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Original article
Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota
  1. Raul Y Tito1,2,3,
  2. Samuel Chaffron4,
  3. Clara Caenepeel5,
  4. Gipsi Lima-Mendez1,2,
  5. Jun Wang1,2,
  6. Sara Vieira-Silva1,2,
  7. Gwen Falony1,2,
  8. Falk Hildebrand6,
  9. Youssef Darzi1,2,
  10. Leen Rymenans1,2,
  11. Chloë Verspecht1,2,
  12. Peer Bork6,7,8,
  13. Severine Vermeire5,
  14. Marie Joossens1,2,
  15. Jeroen Raes1,2
  1. 1 Department of Microbiology and Immunology, Rega Institute, KU Leuven, University of Leuven, Leuven, Belgium
  2. 2 VIB, Center for Microbiology, Leuven, Belgium
  3. 3 Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
  4. 4 Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004, Université de Nantes, École Centrale de Nantes, Nantes, France
  5. 5 Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
  6. 6 European Molecular Biology Laboratory, Heidelberg, Germany
  7. 7 Max Delbrück Centre for Molecular Medicine, Berlin, Germany
  8. 8 Department of Bioinformatics, University of Würzburg, Würzburg, Germany
  1. Correspondence to Professor Jeroen Raes, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven 3000, Belgium; jeroen.raes{at}


Objective Human gut microbiome studies are mainly bacteria- and archaea-oriented, overlooking the presence of single-cell eukaryotes such as Blastocystis, an enteric stramenopiles with worldwide distribution. Here, we surveyed the prevalence and subtype variation of Blastocystis in faecal samples collected as part of the Flemish Gut Flora Project (FGFP), a Western population cohort. We assessed potential links between Blastocystis subtypes and identified microbiota–host covariates and quantified microbiota differentiation relative to subtype abundances.

Design We profiled stool samples from 616 healthy individuals from the FGFP cohort as well as 107 patients with IBD using amplicon sequencing targeting the V4 variable region of the 16S rRNA and 18S rRNA genes. We evaluated associations of Blastocystis, and their subtypes, with host parameters, diversity and composition of bacterial and archaeal communities.

Results Blastocystis prevalence in the non-clinical population cohort was 30% compared with 4% among Flemish patients with IBD. Within the FGFP cohort, out of 69 previously identified gut microbiota covariates, only age was associated with Blastocystis subtype carrier status. In contrast, a strong association between microbiota community composition and Blastocystis subtypes was observed, with effect sizes larger than that of host covariates. Microbial richness and diversity were linked to both Blastocystis prevalence and subtype variation. All Blastocystis subtypes detected in this cohort were found to be less prevalent in Bacteroides enterotyped samples. Interestingly, Blastocystis subtypes 3 and 4 were inversely correlated with Akkermansia, suggesting differential associations of subtypes with host health.

Conclusions These results emphasise the role of Blastocystis as a common constituent of the healthy gut microbiota. We show its prevalence is reduced in patients with active IBD and demonstrate that subtype characterisation is essential for assessing the relationship between Blastocystis, microbiota profile and host health. These findings have direct clinical applications, especially in donor selection for faecal transplantation.

  • Blastocystis
  • Microbiota
  • FGFP

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  • Contributors Conception and design of the study: RYT and JR; data collection: RYT, CC, MJ, SC, JW, SV-S, GF, YD, LR and CV; data preparation: RYT, MJ, CC, JW, SVS, FH and YD; statistical analysis, data analysis and interpretation: RYT, MJ, SC, SVS, GF, GL-M, JW, FH, PB, SV and JR; writing and critical revision of the manuscript: RYT, MJ, SC, GF, SV-S and JR. All authors approved the final version for publication.

  • Funding The FGFP was funded with support of the Flemish government (IWT130359), the Research Fund–Flanders (FWO) Odysseus program (G.0924.09), the King Baudouin Foundation (2012-J80000-004), FP7 METACARDIS HEALTH-F4-2012-305312, VIB, the Rega institute for Medical Research, and KU Leuven. SV-S is supported by Marie Curie Actions FP7 People COFUND–Proposal 267139 (acronym OMICS@VIB). MJ, SV-S, GL-M, SC and JW are supported by postdoctoral (five) fellowships, from the FWO.

  • Competing interests None declared.

  • Patient consent Not required.

  • Ethics approval GFP procedures were approved by the medical ethics committee of the University of Brussels–Brussels University Hospital (approval 143201215505, 5/12/2012). The local ethical committee approved the study (B322201213950/S53684).

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement The datasets generated and analysed during the current study are available upon reasonable request to the corresponding author. In line with the ethical protocol, data will be made available after a data transfer agreement has been signed.

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