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FEMS Microbiol Ecol. 2015 Jul;91(7). pii: fiv072. doi: 10.1093/femsec/fiv072. Epub 2015 Jun 29.

A retrospective metagenomics approach to studying Blastocystis.

Author information

1
Unit of Mycology and Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, DK-2300 Copenhagen, Denmark.
2
The Novo Nordisk Foundation Center for Biosustainability, DK-2970 Hørsholm, Denmark Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
3
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
4
Unit of Mycology and Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, DK-2300 Copenhagen, Denmark run@ssi.dk.

Abstract

Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in coabundance gene groups, which are groups of genes that covary across a selection of 316 human faecal samples, hence representing genes originating from a single subtype. The 316 faecal samples were from 236 healthy individuals, 13 patients with Crohn's disease (CD) and 67 patients with ulcerative colitis (UC). The prevalence of Blastocystis was 20.3% in the healthy individuals and 14.9% in patients with UC. Meanwhile, Blastocystis was absent in patients with CD. Individuals with intestinal microbiota dominated by Bacteroides were much less prone to having Blastocystis-positive stool (Matthew's correlation coefficient = -0.25, P < 0.0001) than individuals with Ruminococcus- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities.

KEYWORDS:

NGS; data mining; eukaryote; gut ecology; microbiota; parasite

PMID:
26130823
DOI:
10.1093/femsec/fiv072
[Indexed for MEDLINE]

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