H. Tilg, A. Moschen, and A. Kaser, Obesity and the Microbiota, Gastroenterology, vol.136, issue.5, pp.1476-1483, 2009.
DOI : 10.1053/j.gastro.2009.03.030

F. Backhed, Programming of Host Metabolism by the Gut Microbiota, Annals of Nutrition and Metabolism, vol.205, issue.s2, pp.44-52, 2011.
DOI : 10.1084/jem.20081800

F. Backhed, R. Ley, J. Sonnenburg, D. Peterson, and J. Gordon, Host-Bacterial Mutualism in the Human Intestine, Science, vol.307, issue.5717, pp.1915-1920, 2005.
DOI : 10.1126/science.1104816

F. Tsai and W. Coyle, The microbiome and obesity: Is obesity linked to our gut flora?, Current Gastroenterology Reports, vol.3, issue.4, pp.307-313, 2009.
DOI : 10.1111/j.1365-2672.1989.tb05105.x

R. Ley, Obesity and the human microbiome, Current Opinion in Gastroenterology, vol.26, issue.1, pp.5-11, 2010.
DOI : 10.1097/MOG.0b013e328333d751

J. Dibaise, H. Zhang, M. Crowell, R. Krajmalnik-brown, and G. Decker, Gut Microbiota and Its Possible Relationship With Obesity, Mayo Clinic Proceedings, vol.83, issue.4, pp.460-469, 2008.
DOI : 10.4065/83.4.460

M. Million, M. Maraninchi, M. Henry, F. Armougom, and H. Richet, Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii, International Journal of Obesity, vol.40, issue.6, pp.817-825, 2011.
DOI : 10.1080/00071669987890
URL : http://www.nature.com/ijo/journal/v36/n6/pdf/ijo2011153a.pdf

M. Rajilic-stojanovic, H. Smidt, and W. De-vos, Diversity of the human gastrointestinal tract microbiota revisited, Environmental Microbiology, vol.64, issue.9, pp.2125-2136, 2007.
DOI : 10.1111/j.1365-2958.2006.05056.x

P. Scanlan and J. Marchesi, Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces, The ISME Journal, vol.70, issue.12, pp.1183-1193, 2008.
DOI : 10.1099/mic.0.26899-0

Y. Nam, H. Chang, K. Kim, S. Roh, and M. Kim, Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people, The Journal of Microbiology, vol.64, issue.5, pp.491-501, 2008.
DOI : 10.1016/S1389-1723(04)00276-2

S. Ott, T. Kuhbacher, M. Musfeldt, P. Rosenstiel, and S. Hellmig, Fungi and inflammatory bowel diseases: Alterations of composition and diversity, Scandinavian Journal of Gastroenterology, vol.67, issue.7, pp.831-841, 2008.
DOI : 10.1038/30492

Y. Chen, Z. Chen, R. Guo, N. Chen, and H. Lu, Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection, Diagnostic Microbiology and Infectious Disease, vol.70, issue.4, pp.492-498, 2011.
DOI : 10.1016/j.diagmicrobio.2010.04.005

Q. Li, C. Wang, Q. Zhang, C. Tang, and N. Li, Use of 18S ribosomal DNA polymerase chain reaction???denaturing gradient gel electrophoresis to study composition of fungal community in 2 patients with intestinal transplants, Human Pathology, vol.43, issue.8, pp.1273-1281, 2012.
DOI : 10.1016/j.humpath.2011.09.017

D. Fredricks, C. Smith, and A. Meier, Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR, Journal of Clinical Microbiology, vol.43, issue.10, pp.5122-5128, 2005.
DOI : 10.1128/JCM.43.10.5122-5128.2005

L. Griffiths, M. Anyim, S. Doffman, M. Wilks, and M. Millar, Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR, Journal of Medical Microbiology, vol.55, issue.9, pp.1187-1191, 2006.
DOI : 10.1099/jmm.0.46510-0

H. Poinar, M. Kuch, K. Sobolik, I. Barnes, and A. Stankiewicz, A molecular analysis of dietary diversity for three archaic Native Americans, Proceedings of the National Academy of Sciences, vol.280, issue.5361, pp.4317-4322, 2001.
DOI : 10.1126/science.280.5361.190

C. Stensvold, M. Lebbad, and J. Verweij, The impact of genetic diversity in protozoa on molecular diagnostics, Trends in Parasitology, vol.27, issue.2, pp.53-58, 2011.
DOI : 10.1016/j.pt.2010.11.005

J. Slapeta, D. Moreira, and P. Lopez-garcia, The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes, Proceedings of the Royal Society B: Biological Sciences, vol.81, issue.1-4, pp.2073-2081, 2005.
DOI : 10.1023/A:1020547517255

J. Pounder, K. Simmon, C. Barton, S. Hohmann, and M. Brandt, Discovering Potential Pathogens among Fungi Identified as Nonsporulating Molds, Journal of Clinical Microbiology, vol.45, issue.2, pp.568-571, 2007.
DOI : 10.1128/JCM.01684-06
URL : http://jcm.asm.org/content/45/2/568.full.pdf

S. Atkins and I. Clark, Fungal molecular diagnostics: a mini review, J Appl Genet, vol.45, pp.3-15, 2004.

W. Dong, J. Liu, Y. J. Wang, L. Zhou, and S. , Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding, PLoS ONE, vol.25, issue.4, p.35071, 2012.
DOI : 10.1371/journal.pone.0035071.s004
URL : http://doi.org/10.1371/journal.pone.0035071

P. Taberlet, L. Gielly, G. Pautou, and J. Bouvet, Universal primers for amplification of three non-coding regions of chloroplast DNA, Plant Molecular Biology, vol.250, issue.5, pp.1105-1109, 1991.
DOI : 10.1007/BF00037152

R. Khatib, K. Riederer, J. Ramanathan, J. Baran, and . Jr, Faecal fungal flora in healthy volunteers and inpatients, Mycoses, vol.27, issue.5, pp.151-156, 2001.
DOI : 10.1099/00222615-29-1-51

S. Goerges, J. Mounier, M. Rea, R. Gelsomino, and V. Heise, Commercial Ripening Starter Microorganisms Inoculated into Cheese Milk Do Not Successfully Establish Themselves in the Resident Microbial Ripening Consortia of a South German Red Smear Cheese, Applied and Environmental Microbiology, vol.74, issue.7, pp.2210-2217, 2008.
DOI : 10.1128/AEM.01663-07
URL : https://hal.archives-ouvertes.fr/hal-00557107

F. Giraud, T. Giraud, G. Aguileta, E. Fournier, and R. Samson, Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing, International Journal of Food Microbiology, vol.137, issue.2-3, pp.204-213, 2010.
DOI : 10.1016/j.ijfoodmicro.2009.11.014

M. Ghannoum, R. Jurevic, P. Mukherjee, F. Cui, and M. Sikaroodi, Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals, PLoS Pathogens, vol.42, issue.1, p.1000713, 2010.
DOI : 10.1371/journal.ppat.1000713.s003

D. Asefa, R. Gjerde, M. Sidhu, S. Langsrud, and C. Kure, Moulds contaminants on Norwegian dry-cured meat products, International Journal of Food Microbiology, vol.128, issue.3, pp.435-439, 2009.
DOI : 10.1016/j.ijfoodmicro.2008.09.024

A. Rodriguez, M. Rodriguez, M. Andrade, and J. Cordoba, Development of a multiplex real-time PCR to quantify aflatoxin, ochratoxin A and patulin producing molds in foods, International Journal of Food Microbiology, vol.155, issue.1-2, pp.10-18, 2012.
DOI : 10.1016/j.ijfoodmicro.2012.01.007

M. Klich, Health effects of Aspergillus in food and air, Toxicology and Industrial Health, vol.263, issue.9-10, pp.657-667, 2009.
DOI : 10.3852/08-078

A. Saleh and . Kabli, Studies on Fungal Communities Associated with Litter of Plant Cover at Al-Taif Province, Saudi Arabia, Met env and Arid Land Agric, Sci, vol.18, pp.87-98, 2007.

J. Valdez, M. Makuch, A. Ordovini, J. Frisvad, and D. Overy, spp. isolated from garlic in two regions in Argentina, Plant Pathology, vol.81, issue.424, pp.352-361, 2009.
DOI : 10.1007/978-1-4615-6391-4

Y. Inoue, Y. Matsuwaki, S. Shin, J. Ponikau, and H. Kita, Nonpathogenic, Environmental Fungi Induce Activation and Degranulation of Human Eosinophils, The Journal of Immunology, vol.175, issue.8, pp.5439-5447, 2005.
DOI : 10.4049/jimmunol.175.8.5439

S. Sonjak, M. Licen, J. Frisvad, and N. Gunde-cimerman, The mycobiota of three dry-cured meat products from Slovenia, Food Microbiology, vol.28, issue.3, pp.373-376, 2011.
DOI : 10.1016/j.fm.2010.09.007

M. Bragulat, M. Abarca, and F. Cabanes, Low occurrence of patulin- and citrinin-producing species isolated from grapes, Letters in Applied Microbiology, vol.13, issue.4, pp.286-289, 2008.
DOI : 10.1080/02652039609374451

G. Westwood, S. Huang, and N. Keyhani, Allergens of the entomopathogenic fungus Beauveria bassiana, Clin Mol Allergy, vol.3, issue.1, 2005.

A. Chai, L. Denning, D. Warn, and P. , in human disease, Critical Reviews in Microbiology, vol.29, issue.4, pp.282-298, 2010.
DOI : 10.1007/s15010-001-9170-9

S. Yim, J. Kim, J. Ko, Y. Lee, and Y. Choe, Molecular Analysis of Malassezia Microflora on the Skin of the Patients with Atopic Dermatitis, Annals of Dermatology, vol.22, issue.1, pp.41-47, 2010.
DOI : 10.5021/ad.2010.22.1.41

Y. Lee, H. Byun, B. Kim, D. Kim, and Y. Lim, Species on the Scalp in Korean Seborrheic Dermatitis Patients, Annals of Dermatology, vol.23, issue.2, pp.156-161, 2011.
DOI : 10.5021/ad.2011.23.2.156

I. Abdullahi, M. Koerbler, H. Stachewicz, and S. Winter, The 18S rDNA sequence of Synchytrium endobioticum and its utility in microarrays for the simultaneous detection of fungal and viral pathogens of potato, Applied Microbiology and Biotechnology, vol.244, issue.3, pp.368-375, 2005.
DOI : 10.1007/s00253-005-1952-z

P. Pandey, J. Siddharth, P. Verma, A. Bavdekar, and M. Patole, Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers, Journal of Biosciences, vol.173, issue.2, pp.221-226, 2012.
DOI : 10.1128/AEM.72.4.2756-2764.2006

M. Hong, J. Kim, H. Bae, N. Lee, and Y. Shin, Atractylodes japonica Koidzumi inhibits the production of proinflammatory cytokines through inhibition of the NF-??B/I??B signal pathway in HMC-1 human mast cells, Archives of Pharmacal Research, vol.274, issue.6, pp.843-851, 2010.
DOI : 10.1007/s12272-010-0606-6

L. Parfrey, W. Walters, and R. Knight, Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions, Frontiers in Microbiology, vol.2, p.153, 2011.
DOI : 10.3389/fmicb.2011.00153

S. Wright, Protozoan Infections of the Gastrointestinal Tract, Infectious Disease Clinics of North America, vol.26, issue.2, pp.2323-2339, 2012.
DOI : 10.1016/j.idc.2012.03.009

B. Kullberg, O. Lashof, and A. , Epidemiology of opportunistic invasive mycoses, Eur J Med Res, vol.7, issue.5, pp.183-191, 2002.

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1038/scientificamerican1179-98

J. Leeming and F. Notman, Improved methods for isolation and enumeration of Malassezia furfur from human skin, J Clin Microbiol, vol.25, pp.2017-2019, 1987.

V. Thomas, K. Herrera-rimann, D. Blanc, and G. Greub, Biodiversity of Amoebae and Amoeba-Resisting Bacteria in a Hospital Water Network, Applied and Environmental Microbiology, vol.72, issue.4, pp.2428-2438, 2006.
DOI : 10.1128/AEM.72.4.2428-2438.2006

J. Schroeder, G. Booton, J. Hay, I. Niszl, and D. Seal, Use of Subgenic 18S Ribosomal DNA PCR and Sequencing for Genus and Genotype Identification of Acanthamoebae from Humans with Keratitis and from Sewage Sludge, Journal of Clinical Microbiology, vol.39, issue.5, pp.1903-1911, 2001.
DOI : 10.1128/JCM.39.5.1903-1911.2001

H. Santos, R. Bandea, L. Martins, H. De-macedo, and R. Peralta, Differential identification of Entamoeba spp. based on the analysis of 18S rRNA, Parasitology Research, vol.8, issue.4, pp.883-888, 2010.
DOI : 10.1590/S1413-86702007000300013

M. Kuiper, R. Valster, B. Wullings, H. Boonstra, and H. Smidt, Quantitative Detection of the Free-Living Amoeba Hartmannella vermiformis in Surface Water by Using Real-Time PCR, Applied and Environmental Microbiology, vol.72, issue.9, pp.5750-5756, 2006.
DOI : 10.1128/AEM.00085-06

M. Pelandakis and P. Pernin, Use of Multiplex PCR and PCR Restriction Enzyme Analysis for Detection and Exploration of the Variability in the Free-Living Amoeba Naegleria in the Environment, Applied and Environmental Microbiology, vol.68, issue.4, pp.2061-2065, 2002.
DOI : 10.1128/AEM.68.4.2061-2065.2002

A. Dopheide, G. Lear, R. Stott, and G. Lewis, Molecular Characterization of Ciliate Diversity in Stream Biofilms, Applied and Environmental Microbiology, vol.74, issue.6, pp.1740-1747, 2008.
DOI : 10.1128/AEM.01438-07

J. Provan, S. Murphy, and C. Maggs, Universal plastid primers for Chlorophyta and Rhodophyta, European Journal of Phycology, vol.51, issue.1, pp.43-50, 2004.
DOI : 10.1017/S0967026202003827
URL : http://www.tandfonline.com/doi/pdf/10.1080/09670260310001636668?needAccess=true

S. Senapin, K. Phiwsaiya, P. Kiatmetha, and B. Withyachumnarnkul, Development of primers and a procedure for specific identification of the diatom Thalassiosira weissflogii, Aquaculture International, vol.5, issue.4, pp.693-704, 2010.
DOI : 10.1007/s10126-002-0075-0

S. Lin, H. Zhang, Y. Hou, L. Miranda, and D. Bhattacharya, Development of a Dinoflagellate-Oriented PCR Primer Set Leads to Detection of Picoplanktonic Dinoflagellates from Long Island Sound, Applied and Environmental Microbiology, vol.72, issue.8, pp.5626-5630, 2006.
DOI : 10.1128/AEM.00586-06

M. Kolisko, J. Silberman, I. Cepicka, N. Yubuki, and K. Takishita, A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats, Environmental Microbiology, vol.161, pp.2700-2710, 2010.
DOI : 10.1093/oxfordjournals.molbev.a003732

A. Mullner, D. Angeler, R. Samuel, E. Linton, and R. Triemer, Phylogenetic analysis of phagotrophic, phototrophic and osmotrophic euglenoids by using the nuclear 18S rDNA sequence, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.51, issue.3, pp.783-791, 2001.
DOI : 10.1099/00207713-51-3-783

M. Desquesnes, G. Mclaughlin, A. Zoungrana, and A. Davila, Detection and identification of Trypanosoma of African livestock through a single PCR based on internal transcribed spacer 1 of rDNA, International Journal for Parasitology, vol.31, issue.5-6, pp.610-614, 2001.
DOI : 10.1016/S0020-7519(01)00161-8

H. Callahan, R. Litaker, and E. Noga, Molecular Taxonomy of the Suborder Bodonina (Order Kinetoplastida), Including the Important Fish Parasite, Ichthyobodo necator, The Journal of Eukaryotic Microbiology, vol.17, issue.2, pp.119-128, 2002.
DOI : 10.1016/S0166-6851(98)00184-4

N. Chabchoub, R. Abdelmalek, F. Mellouli, F. Kanoun, and M. Thellier, Genetic identification of intestinal microsporidia species in immunocompromised patients in Tunisia, Am J Trop Med Hyg, vol.80, pp.24-27, 2009.
URL : https://hal.archives-ouvertes.fr/pasteur-00859425

D. Hayes, R. Anderson, and R. Walker, Identification of Trichomonadid Protozoa from the Bovine Preputial Cavity by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism Typing, Journal of Veterinary Diagnostic Investigation, vol.36, issue.4, pp.390-394, 2003.
DOI : 10.1177/104063870301500104

H. Mirhendi, K. Makimura, K. Zomorodian, T. Yamada, and T. Sugita, A simple PCR-RFLP method for identification and differentiation of 11 Malassezia species, Journal of Microbiological Methods, vol.61, issue.2, pp.281-284, 2005.
DOI : 10.1016/j.mimet.2004.11.016

T. White, T. Burns, S. Lee, and J. Taylor, Amplification and direct sequencing of fungal ribosomal RNA genes for phylognetics. PCR protocols: a guide and applications, pp.315-322, 1990.

T. Stoeck, B. Hayward, G. Taylor, R. Varela, and S. Epstein, A Multiple PCR-primer Approach to Access the Microeukaryotic Diversity in Environmental Samples, Protist, vol.157, issue.1, pp.31-43, 2006.
DOI : 10.1016/j.protis.2005.10.004