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Single-Microbe Genomics: One Workflow, One Kit

11 June - 2025
Single-Microbe Genomics: One Workflow, One Kit

Microbial communities are rich and complex. Whether you're studying the gut, soil or any environments, metagenomics can tell you who’s there. But it still struggles with what each cell is doing, how microbes differ within populations, or how mobile elements like plasmids are spreading.

When we launched the Single-Microbe DNA Barcoding Kit, based on Semi-Permeable Capsule (SPC) technology, the goal was clear: to unlock strain-level insights from complex microbial communities by enabling high-throughput, high-quality single-cell genomics, without a need of microfluidics background.

Now, we’re making that experience even more complete. The updated Single-Cell Microbial WGS Kit now delivers a fully optimized solution: from a microbial sample all the way to a sequencing-ready barcoded library, in a single streamlined workflow.

Single-Cell Microbial WGS Kit

What’s New?

Library preparation reagents are now included
You no longer need to source or validate separate library prep kits. Everything required for barcoding and preparing your single-amplified genome (SAG) libraries for Illumina sequencing is included in the box.

Built-in flexibility with test-before-you-commit design
The kit contains reagents for an optional optimization step, so you can run a small-scale whole genome amplification (WGA) with your sample and confirm that sufficient SAGs are generated before proceeding to the full workflow. It's a safeguard for your time, sample, and sequencing budget.

Smaller kit size, same output power
The updated format covers 2 runs, with up to 8 samples each, making it easier to design pilot studies, fieldwork, or comparative experiments without committing to large-scale processing all at once.

No change in price per run
The update comes with almost no change in cost per run, but significantly more value and flexibility for your experimental design.

Single-Cell Microbial WGS Kit

Traditional approaches like 16S or bulk metagenomics offer a broad view, but they fall short when you need strain-level resolution, functional gene context, or a clear view of microbial dark matter. The Single-Cell Microbial WGS Kit workflow bridges that gap.

With our solution you can generate thousands of single-amplified genomes (SAGs) in parallel, directly from your sample, with:

  • Recovery of high-quality genomes even from low-abundance species.
  • Strain-resolved microbial profiling, without culturing.
  • Absolute abundance quantification.
  • Association of mobile elements (plasmids, phages) with specific hosts.
  • Applications for community dynamics, antibiotic resistance tracking, and novel genome discovery.
And all of this, without needing microfluidics experience. The Single-Cell Microbial WGS Kit is used with our Flux system, which handles up to 8 different samples at once and encapsulates thousands of single microbe cells into SPCs in just 30 minutes – no microfluidics experience required. The entire encapsulation step can even be done outside the lab, powered by a portable battery, and samples can be safely stored until you’re ready to proceed.

From a microbial sample to a sequencing-ready library. All in one kit. Explore the updated kit here.