The microbiome can both positively and negatively affect host health, with broader effects on ecosystems and evolution. Prokaryotic members of the microbiome are commonly studied by sequencing 16S rRNA fragments, but eukaryotic members are hard to study because their analogous 18S rRNA fragments are vastly outnumbered by those of the host. To solve this problem, researchers recently developed a new method, CRISPR-Cas Selective Amplicon Sequencing (CCSAS). In CCSAS, a single-guide RNA specific to the host taxon directs the enzyme Cas9 to cleave host 18S rRNA, preventing its amplification and detection, while the 18S rRNA of eukaryotic microbes like fungi and protists is left intact. The researchers tested the method by investigating the eukaryotic microbiome in settled oyster larvae (spat). CCSAS uncovered a diverse array of eukaryotic microbes with much less host (metazoan) fragment contamination than alternative methods. Notably, some unique sequences were identified by each method, suggesting that a combination of methods may yield the most complete results. To facilitate widespread use of CCSAS, the researchers also designed single-guide RNA that works for 16,000 plant and animal taxa, thus providing a new high-throughput and cost-effective way to characterize eukaryotic microbiomes with improved accuracy.