Birtles, Characterization of novel bovine gastrointestinal tract Treponema isolates and comparison with bovine digital dermatitis treponemes, Applied and Environmental Microbiology, vol.77, pp.138-147, 2011.

A. Gomez, K. Petrzelkova, C. J. Yeoman, M. B. Burns, and K. R. Amato, Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers, p.19232, 2015.

M. Kanehisa and S. Goto, KEGG: kyoto encyclopedia of genes and genomes, Nucleic acids research, vol.28, p.10592173, 2000.

M. G. Langille, J. Zaneveld, J. G. Caporaso, D. Mcdonald, and D. Knights, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nature biotechnology, vol.31, p.23975157, 2013.

I. Cho, S. Yamanishi, L. Cox, B. A. Methé, and J. Zavadil, Antibiotics in early life alter the murine colonic microbiome and adiposity, Nature, vol.488, pp.621-626, 2012.

C. J. Meehan and R. G. Beiko, A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria, Genome Biology and Evolution, vol.6, p.24625961, 2014.

X. Ze, S. H. Duncan, P. Louis, and H. J. Flint, Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon, The ISME journal, vol.6, pp.1535-1543, 2012.

R. M. Anthony, L. I. Rutitzky, J. F. Urban, M. J. Stadecker, and W. C. Gause, Protective immune mechanisms in helminth infection, Nature Reviews Immunology, vol.7, p.18007680, 2007.

J. Fleming and J. Weinstock, Clinical Trials of Helminth Therapy in Autoimmune Diseases: Rationale and Findings, 2015.

J. L. Round, R. M. O'connell, and S. K. Mazmanian, Coordination of tolerogenic immune responses by the commensal microbiota, Journal of autoimmunity, vol.34, 2010.

J. M. Kinross, A. W. Darzi, and J. K. Nicholson, Gut microbiome-host interactions in health and disease, Genome Med, vol.3, p.21392406, 2011.

D. Pagliari, C. A. Piccirillo, A. Larbi, and R. Cianci, The Interactions between Innate Immunity and Microbiota in Gastrointestinal Diseases, Journal of Immunology Research, 2015.

M. J. Blaser and S. Falkow, What are the consequences of the disappearing human microbiota?, Nature Reviews Microbiology, vol.7, pp.887-894, 2009.

N. Segata, Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity, Current Biology, vol.25, pp.611-613, 2015.

J. Mcgrady-steed and P. J. Morin, Biodiversity, density compensation, and the dynamics of populations and functional groups, Ecology, vol.81, pp.361-373, 2000.

K. S. Mccann, The diversity-stability debate, Nature, vol.405, p.10821283, 2000.

D. Tilman and J. A. Downing, Biodiversity and stability in grasslands, pp.3-7, 1996.

J. U. Scher, A. Sczesnak, R. S. Longman, N. Segata, and C. Ubeda, Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis, vol.2, p.24192039, 2013.

A. N. Mccoy, F. Araujo-perez, A. Azcarate-peril, J. J. Yeh, and R. S. Sandler, Fusobacterium is associated with colorectal adenomas, Plos One, vol.8, p.23335968, 2013.

M. B. Burns, J. Lynch, T. K. Starr, D. Knights, and R. Blekhman, Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment, p.9431, 2014.

A. M. Nsubuga, M. M. Robbins, A. D. Roeder, P. A. Morin, and C. Boesch, Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method, Molecular Ecology, vol.13, p.15189228, 2004.

L. Cai, L. Ye, A. Tong, S. Lok, and T. Zhang, Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets, Plos One, vol.8, p.23341963, 2013.

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

T. Mago? and S. L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011.

J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, and F. D. Bushman, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.7, p.20383131, 2010.

D. Mcdonald, M. N. Price, J. Goodrich, E. P. Nawrocki, and T. Z. Desantis, An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, The ISME journal, vol.6, p.22134646, 2012.

D. P. Faith, Conservation evaluation and phylogenetic diversity, Biological conservation, vol.61, pp.1-10, 1992.

C. E. Shannon, A mathematical theory of communication, ACM SIGMOBILE Mobile Computing and Communications Review, vol.5, pp.3-55, 2001.

E. H. Simpson, Measurement of diversity, Nature, 1949.

M. J. Anderson, Permutational multivariate analysis of variance, 2005.

J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, and P. R. Minchin, Package 'vegan'. Community ecology package, 2013.

F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, and B. Thirion, Scikit-learn: Machine learning in Python, The Journal of Machine Learning Research, vol.12, pp.2825-2830, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00650905