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Lithuanian Startup Atrandi Biosciences Debuts Microbial Single-Cell DNA Sequencing Platform


NEW YORK – Atrandi Biosciences has launched a new microfluidics platform and accompanying kit to support high-throughput microbial single-cell DNA sequencing.

The Vilnius, Lithuania-based company is also preparing to raise a Series A financing round to establish its technology in other application areas, according to Juozas Nainys, its founder and CEO.

Last year, the firm, formerly called Droplet Genomics, raised $4.8 million in venture capital led by Vsquared Ventures, a Munich, Germany-based deep tech fund, which was joined by Metaplanet, a Tallinn, Estonia-based fund focused on biotech, and Practica Capital, a Vilnius-based VC and early investor in Atrandi.

Atrandi's new instrument, called Flux, can sort single cells into semipermeable capsules, or SPCs, which consist of an aqueous core encased within a hydrogel shell. It can process up to eight samples simultaneously, compartmentalizing as many as 100,000 single cells into SPCs in about half an hour.

SPCs can exchange reagents while keeping the cells apart. For example, cell lysis components can be washed out while genomic DNA is retained. Once generated, SPCs are suitable for most downstream reactions, which can be performed in bulk using standard laboratory equipment.

The company is marketing the Flux instrument along with a DNA barcoding kit for single microbes to microbiologists for the study of microbial communities. The kit supports the labeling of up to 10,000 microbial genomes for library preparation and sequencing, the company said.

According to Nainys, Atrandi's SPC technology has been years in development, and it is one of the reasons the company changed its name last year from Droplet Genomics, as it was pivoting away from droplets.

The company decided to go after the microbiology market first because it is underserved and yet experiencing growth, he said.

"The microbial metagenomics market is growing at 18 percent year over year," Nainys said, as are related publications. "People realize that microbes hold the answer to a lot of questions around human health."

Nainys said the workflow is priced at less than $1 per cell, including sequencing costs. The price for the Flux is region dependent, he added, but in general, it costs less than $25,000.

Flux currently works with Illumina, PacBio, and Oxford Nanopore sequencing workflows but could be adapted for other sequencing platforms, he said.

While the capsule technology offers the same throughput and scalability as droplets, it is more versatile, Nainys said. For example, reagents added to droplets cannot be removed, while capsules allow for "seamless reagent exchange without loss of sample compartmentalization," he said.

Atrandi first entered the genomics market with droplet technologies, launching two systems, the Styx, which provides fluorescence-activated droplet and capsule detection, and the Onyx, a microfluidic system that supports droplet generation and manipulation.

The Styx, launched in 2021, could support millions of functional assays per day for metagenomics studies, DNA-encoded library screening, in vitro evolution studies, and functional antibody discovery. The Onyx, launched a few years prior, has been used for sequencing library generation and functional assays, while Styx is used for screening libraries in droplets.

The release of the SPC technology also coincided with other changes at the company.

Last year's funding allowed Atrandi to double its headcount from about 33 people at the end of 2022 to 60 at the start of this year. It also incorporated in Delaware, while making a few hires across the US to build out its business in the US.

"The US is one of the main markets for life sciences and for emerging technologies, particularly single-cell analysis," Nainys said. "We've been selling into the US market since the beginning, but we wanted to have a presence there to better support our clients."

One of those clients is Ramunas Stepanauskas, a senior research scientist at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine, and director of the Bigelow Laboratory’s Single Cell Genomics Center (SCGC). Stepanauskas is also Lithuanian and knows one of Atrandi's founders, but has no connection to the company.

He has primarily been using flow cytometry to sort cells and drop them into 384-well plates for robotic liquid handling, followed by amplification and next-generation sequencing. The Bigelow Laboratory established SCGC on the back of that platform in 2009, and while it continues to innovate on it, it remains the center's "main workhorse."

Stepanauskas' collaboration with Atrandi has given the center the ability to scale up analysis while reducing cost. "It looks like we may be able to increase the throughput by roughly tenfold" or even more, he said.

In addition to cost and throughput, Stepanauskas also cited the Flux platform's ease of use. At least one other company focuses on the market for microbial single-cell sequencing: Tokyo's BitBiome, which offers a research platform based on its Bit-Map single-cell microbial genome analysis technology.

"Scale is of the essence," said Stepanauskas. "The number and diversity of microbes in nature is astonishing, and the tools we have been using so far are not adequate to really represent nature."

Stepanauskas mostly works on marine microbes drawn from the ocean, particularly below the sunlit surface layer. He studies their capacity to fix carbon and what energy sources they use for that purpose. But he has also studied microbial communities in deep subsurface, soil, and even NASA spacecrafts.

One project Stepanauskas currently leads is the creation of the Global Ocean Reference Genomes Database, with primary financial support from the Simons Foundation. One of the goals of the project is to map out, at single-cell resolution, the genomic composition of unicellular microorganisms that "dominate marine ecosystems, drive global cycles of carbon and other elements, and harbor enormous biotechnological potential," he said. SCGC will likely use the Flux instrument and barcoding kit in the next stage of this program, which involves collaborations with over 10 organizations around the globe.

According to Atrandi's Nainys, the company's interest in the microbiology market is just the start. "We have planned a lot of products in different spaces," he said.

With new funding, the company is also eyeing the application of its SPC technology in oncology and cell-line editing. It also has long-term technology plans around multiomics and supporting multimodal analysis of imaging data with next-generation sequencing data, he added.