U. Esser and T. Roth, Regent's Park, Zoological Society of London We would like to acknowledge the following people for their work collecting fecal samples from wild primates, National Zoo

K. Amato, S. Van-belle, D. Fiore, A. Estrada, A. Stumpf et al., Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate, Microbial Ecology, vol.76, issue.1, pp.1-9, 2017.
DOI : 10.1016/j.ebiom.2016.01.032

A. Amir, D. Mcdonald, J. Navas-molina, E. Kopylova, J. Morton et al., Deblur rapidly resolves singlenucleotide community sequence patterns, pp.191-207, 2017.

E. Biagi, C. Franceschi, S. Rampelli, M. Severgnini, R. Ostan et al., Gut Microbiota and Extreme Longevity, Current Biology, vol.26, issue.11, pp.1480-1485, 2016.
DOI : 10.1016/j.cub.2016.04.016

J. Caporaso, C. Lauber, W. Walters, D. Berg-lyons, J. Huntley et al., Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, The ISME Journal, vol.6, issue.8, pp.1621-1625, 2012.
DOI : 10.1038/ismej.2010.160

J. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. Bushman et al., QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-341, 2010.
DOI : 10.1038/nmeth.f.303

A. Clark, A. Silva-fletcher, M. Fox, M. Kreuzer, and M. Clauss, Survey of feeding practices, body condition and faeces consistency in captive ant-eating mammals in the UK, J Zoo Aqua Res, vol.4, pp.183-95, 2016.

M. Clauss and E. Dierenfeld, The Nutrition of ???Browsers???, Zoo and Wild Animal Medicine, pp.444-54, 2008.
DOI : 10.1016/B978-141604047-7.50058-0

J. Clayton, P. Vangay, H. Huang, T. Ward, B. Hillmann et al., Captivity humanizes the primate microbiome, Proceedings of the National Academy of Sciences, vol.18, issue.3, pp.10376-81, 2016.
DOI : 10.1093/bioinformatics/btg412

L. David, C. Maurice, R. Carmody, D. Gootenberg, J. Button et al., Diet rapidly and reproducibly alters the human gut microbiome, Nature, vol.24, issue.7484, pp.559-63, 2014.
DOI : 10.1111/j.1365-294X.1993.tb00005.x

D. Filippo, C. Cavalieri, D. , D. Paola, M. Ramazzotti 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.10, issue.23, pp.14691-14697, 2010.
DOI : 10.1023/A:1026096204727

F. Delsuc, J. Metcalf, W. Parfrey, L. Song, S. Gonz-alez et al., Convergence of gut microbiomes in myrmecophagous mammals, Molecular Ecology, vol.108, issue.Suppl. 1, pp.1301-1318, 2014.
DOI : 10.1073/pnas.1017956108

A. Estrada, P. Garber, A. Rylands, C. Roos, E. Fernandez-duque et al., Impending extinction crisis of the world???s primates: Why primates matter, Science Advances, vol.53, issue.2, p.1600946, 2017.
DOI : 10.1111/1365-2664.12452

C. Evans, K. Lepard, J. Kwak, M. Stancukas, S. Laskowski et al., Exercise Prevents Weight Gain and Alters the Gut Microbiota in a Mouse Model of High Fat Diet-Induced Obesity, PLoS ONE, vol.11, issue.3, p.92193, 2014.
DOI : 10.1371/journal.pone.0092193.s008

M. Fischbach and J. Segre, Signaling in Host-Associated Microbial Communities, Cell, vol.164, issue.6, pp.1288-300, 2016.
DOI : 10.1016/j.cell.2016.02.037

J. Goodrich, J. Waters, A. Poole, J. Sutter, O. Koren et al., Human Genetics Shape the Gut Microbiome, Cell, vol.159, issue.4, pp.789-99, 2014.
DOI : 10.1016/j.cell.2014.09.053

G. Henderson, F. Cox, S. Ganesh, A. Jonker, W. Young et al., Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range, Scientific Reports, vol.5, issue.1, p.14567, 2015.
DOI : 10.1186/1756-0381-5-19

D. Hird, J. Anderson, and J. Bielitzki, Diarrhea in nonhuman primates: a survey of primate colonies for incidence rates and clinical opinion, Lab Anim Sci, vol.34, pp.465-70, 1984.

E. Hyde, J. Navas-molina, S. Song, J. Kueneman, G. Ackermann et al., ABSTRACT, mSystems, vol.1, issue.4, pp.46-62, 2016.
DOI : 10.1128/mSystems.00046-16

K. Kohl and M. Dearing, Wild-caught rodents retain a majority of their natural gut microbiota upon entrance into captivity, Environmental Microbiology Reports, vol.146, issue.2, pp.191-196, 2014.
DOI : 10.1016/j.vetmic.2010.05.024

T. Kubasova, L. Davidova-gerzova, E. Merlot, M. Medvecky, O. Polansky et al., Housing Systems Influence Gut Microbiota Composition of Sows but Not of Their Piglets, PLOS ONE, vol.82, issue.1, p.170051, 2017.
DOI : 10.1371/journal.pone.0170051.s001

URL : https://hal.archives-ouvertes.fr/hal-01594935

J. Kueneman, D. Woodhams, R. Harris, H. Archer, R. Knight et al., Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity, Proceedings of the Royal Society B: Biological Sciences, vol.7, issue.1839, p.20161553, 2016.
DOI : 10.3389/fmicb.2016.00068

R. Ley, M. Hamady, C. Lozupone, P. Turnbaugh, R. Ramey et al., Evolution of Mammals and Their Gut Microbes, Science, vol.99, issue.12, pp.1647-51, 2008.
DOI : 10.1073/pnas.102164299

A. Loudon, D. Woodhams, L. Parfrey, H. Archer, R. Knight et al., Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus), The ISME Journal, vol.39, issue.4, pp.830-870, 2014.
DOI : 10.1016/j.dld.2007.04.003

M. Mcfall-ngai, M. Hadfield, T. Bosch, H. Carey, T. Domazet-lo-so et al., Animals in a bacterial world, a new imperative for the life sciences, Proceedings of the National Academy of Sciences, vol.110, issue.9, pp.3229-3265, 2013.
DOI : 10.1016/j.copbio.2011.11.028

URL : https://hal.archives-ouvertes.fr/hal-00972300

M. Morotomi, F. Nagai, H. Sakon, and R. Tanaka, Paraprevotella clara gen. nov., sp. nov. and Paraprevotella xylaniphila sp. nov., members of the family 'Prevotellaceae' isolated from human faeces, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.45, issue.4, pp.1895-900, 2009.
DOI : 10.1099/00207713-45-4-832

B. Muegge, J. Kuczynski, D. Knights, J. Clemente, A. Gonz-alez et al., Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans, Science, vol.8, issue.11, pp.970-974, 2011.
DOI : 10.1371/journal.pbio.1000546

J. Oksanen, F. Blanchet, R. Kindt, P. Legendre, P. Minchin et al., vegan: Community ecology package. CRAN-The Comprehensive R Archive Network, 2016.

K. Ormerod, D. Wood, N. Lachner, S. Gellatly, J. Daly et al., Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals, Microbiome, vol.15, issue.12, p.36, 2016.
DOI : 10.1186/s13059-014-0550-8

E. Rosenberg, The Family Prevotellaceae, The prokaryotes, pp.825-832, 2014.
DOI : 10.1007/978-3-642-38954-2_131

M. Serino, E. Luche, S. Gres, A. Baylac, M. Bergé et al., Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota, Gut, vol.61, issue.4, pp.543-53, 2012.
DOI : 10.1136/gutjnl-2011-301012

URL : https://hal.archives-ouvertes.fr/inserm-00726182

E. Sonnenburg, S. Smits, M. Tikhonov, S. Higginbottom, N. Wingreen et al., Diet-induced extinctions in the gut microbiota compound over generations, Nature, vol.19, issue.7585, pp.212-217, 2016.
DOI : 10.1093/protein/gzl044

X. Sun, Z. Hu, W. Jia, C. Duan, and L. Yang, Decaying Cyanobacteria decrease N2O emissions related to diversity of intestinal denitrifiers of Chironomus plumosus, Journal of Limnology, vol.73, issue.AoP, 2014.
DOI : 10.4081/jlimnol.2014.1072

L. Taylor, C. Schwitzer, N. Owen-smith, M. Kreuzer, and M. Clauss, Feeding practices for captive greater kudus (Tragelaphus strepsiceros) in UK collections as compared to diets of free-ranging specimens, J Zoo Aqua Res, vol.1, pp.7-13, 2013.

M. Tucker, ) under experiment, Laboratory Animals, vol.18, issue.4, pp.351-359, 1984.
DOI : 10.1258/002367784780865397

J. Tung, L. Barreiro, M. Burns, J. Grenier, J. Lynch et al., Author response, eLife, vol.44, p.5224, 2015.
DOI : 10.7554/eLife.05224.023

E. Van-opstal and S. Bordenstein, Rethinking heritability of the microbiome, Science, vol.349, issue.6253, pp.1172-1175, 2015.
DOI : 10.1126/science.1240659

H. Wickham, ggplot: An implementation of the grammar of graphics in R. R package version 0.4, 2009.

H. Wilman, J. Belmaker, J. Simpson, C. De-la-rosa, M. Rivadeneira et al., EltonTraits 1.0: Species-level foraging attributes of the world's birds and mammals, Ecology, vol.95, issue.7, p.2027, 2014.
DOI : 10.1890/13-1917.1

G. Wu, J. Chen, C. Hoffmann, K. Bittinger, Y. Chen et al., Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science, vol.107, issue.33, pp.105-113, 2011.
DOI : 10.1073/pnas.1005963107

T. Yatsunenko, F. Rey, M. Manary, I. Trehan, M. Dominguez-bello et al., Human gut microbiome viewed across age and geography, Nature, vol.2, pp.222-229, 2012.
DOI : 10.1198/106186005X59243