K. S. Tan, New insights on classification, identification, and clinical relevance of Blastocystis spp, Clin. Microbiol. Rev, vol.21, pp.639-665, 2008.

C. G. Clark, M. Van-der-giezen, M. A. Alfellani, and C. R. Stensvold, Recent developments in Blastocystis research, Adv. Parasitol, vol.82, pp.1-32, 2013.

, Scientific RepoRts |, vol.6

A. Bart, Diagnosis and subtype analysis of Blastocystis sp. in 442 patients in a hospital setting in the Netherlands, BMC Infect. Dis, vol.13, p.389, 2013.

I. Wawrzyniak, Blastocystis, an unrecognized parasite: an overview of pathogenesis and diagnosis, Ther. Adv. Infect. Dis, vol.1, pp.167-178, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01071806

D. El-safadi, Children of Senegal River Basin show the highest prevalence of Blastocystis sp. ever observed worldwide, BMC Infect. Dis, vol.14, p.164, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-00981310

K. F. Boorom, Oh my aching gut: irritable bowel syndrome, Blastocystis, and asymptomatic infection, Parasit. Vectors, vol.1, p.40, 2008.

K. S. Tan, H. Mirza, J. D. Teo, B. Wu, and P. A. Macary, Current views on the clinical relevance of Blastocystis spp, Curr. Infect. Dis. Rep, vol.12, pp.28-35, 2010.

P. Poirier, I. Wawrzyniak, C. P. Vivarès, F. Delbac, and H. El-alaoui, New insights into Blastocystis spp.: A potential link with irritable bowel syndrome, PLos Pathog, vol.8, p.1002545, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00814144

P. D. Scanlan, Blastocystis: Past pitfalls and future perspectives, Trends Parasitol, vol.28, pp.327-334, 2012.

F. Denoeud, Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite, Genome Biol, vol.12, p.29, 2011.
URL : https://hal.archives-ouvertes.fr/inserm-00617212

I. Wawrzyniak, Characterization of two cysteine proteases secreted by Blastocystis ST7, a human intestinal parasite, Parasitol. Int, vol.61, pp.437-442, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00814173

I. Wawrzyniak, Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1, Genom. Data, vol.4, pp.22-23, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01247485

M. X. Lim, Differential regulation of proinflammatory cytokine expression by mitogen-activated protein kinases in macrophages in response to intestinal parasite infection, Infect. Immun, vol.82, pp.4789-4801, 2014.

Z. Wu, H. Mirza, and K. S. Tan, Intra-subtype variation in enteroadhesion accounts for differences in epithelial barrier disruption and is associated with metronidazole resistance in Blastocystis subtype-7, PLos Negl. Trop. Dis, vol.8, pp.27-31, 2014.

Z. Wu, H. Mirza, J. D. Teo, and K. S. Tan, Strain-dependent induction of human enterocyte apoptosis by Blastocystis disrupts epithelial barrier and ZO-1 organization in a caspase 3-and 9-dependent manner, Biomed Res. Int, p.209163, 2014.

P. D. Scanlan and J. R. Marchesi, Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culturedependent and -independent analysis of faeces, ISME J, vol.2, pp.1183-1193, 2008.

P. D. Scanlan, The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota, FEMS Microbiol. Ecol, vol.90, pp.326-330, 2014.

A. M. Petersen, Active ulcerative colitis associated with low prevalence of Blastocystis and Dientamoeba fragilis infection, Scand. J. Gastroenterol, vol.48, pp.638-639, 2013.

L. R. Krogsgaard, A. L. Engsbro, C. R. Stensvold, H. V. Nielsen, and P. Bytzer, The prevalence of intestinal parasites is not greater among individuals with irritable bowel syndrome: a population-based case-control study, Clin. Gastroenterol. Hepatol, vol.13, pp.507-513, 2015.

N. G. Rossen, Low prevalence of Blastocystis sp. in active ulcerative colitis patients, Eur. J. Clin. Microbiol. Infect. Dis, vol.34, pp.1039-1044, 2015.

C. Manichanh, N. Borruel, F. Casellas, and F. Guarner, The gut microbiota in IBD, Nat. Rev. Gastroenterol. Hepatol, vol.9, pp.599-608, 2012.

A. Lyra and S. Lahtinen, Dysbiosis of the intestinal microbiota in IBS in Current concepts in colonic disorders, pp.261-276, 2012.

T. A. Pham and T. D. Lawley, Emerging insights on intestinal dysbiosis during bacterial infections, Curr. Opin. Microbiol, vol.17, pp.67-74, 2014.

M. Raetz, Parasite-induced TH1 cells and intestinal dysbiosis cooperate in IFN-? -dependent elimination of Paneth cells, Nat. Immunol, vol.14, pp.136-142, 2013.

M. F. Torres, Influence of bacteria from the duodenal microbiota of patients with symptomatic giardiasis on the pathogenicity of Giardia duodenalis in gnotoxenic mice, J. Med. Microbiol, vol.49, pp.209-215, 2000.

J. M. Galván-moroyoqui, M. Del-carmen-domínguez-robles, E. Franco, and I. Meza, The interplay between Entamoeba and enteropathogenic bacteria modulates epithelial cell damage, PLos Negl. Trop. Dis, vol.2, p.266, 2008.

A. K. Verma, R. Verma, V. Ahuja, and J. Paul, Real-time analysis of gut flora in Entamoeba histolytica infected patients of Northern India, BMC Microbiol, vol.12, p.183, 2012.

S. Lindgreen, K. L. Adair, and P. Gardner, An evaluation of the accuracy and speed of metagenome analysis tools, Sci. Rep, vol.6, p.19233, 2015.

A. Esposito and M. Kirschberg, How many 16S-based studies should be included in a metagenomic conference? It may be a matter of etymology, FEMS Microbiol. Lett, vol.351, pp.145-146, 2014.

D. H. Parks, G. W. Tyson, P. Hugenholtz, and R. G. Beiko, STAMP: Statistical analysis of taxonomic and functional profiles, Bioinformatics, vol.30, pp.3123-3124, 2014.

L. R. Lopetuso, F. Scaldaferri, V. Petito, and A. Gasbarrini, Commensal Clostridia: leading players in the maintenance of gut homeostasis, Gut Pathog, vol.5, p.23, 2013.

C. Nourrisson, Blastocystis is associated with decrease of fecal microbiota protective bacteria: comparative analysis between patients with irritable bowel syndrome and control subjects, PLos One, vol.9, p.111868, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01111985

L. O. Andersen, I. Bonde, H. B. Nielsen, and C. R. Stensvold, A retrospective metagenomics approach to studying Blastocystis, FEMS Microbiol. Ecol, vol.91, p.72, 2015.

A. Hevia, Intestinal dysbiosis associated with systemic lupus erythematosus, MBio, vol.5, pp.1548-1562, 2014.

C. Milani, Assessing the fecal microbiota: an optimized Ion Torrent 16S rRNA gene-based analysis protocol, PLos One, vol.8, p.68739, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01190517

S. E. Winter and A. J. Bäumler, Why related bacterial species bloom simultaneously in the gut: Principles underlying the 'like will to like' concept, Cell. Microbiol, vol.16, pp.179-184, 2014.

G. Loh and M. Blaut, Role of commensal gut bacteria in inflammatory bowel diseases, Gut Microbes, vol.3, pp.544-555, 2012.

J. R. Brestoff and D. Artis, Commensal bacteria at the interface of host metabolism and the immune system, Nat. Immunol, vol.14, pp.676-684, 2013.

H. M. Hamer, Review article: The role of butyrate on colonic function, Aliment. Pharmacol. Ther, vol.27, pp.104-119, 2008.

J. Tan, The role of short-chain fatty acids in health and disease, Adv. Immunol, vol.121, pp.91-119, 2014.

K. Machiels, A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis, Gut, vol.63, pp.1275-1283, 2013.

H. Sokol, Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients, Proc. Natl. Acad. Sci. USA 105, pp.16731-16736, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00652961

P. D. Scanlan and C. R. Stensvold, Blastocystis: getting to grips with our guileful guest, Trends Parasitol, vol.29, pp.523-529, 2013.

M. J. Broadhurst, Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon, PLos Pathog, vol.8, p.1003000, 2012.

S. C. Lee, Helminth colonization is associated with increased diversity of the gut microbiota, PLos Negl. Trop. Dis, vol.8, p.2880, 2014.

C. Cantacessi, Impact of experimental hookworm infection on the human gut microbiota, J. Infect. Dis, vol.210, pp.1-4, 2014.

J. Luke?, R. Kuchta, T. Scholz, and K. Pomajbíková, Self-) infections with parasites: re-interpretations for the present, Trends Parasitol, vol.30, pp.377-385, 2014.

, Scientific RepoRts |, vol.6

O. Koren, A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets, PLos Comput. Biol, vol.9, p.1002863, 2013.

D. Knights, Rethinking 'enterotypes', Cell Host Microbe, vol.16, pp.433-437, 2014.

P. Poirier, Development and evaluation of a real-time PCR assay for detection and quantification of Blastocystis parasites in human stool samples: Prospective study of patients with hematological malignancies, J. Clin. Microbiol, vol.49, pp.975-983, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00825471

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2013.

H. Maeda, Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria, FEMS Immunol. Med. Microbiol, vol.39, pp.81-86, 2003.

P. D. Schloss, Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol, vol.75, pp.7537-7541, 2009.

Y. Cai, Y. Sun, and . Esprit-tree, Hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time, Nucleic Acids Res, vol.39, p.95, 2011.

J. Goecks, A. Nekrutenko, and J. Taylor, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, vol.11, p.86, 2010.

C. Quast, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2013.

Q. Wang, G. M. Garrity, J. M. Tiedje, and J. R. Cole, Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol, vol.73, pp.5261-5267, 2007.

D. Mcdonald, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, Gigascience, vol.1, p.7, 2012.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

J. G. Caporaso, QIIME allows analysis of high-throughput community sequencing data, Nat. methods, vol.7, pp.335-336, 2010.

P. J. Mcmurdie and S. Holmes, Waste not, want not: why rarefying microbiome data is inadmissible, PLos Comput. Biol, vol.10, p.1003531, 2014.

S. Lê, J. Josse, and F. Husson, FactoMineR : An R package for multivariate analysis, J. Stat. Softw, vol.25, pp.1-18, 2008.

, Scientific RepoRts |, vol.6

, Consortia The Blastocystis Investigation Group

, Philippe Poirier 7,8 , Ivan Wawrzyniak 8 , Frédéric Delbac 8 , Christelle Morelle 9, Guillaume Desoubeaux, vol.7, p.17

, Centre AZM pour la Recherche en Biotechnologies et ses applications

. Département-de-parasitologie-mycologie, 11 Laboratoire de Parasitologie-Mycologie, vol.13

. Service-de-parasitologie, Groupe Hospitalier Pellegrin