J. Lagier, M. Million, and P. Hugon, Human Gut Microbiota: Repertoire and Variations, Frontiers in Cellular and Infection Microbiology, vol.2, p.136, 2012.
DOI : 10.3389/fcimb.2012.00136

URL : http://journal.frontiersin.org/article/10.3389/fcimb.2012.00136/pdf

J. Chang, D. Antonopoulos, and A. Kalra, ???Associated Diarrhea, The Journal of Infectious Diseases, vol.38, issue.3, pp.435-443, 2008.
DOI : 10.1016/S0140-6736(89)92749-9

D. Frank, A. St-amand, and R. Feldman, Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases, Proceedings of the National Academy of Sciences, vol.72, issue.10, pp.13780-13785, 2007.
DOI : 10.1128/AEM.00378-06

H. Sokol, P. Seksik, and L. Rigottier-gois, Specificities of the fecal microbiota in inflammatory bowel disease, Inflammatory Bowel Diseases, vol.67, issue.2, pp.106-117, 2006.
DOI : 10.1128/AEM.67.10.4939-4942.2001

P. Turnbaugh, R. Ley, and M. Mahowald, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, vol.20, issue.7122, pp.1027-131, 2006.
DOI : 10.1038/nature05414

H. Zhang, J. Dibaise, and A. Zuccolo, Human gut microbiota in obesity and after gastric bypass, Proceedings of the National Academy of Sciences, vol.89, issue.6, pp.2365-70, 2009.
DOI : 10.1002/bit.20347

N. Larsen, F. Vogensen, . Van-den, and F. Berg, Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults, PLoS ONE, vol.5, issue.2, p.9085, 2010.
DOI : 10.1371/journal.pone.0009085.s003

J. Qin, Y. Li, and Z. Cai, A metagenome-wide association study of gut microbiota in type 2 diabetes, Nature, vol.334, issue.7418, pp.55-60, 2012.
DOI : 10.1126/science.1208344

URL : https://hal.archives-ouvertes.fr/hal-01204262

M. Tong, I. Mchardy, and P. Ruegger, Reprograming of gut microbiome energy metabolism by the FUT2 Crohn???s disease risk polymorphism, The ISME Journal, vol.4, issue.11, pp.2193-206, 2014.
DOI : 10.1080/089106001750462669

C. Lozupone, M. Li, and T. Campbell, Alterations in the Gut Microbiota Associated with HIV-1 Infection, Cell Host & Microbe, vol.14, issue.3, pp.329-368, 2013.
DOI : 10.1016/j.chom.2013.08.006

E. Mutlu, A. Keshavarzian, and J. Losurdo, A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects, PLoS Pathogens, vol.67, issue.2, p.1003829, 2014.
DOI : 10.1371/journal.ppat.1003829.s025

I. Mchardy, X. Li, and M. Tong, HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota, Microbiome, vol.1, issue.1, p.26, 2013.
DOI : 10.1038/nature11319

E. Von-rosenvinge, Y. Song, and J. White, Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota, The ISME Journal, vol.64, issue.7, pp.1354-66, 2013.
DOI : 10.1016/j.autrev.2010.11.009

S. Dillon, E. Lee, and C. Kotter, An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia, Mucosal Immunology, vol.29, issue.4, pp.983-94, 2014.
DOI : 10.1089/aid.2013.0115

I. Vujkovic-cvijin, R. Dunham, and S. Iwai, Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism, Science Translational Medicine, vol.44, issue.193, pp.193-91, 0193.
DOI : 10.1093/nar/gkr201

M. Jenabian, M. El-far, and K. Vyboh, Immunosuppressive Tryptophan Catabolism and Gut Mucosal Dysfunction Following Early HIV Infection, Journal of Infectious Diseases, vol.212, issue.3, pp.355-66, 2015.
DOI : 10.1371/journal.ppat.1003890

URL : https://academic.oup.com/jid/article-pdf/212/3/355/5239165/jiv037.pdf

G. Marchetti, G. Bellistrì, and E. Borghi, Microbial translocation is associated with sustained failure in CD4+ T-cell reconstitution in HIV-infected patients on long-term highly active antiretroviral therapy, AIDS, vol.22, issue.15, pp.2035-2043, 2008.
DOI : 10.1097/QAD.0b013e3283112d29

C. Lozupone, M. Rhodes, and C. Neff, HIV-induced alteration in gut microbiota, Gut Microbes, vol.57, issue.4, pp.562-70, 2014.
DOI : 10.1038/ismej.2011.139

C. Ellis, Z. Ma, and S. Mann, Molecular Characterization of Stool Microbiota in HIV-Infected Subjects by Panbacterial and Order-Level 16S Ribosomal DNA (rDNA) Quantification and Correlations With Immune Activation, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.57, issue.5, p.363, 2011.
DOI : 10.1097/QAI.0b013e31821a603c

J. Vázquez-castellanos, S. Serrano-villar, and A. Latorre, Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals, Mucosal Immunology, vol.35, issue.4, pp.760-72, 2015.
DOI : 10.18637/jss.v035.i03

R. Ferreira, N. Gill, and B. Willing, The Intestinal Microbiota Plays a Role in Salmonella-Induced Colitis Independent of Pathogen Colonization, PLoS ONE, vol.61, issue.5, p.20338, 2011.
DOI : 10.1371/journal.pone.0020338.s002

A. Gori, C. Tincati, and G. Rizzardini, Early Impairment of Gut Function and Gut Flora Supporting a Role for Alteration of Gastrointestinal Mucosa in Human Immunodeficiency Virus Pathogenesis, Journal of Clinical Microbiology, vol.46, issue.2, pp.757-765, 2008.
DOI : 10.1128/JCM.01729-07

R. Sharma, C. Young, and J. Neu, Molecular Modulation of Intestinal Epithelial Barrier: Contribution of Microbiota, Journal of Biomedicine and Biotechnology, vol.3, issue.4, p.305879, 2010.
DOI : 10.1038/nri1057

M. Million, T. Alou, M. Khelaifia, and S. , Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition, Scientific Reports, vol.283, issue.1, p.26051, 2016.
DOI : 10.1002/9780470743386.ch20

URL : https://hal.archives-ouvertes.fr/hal-01439070

A. Mangili, D. Murman, and A. Zampini, Nutrition and HIV Infection: Review of Weight Loss and Wasting in the Era of Highly Active Antiretroviral Therapy from the Nutrition for Healthy Living Cohort, Clinical Infectious Diseases, vol.38, issue.4, pp.836-878, 2006.
DOI : 10.1097/01.qai.0000152647.89008.2b

E. Von-elm, D. Altman, and M. Egger, The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement, Epidemiology, vol.18, issue.6, pp.806-814, 2007.
DOI : 10.1097/EDE.0b013e3181577654

T. Magoç and S. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.5, issue.7, pp.2957-63, 2011.
DOI : 10.1371/journal.pone.0011840

J. Caporaso, J. Kuczynski, and J. Stombaugh, 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

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.22, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btl158

C. Quast, E. Pruesse, and P. Yilmaz, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.35, issue.D1, pp.590-596, 2013.
DOI : 10.1093/nar/gkl856

S. Altschul, W. Gish, and W. Miller, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

L. Guillou, D. Bachar, and S. Audic, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucleic Acids Research, vol.20, issue.D1, pp.597-604, 2013.
DOI : 10.1093/bioinformatics/bth226

URL : https://hal.archives-ouvertes.fr/hal-01253994

A. Boissière, M. Tchioffo, and D. Bachar, Midgut Microbiota of the Malaria Mosquito Vector Anopheles gambiae and Interactions with Plasmodium falciparum Infection, PLoS Pathogens, vol.1, issue.5, p.1002742, 2012.
DOI : 10.1371/journal.ppat.1002742.s005

T. Stoeck, A. Behnke, and R. Christen, Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities, BMC Biology, vol.7, issue.1, p.72, 2009.
DOI : 10.1186/1741-7007-7-72

URL : https://hal.archives-ouvertes.fr/hal-00484166

S. Terrat, R. Christen, and S. Dequiedt, Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure, Microbial Biotechnology, vol.62, issue.1, pp.135-176, 2012.
DOI : 10.1128/AEM.01063-10

URL : https://hal.archives-ouvertes.fr/hal-01546177

P. Mcmurdie and S. Holmes, Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible, PLoS Computational Biology, vol.334, issue.8, p.1003531, 2014.
DOI : 10.1371/journal.pcbi.1003531.s002

S. Squizzato, Y. Park, and N. Buso, The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI, Nucleic Acids Research, vol.43, issue.W1, pp.585-593, 2015.
DOI : 10.1093/nar/gkq313

K. Hutcheson, A test for comparing diversities based on the shannon formula, Journal of Theoretical Biology, vol.29, issue.1, pp.151-155, 1970.
DOI : 10.1016/0022-5193(70)90124-4

N. Segata, J. Izard, and L. Waldron, Metagenomic biomarker discovery and explanation, Genome Biology, vol.12, issue.6, p.60, 2011.
DOI : 10.1101/gr.112730.110

URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2011-12-6-r60?site=genomebiology.biomedcentral.com

K. Rothman, No Adjustments Are Needed for Multiple Comparisons, Epidemiology, vol.1, issue.1, pp.43-49, 1990.
DOI : 10.1097/00001648-199001000-00010

D. Dinh, G. Volpe, and C. Duffalo, Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection, Journal of Infectious Diseases, vol.64, issue.1, pp.19-27, 2015.
DOI : 10.1053/j.gastro.2010.11.049

S. Ott, M. Musfeldt, and D. Wenderoth, Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease, Gut, vol.53, issue.5, pp.685-93, 2004.
DOI : 10.1136/gut.2003.025403

X. Ze, S. Duncan, and P. Louis, Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon, The ISME Journal, vol.34, issue.8, pp.1535-1578, 2012.
DOI : 10.1002/mnfr.200500026

S. Dillon, E. Lee, and C. Kotter, Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection, Mucosal Immunology, vol.762, issue.1, pp.24-37, 2016.
DOI : 10.1016/j.clim.2008.12.003

S. Sankaran, M. George, and E. Reay, Rapid Onset of Intestinal Epithelial Barrier Dysfunction in Primary Human Immunodeficiency Virus Infection Is Driven by an Imbalance between Immune Response and Mucosal Repair and Regeneration, Journal of Virology, vol.82, issue.1
DOI : 10.1128/JVI.01449-07

W. Jia, R. Whitehead, and L. Griffiths, Is the abundance of Faecalibacterium prausnitzii???relevant to Crohn's disease?, FEMS Microbiology Letters, vol.276, issue.(s, pp.138-182, 2010.
DOI : 10.1111/j.1574-6968.2010.02057.x

H. Sokol, P. Seksik, and J. Furet, Low counts of Faecalibacterium prausnitzii in colitis microbiota, Inflammatory Bowel Diseases, vol.40, issue.8, pp.1183-1192, 2009.
DOI : 10.1128/JCM.40.12.4423-4427.2002

URL : https://hal.archives-ouvertes.fr/hal-00657435

H. Sokol, B. Pigneur, and L. Watterlot, Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients, Proceedings of the National Academy of Sciences, vol.41, issue.4, pp.16731-16737, 2008.
DOI : 10.1136/gut.41.4.487

URL : https://hal.archives-ouvertes.fr/hal-00652961

F. Van-immerseel, R. Ducatelle, D. Vos, and M. , Butyric acid-producing anaerobic bacteria as a novel probiotic treatment approach for inflammatory bowel disease, Journal of Medical Microbiology, vol.298, issue.5-6, pp.141-144, 2010.
DOI : 10.1016/j.ijmm.2007.07.016

C. Stephensen, G. Marquis, and R. Jacob, Vitamins C and E in adolescents and young adults with HIV infection, The American Journal of Clinical Nutrition, vol.9, issue.2, pp.870-879, 2006.
DOI : 10.1179/135100004225004814

J. Allard, E. Aghdassi, and J. Chau, Effects of vitamin E and C supplementation on oxidative stress and viral load in HIV-infected subjects, AIDS, vol.12, issue.13, pp.1653-1662, 1998.
DOI : 10.1097/00002030-199813000-00013

S. Mburu, J. Marnewick, and A. Abayomi, Study, Clinical and Developmental Immunology, vol.25, issue.5, p.631063, 2013.
DOI : 10.1186/1475-2891-2-1

C. Sappey, S. Legrand-poels, and M. Best-belpomme, Stimulation of Glutathione Peroxidase Activity Decreases HIV Type 1 Activation after Oxidative Stress, AIDS Research and Human Retroviruses, vol.10, issue.11, pp.1451-61, 1994.
DOI : 10.1089/aid.1994.10.1451

N. Dione, S. Khelaifia, L. Scola, and B. , A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology, Clinical Microbiology and Infection, vol.22, issue.1, pp.53-61, 2016.
DOI : 10.1016/j.cmi.2015.10.032

URL : https://hal.archives-ouvertes.fr/hal-01459959