Genetic diversity of commensal Blastocystis gut protists reveals strain-specific changes in host-interfacing pathways

The human gut microbiome is a microbial ecosystem containing bacteria, archaea, viruses, and microbial eukaryotes. The most common human gut microbial eukaryote is the commensal protist Blastocystis, with an estimated prevalence in industrialized countries at 25%. While the presence of Blastocystis is associated with a significant reduction in pro-inflammatory bacteria and with reduced gut inflammation, little is understood about its role in the gut microbiome and its fundamental biology. Genetic evidence suggests that Blastocystis comprise a group of genetically diverse subtypes, but we lack high quality genomic data for these subtypes and understanding of their functional similarities and differences. Here, we cultivate 6 Blastocystis strains spanning the genetic diversity of the genus and generate contiguous, annotated genomes using a combination of long-read DNA sequencing, Hi-C, and RNA-seq. These genomes range in size from 14-25 Mb and have protein-coding genes with unusual features, including a frequent lack of canonical stop codons and a regular intron length of exactly 30 base pairs. Through comparison with the genomes of closely related stramenopiles, we find a pattern of genome reduction and gene duplication in Blastocystis, as well as genomic organization patterns that likely arose during the transitions from a free-living lifestyle to an obligate within-host lifestyle and in transitions between host species. We find substantial strain and subtype-specific gene duplications, including those of likely host-interfacing genes such as those involved in cell-cell adhesion and cell surface glycan production. Together, these genomes and our analyses reveal the adaptations Blastocystis has undergone to thrive in the gut microbiome. These results identify substantial biological variability between subtypes of Blastocystis which are likely to drive differences in interactions with other gut microbiota and the host.