P. Hugon, J. Lagier, and P. Colson, repertoire of human gut microbes, Microb Pathog, vol.106, pp.103-115, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01478556

M. K. Mirzaei and M. Cf, Ménage à trois in the human gut: interactions between host, bacteria and phages, Nat Rev Microbiol, vol.15, pp.397-408, 2017.

P. Manrique, M. Dills, and M. J. Young, the human gut phage community and its implications for health and disease, Viruses, vol.9, p.141, 2017.

. Bedarf, F. Hildebrand, and . Coelho-lp, Functional implications of microbial and viral gut metagenome changes in early stage l-DOPa-naïve Parkinson's disease patients

, Genome Med, vol.9, p.39, 2017.

C. Stensvold-cr and . Cg, current status of blastocystis: a personal view, Parasitol Int, vol.65, pp.763-71, 2016.

. Coyle-cm, J. Varughese, and . Weiss-lm, Blastocystis: to treat or not to treat?, Clin Infect Dis, vol.54, pp.105-115, 2012.

. Wawrzyniak-i, P. Poirier, and . Viscogliosi-e, an unrecognized parasite: an overview of pathogenesis and diagnosis, Ther Adv Infect Dis, vol.1, pp.167-78, 2013.

H. Cammarota-g,-ianiro-g,-tilg, european consensus conference on faecal microbiota transplantation in clinical practice, Gut, vol.66, pp.569-80, 2017.

P. D. Scanlan and M. Stensvold-cr,-rajili?-stojanovi?, the microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota, FEMS Microbiol Ecol, vol.90, pp.326-356, 2014.

J. Stensvold-cr and K. Jirk?-pomajbíková, are human intestinal eukaryotes beneficial or commensals?, PLoS Pathog, vol.11, p.1005039, 2015.

P. D. Scanlan and M. , Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and-independent analysis of faeces, Isme J, vol.2, pp.1183-93, 2008.

J. D. Ramírez, . Flórez-c, and M. Olivera, Blastocystis subtyping and its association with intestinal parasites in children from different geographical regions of colombia, PLoS One, vol.12, p.172586, 2017.

F. Beghini, . Pasolli-e, and . Truong-td, large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome, Isme J, vol.11, pp.2848-63, 2017.

B. Curtis, lateral gene transfer in the adaptation of the anaerobic parasite blastocystis to the gut, Curr Biol, vol.27, pp.807-827, 2017.

H. B. Andersen-lo,-bonde-i,-nielsen, a retrospective metagenomics approach to studying Blastocystis, FEMS Microbiol Ecol, vol.91, pp.1-9, 2015.

, colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota, Sci Rep, vol.6, p.25255, 2016.

. Falony-g, M. Joossens, and S. Vieira-silva, Population-level analysis of gut microbiome variation, Science, vol.352, pp.560-564, 2016.

D. Vandeputte and . Vanleeuwen-r, Practical considerations for large-scale gut microbiome studies, FEMS Microbiol Rev, vol.41, pp.154-67, 2017.

W. Wa and . Caporaso-jg, PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers, Bioinformatics, vol.27, pp.1159-61, 2011.

H. Tito-ry and M. Joossens, Brief report: dialister as a microbial marker of disease activity in spondyloarthritis, Arthritis Rheumatol, vol.69, pp.114-135, 2017.

F. Hildebrand and . Voigt-ay, lotuS: an efficient and user-friendly OtU processing pipeline, Microbiome, vol.2, p.30, 2014.
DOI : 10.1186/2049-2618-2-30
URL : https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/2049-2618-2-30

. Edgar-rc, UParSe: highly accurate OtU sequences from microbial amplicon reads, Nat Methods, vol.10, pp.996-1004, 2013.

P. Mn and P. S. Dehal, Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix, Mol Biol Evol, vol.26, pp.1641-50, 2009.

. Tito-ry, Gut, vol.0, pp.1-10, 2018.

D. Bachar and S. , the Protist ribosomal reference database (Pr2): a catalog of unicellular eukaryote small sub-unit rrna sequences with curated taxonomy, Nucleic Acids Res, vol.41, pp.597-604, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01253994

Q. Wang and J. M. , naive Bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy, Appl Environ Microbiol, vol.73, pp.5261-5268, 2007.

S. M. Scicluna, B. , and C. Cg, Dna barcoding of blastocystis, Protist, vol.157, pp.77-85, 2006.

C. Stensvold-cr and . Cg, Molecular identification and subtype analysis of blastocystis, Curr Protoc Microbiol, vol.43, pp.20-22, 2016.

K. D. Pruitt, M. Tatusova-t, and . Dr, ncBi reference sequences (refSeq): a curated nonredundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res, vol.35, pp.61-66, 2007.

S. Kumar and K. Stecher-g,-tamura, Mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

D. Mcdonald, . Hyde-e, and J. W. Debelius, american gut: an Open Platform for citizen Science Microbiome research, mSystems, vol.3, pp.31-49, 2018.

J. K. Goodrich, W. Jl, and . Poole-ac, Human genetics shape the gut microbiome, Cell, vol.159, pp.789-99, 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.975-83, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00825471

. Stensvold, Blastocystis: genetic diversity and molecular methods for diagnosis and epidemiology, Trop Parasitol, vol.3, pp.26-34, 2013.

P. J. Mcmurdie and S. Holmes, phyloseq: an r package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, p.61217, 2013.

J. Oksanen and P. Kindt-r,-legendre, the vegan package, Community ecology package, vol.10, pp.631-638, 2007.

Y. Benjamini and Y. Hochberg, controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc Series B Stat Methodol, pp.289-300, 1995.

K. Faust, conet app: inference of biological association networks using cytoscape, F1000Res, vol.5, p.1519, 2016.

M. B. Brown, 400: a method for combining non-independent, one-sided tests of significance, Biometrics, vol.31, pp.987-92, 1975.

J. Halfvarson, . Brislawn-cj, and . Lamendella-r, Dynamics of the human gut microbiome in inflammatory bowel disease, Nat Microbiol, vol.2, p.17004, 2017.

S. M. , the role of Blastocystis sp. and Dientamoeba fragilis in irritable bowel syndrome: a systematic review and meta-analysis, Parasitol Res, vol.116, pp.1-11, 2017.

P. Poirier and W. , Vivarès cP, et al. new insights into Blastocystis spp.: a potential link with irritable bowel syndrome, PLoS Pathog, vol.8, p.1002545, 2012.

D. Mc and J. Wisnewsky, akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology, Gut, vol.65, pp.426-462, 2015.

, Belzer c, geurts l, et al. cross-talk between akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proc Natl Acad Sci U S A, vol.110, pp.9066-71, 2013.

H. Plovier, Druart c, et al. a purified membrane protein from akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice, Nat Med, vol.23, pp.107-120, 2017.

D. Vandeputte, . Falony-g, and S. Vieira-silva, Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates, Gut, vol.65, pp.57-62, 2016.

. Stensvold-cr, D. B. Christiansen, and O. Ke, Blastocystis sp. subtype 4 is common in Danish Blastocystis-positive patients presenting with acute diarrhea, Am J Trop Med Hyg, vol.84, pp.883-888, 2011.

M. V. Domínguez-márquez and . Guna-r,-muñoz-c, High prevalence of subtype 4 among isolates of Blastocystis hominis from symptomatic patients of a health district of Valencia (Spain), Parasitol Res, vol.105, pp.949-55, 2009.

H. M. Roager, B. Hansen-lb, and . Mi, colonic transit time is related to bacterial metabolism and mucosal turnover in the gut, Nat Microbiol, vol.1, p.16093, 2016.

S. Vieira-silva, F. G. Darzi, and Y. , Species-function relationships shape ecological properties of the human gut microbiome, Nat Microbiol, vol.1, p.16088, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01518385

. Le-chatelier-e,-nielsen-t and J. Qin, richness of human gut microbiome correlates with metabolic markers, Nature, vol.500, pp.541-547, 2013.

O. 'brien-andersen-l, K. Ab, and H. M. Roager, associations between common intestinal parasites and bacteria in humans as revealed by qPcr, Eur J Clin Microbiol Infect Dis, vol.35, pp.1427-1458, 2016.

J. Qin and J. Li-r,-raes, a human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010.
URL : https://hal.archives-ouvertes.fr/cea-00908974

D. Vandeputte and K. Kathagen-g,-d'hoe, Quantitative microbiome profiling links gut community variation to microbial load, Nature, p.551, 2017.

M. Schneeberger, akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice, Sci Rep, vol.5, p.16643, 2015.

. Terveer-em and Y. H. Van-beurden, Faecal microbiota transplantation in clinical practice, Gut, vol.67, 2018.