A retrospective metagenomics approach to studying Blastocystis

FEMS Microbiology Ecology

Volumn 91, Issue 7, 2015, Pages 1-9

  Andersen, Lee O'Brien ^a   Bonde, Ida ^b,c   Nielsen, H B Henrik Bjorn ^c   Stensvold, Christen Rune ^a  

^a STATENS SERUM INSTITUT   (Denmark)

^b Chalmers University of Technology   (Denmark)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Data mining; Eukaryote; Gut ecology; Microbiota; NGS; Parasite

Indexed keywords

DATA MINING; DATA SET; EUKARYOTE; GENE EXPRESSION; GENOMICS; MICROBIAL COMMUNITY; PARASITE;

BACTERIA (MICROORGANISMS); BACTEROIDES; BLASTOCYSTIS; EUKARYOTA; PREVOTELLA; RUMINOCOCCUS;

ADULT; BACTEROIDES; BLASTOCYSTIS; CROHN DISEASE; FECES; FEMALE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MALE; METAGENOMICS; MICROBIOLOGY; MIDDLE AGED; PARASITOLOGY; RETROSPECTIVE STUDY; ULCERATIVE COLITIS;

ADULT; BACTEROIDES; BLASTOCYSTIS; COLITIS, ULCERATIVE; CROHN DISEASE; FECES; FEMALE; HUMANS; MALE; METAGENOMICS; MIDDLE AGED; RETROSPECTIVE STUDIES;

EID: 84949209280     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1093/femsec/fiv072     Document Type: Article

References (33)

1. Alfellani MA, Stensvold CR, Vidal-Lapiedra A, et al. Variable geographic distribution of Blastocystis subtypes and its potential implications. Acta Trop 2013a;126:11-8.
2. Alfellani MA, Taner-Mulla D, Jacob AS, et al. Genetic diversity of Blastocystis in livestock and zoo animals. Protist 2013b;164:497-509.
3. Andersen LO, Vedel Nielsen H, Stensvold CR. Waiting for the human intestinal Eukaryotome. ISME J 2013;7:1253-5.
4. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.
5. Clark CG, van der Giezen M, Alfellani MA, et al. Recent developments in Blastocystis research. Adv Parasit 2013;82:1-32.
6. Denoeud F, Roussel M, Noel B, et al. Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biol 2011;12:R29.
7. Domínguez-Márquez MV, Guna R, Muñoz C, et al. High prevalence of subtype 4 among isolates of Blastocystis hominis from symptomatic patients of a health district of Valencia (Spain). Parasitol Res 2009;105:949-55.
8. Engsbro AL, Stensvold CR, Nielsen HV, et al. Treatment of Dientamoeba fragilis in patients with irritable Bowel syndrome. Am J Trop Med Hyg 2012;87:1046-52.
9. Forsell J, Granlund M, Stensvold CR, et al. Subtype analysis of Blastocystis isolates in Swedish patients. Eur J Clin Microbiol 2012;31:1689-96.
10. Knights D, Ward TL, McKinlay CE, et al. Rethinking "enterotypes". Cell Host Microbe 2014;16:433-7.
11. Koren O, Knights D, Gonzalez A, et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 2013;9:e1002863.
12. Krogsgaard LR, Engsbro AL, Stensvold CR, et al. The prevalence of intestinal parasites is not greater among individuals with irritable Bowel syndrome: a population-based case-control study. Clin Gastroenterol H 2015;13:507-13.
13. McCallum A, Nigam K, Ungar LH. Efficient Clustering of High- Dimensional Data Sets With Application to Reference Matching. Boston, MA, USA: ACM, 2000, 169-78.
14. Malheiros AF, Stensvold CR, Clark CG, et al. Short report: molecular characterization of Blastocystis obtained from members of the indigenous Tapirape ethnic group from the Brazilian Amazon region, Brazil. Am J Trop Med Hyg 2011;85:1050-3.
15. Nielsen HB, Almeida M, Juncker AS, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 2014;32:822-8.
16. Nourrisson C, Scanzi J, Pereira B, et al. Blastocystis is associated with decrease of fecal microbiota protective bacteria: comparative analysis between patients with irritable bowel syndrome and control subjects. PLoS One 2014;9:e111868.
17. Pérez-Brocal V, Clark CG. Analysis of two genomes from the mitochondrion-like organelle of the intestinal parasite Blastocystis: complete sequences, gene content, and genome organization. Mol Biol Evol 2008;25:2475-82.
18. Petersen AM, Stensvold CR, Mirsepasi H, et al. Active ulcerative colitis associated with low prevalence of Blastocystis and Dientamoeba fragilis infection. Scand J Gastroentero 2013;48:638-9.
19. Poirier P, Wawrzyniak I, Albert A, et al. 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 2011;49:975-83.
20. Scanlan PD, Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2008;2:1183-93.
21. Scanlan PD, Stensvold CR. Blastocystis: getting to grips with our guileful guest. Trends Parasitol 2013;29:523-9.
22. Scanlan PD, Stensvold CR, Rajilić-Stojanović M, et al. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS Microbiol Ecol 2014;90:326-30.
23. Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gutmicrobiota analysis of Crohn disease patients. P Natl Acad Sci USA 2008;105:16731-6.
24. Stensvold CR. Comparison of sequencing (barcode region) and sequence-tagged-site PCR for Blastocystis subtyping. J Clin Microbiol 2013;51:190-4.
25. Stensvold CR, Ahmed UN, Andersen LO, et al. Development and evaluation of a genus-specific, probe-based, internal process controlled real-time PCR assay for sensitive and specific detection of Blastocystis. J Clin Microbiol 2012a;50: 1847-51.
26. Stensvold CR, Alfellani M, Clark CG. Levels of genetic diversity vary dramatically between Blastocystis subtypes. Infect Genet Evol 2012b;12:263-73.
27. Stensvold CR, Christiansen DB, Olsen KE, et al. Blastocystis sp. subtype 4 is common in Danish Blastocystis-positive patients presenting with acute diarrhea. Am J Trop Med Hyg 2011;84:883-5.
28. Stensvold CR, Lewis HC, Hammerum AM, et al. Blastocystis: unravelling potential risk factors and clinical significance of a common but neglected parasite. Epidemiol Infect 2009a;137:1655-63.
29. Stensvold CR, Nielsen HV, Mølbak K, et al. Pursuing the clinical significance of Blastocystis-diagnostic limitations. Trends Parasitol 2009b;25:23-9.
30. Stensvold CR, Suresh GK, Tan KSW, et al. Terminology for Blastocystis subtypes - a consensus. Trends Parasitol 2007a;23: 93-6.
31. Stensvold CR, Traub RJ, von Samson-Himmelstjerna G, et al. Blastocystis: subtyping isolates using pyrosequencing technology. Exp Parasitol 2007b;116:111-9.
32. Tan KS. New insights on classification, identification, and clinical relevance of Blastocystis spp. Clin Microbiol Rev 2008;21:639-65.
33. Wawrzyniak I, Courtine D, Osman M, et al. Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1. Genomics Data 2015;4:22-3.