Investigating the role of the anaerobic protist Blastocystis in the gut microbiome by metagenomic analysis

Abstract

Blastocystis are amongst the most prevalent microbial eukaryotes inhabiting the gastrointestinal tracts of mammals. A bioinformatic workflow was developed to detect Blastocystis in gut metagenomic data and applied to 996 publicly available metagenomic sequencing datasets from fecal samples of humans and animals. Blastocystis incidence was determined to be 52.7% in human and 62.6% in animal samples. A Blastocystis subtype-specific distribution was observed both in human and animal carriers and associations between microbial community composition and subtypes was confirmed for humans. Specifically, the Methanobrevibacter genus, Prevotella copri, and species from the Firmicutes phylum were positively associated with the presence of Blastocystis. A tool, Eukfinder, was designed to recover protistan genome sequences from metagenomic data and successfully retrieved five near-complete nuclear genomes and mitochondrial genomes of Blastocystis. Overall, these bioinformatic workflows for analysis of metagenomic data performed well to detect difficult-to-cultivate protists, investigate their genomic diversity and their impact on prokaryotic microbiota.