Determining “who’s there” in a microbial community (i.e., which microbes are present, which genes they carry) is a fundamental question in microbiome research…but this question can be REALLY hard to answer! 🦠 Current state-of-the-art methods lack the resolution to accurately differentiate strains and/or are too expensive/low-throughput for routine use. 💸

In collaboration with the HenLab at UmU, we developed a novel single-cell metagenomic sequencing (scMetaG) method, capable of generating up to 1 million single-amplified genomes (SAGs) from a single sample! 🧬 Our scMetaG method relies on novel microfluidic technology to encapsulate single bacterial cells within semi-permeable capsules (SPCs), allowing us to obtain single-cell resolution genomic data at scale. 🫧

To analyze the massive amount of novel data produced by our scMetaG method, we further developed the world’s first bioinformatic toolkit for complete, end-to-end analysis of high-throughput scMetaG data, specifically: (i) Bascet, a command-line suite designed to scale to massive scMetaG datasets (>1 million cells); (ii) Zorn, an R package/workflow manager that integrates with popular single-cell tools (e.g., Seurat, Signac) to enable reproducible scMetaG data analysis, exploration, and visualization! 🧺

We’re so excited to introduce scMetaG to the community! To read more about our methods, check out our scMetaG preprint! And feel free to try out an early version of Bascet/Zorn for yourself! 🧺