Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data

Area of Science:

• Metagenomics
• Bioinformatics
• Microbial Eukaryotes

Background:

• Whole-genome shotgun (WGS) metagenomic sequencing is powerful for microbial genome reconstruction.
• Protistan genome recovery from WGS data is challenging due to genome size and complexity.
• Existing methods limit the exploration of microbial eukaryotic diversity in metagenomes.

Purpose of the Study:

• To develop a bioinformatics pipeline, Eukfinder, for identifying and assembling eukaryotic genomes from WGS metagenomic data.
• To enable the recovery of high-quality nuclear and mitochondrial eukaryotic genomes.
• To facilitate reference-independent and cultivation-free studies of microbial eukaryotes.

Main Methods:

• Eukfinder utilizes specialized databases for read/contig classification.
• A complementary binning workflow aids in genome recovery.
• The pipeline was tested on simulated and real human gut microbiome WGS data, including the protist *Blastocystis*.

Main Results:

• Eukfinder successfully identified eukaryotic sequences and recovered near-complete genomes.
• The pipeline demonstrated effectiveness in recovering diverse *Blastocystis* subtypes.
• Eukfinder outperformed other workflows in eukaryotic genome recovery under sufficient sequencing depth.

Conclusions:

• Eukfinder is a valuable tool for advancing the study of microbial eukaryotes.
• It enables the recovery of high-quality eukaryotic genomes from environmental WGS samples.
• This expands the availability of reference genomes for gut microbiome and other ecosystem research.