New Genomic Method Unlocks Hidden Diversity In Ocean Microbes And Viruses

A caller method vastly improves connected nan existing attack for single-cell familial sequencing, enabling scientists to publication nan genomes of individual cells and viral particles successful nan situation much quickly, efficiently, and cost-effectively.

In a caller study successful Nature Microbiology, researchers from Bigelow Laboratory for Ocean Sciences and Atrandi Biosciences supply nan first biology exertion of nan approach, which they telephone biology microcompartment genomics. Sequencing nan microbiome successful a sample of aboveground seawater from nan Gulf of Maine, nan researchers showcased nan method's advantages compared to accepted processes, peculiarly for studying nan divers and analyzable world of marine viruses.

This activity demonstrates really we tin summation nan throughput of azygous particle genomics, expanding not conscionable nan amount but besides nan value of nan data. You tin study your full microbe organization successful this broad mode that has not been imaginable - astatine reduced costs without sacrificing quality."

Alaina Weinheimer, a postdoctoral chap and paper's lead author

The accepted method, revolutionized by Bigelow Laboratory's Single Cell genomics Center, involves sorting each nan individual particles successful a sample into their ain good connected a microplate. That enables scientists to process 384 particles successful 1 run. The caller attack increases that throughput by an bid of magnitude. In nan study, nan researchers obtained genomic sequences from complete 2,000 particles successful conscionable 300 nanoliters, aliases little than a millionth of a liter, of seawater.

Microcompartment genomics relies connected caller advances successful microfluidic technology. A sample is compartmentalized into thousands of tiny, semipermeable bubbles, each containing a trillionth of a liter of water. Single cells aliases particles are randomly sampled into individual compartments, and reagents are utilized to make tons of copies of nan DNA. That amplified DNA is past tagged pinch a unsocial barcode. When nan bubbles are dissolved, and each nan worldly is mixed to beryllium sequenced, that barcode is utilized to stitch together corresponding sequences into a complete genome.

Though this first exertion uses seawater, Weinheimer said that early testing shows that nan process besides useful connected sediment and ungraded samples, which tin beryllium difficult to study pinch methods that struggle to differentiate cells from non-biological particles.

The attack does not usage travel cytometry, for illustration nan modular single-cell sequencing method. That intends that scientists suffer immoderate of nan descriptive information that travel cytometry provides, but nan advantage is that there's nary size-based pre-sorting required, truthful immoderate particle of immoderate size tin beryllium sequenced. 

"This attack omits immoderate size selection, truthful we tin process everything from ample microbes to nan tiniest of viruses, aliases moreover free-floating DNA, simultaneously," Weinheimer said. "You're looking astatine nan microbial organization successful a very holistic way."

"Nature's microbial world remains afloat of mysteries, owed to its utmost biodiversity and nan mini beingness scales that makes it difficult to study," added Ramunas Stepanauskas, head of SCGC and elder writer connected nan caller study. "Environmental microcompartment genomics creates wholly caller opportunities for nan study of that world."

This rapid, size-agnostic attack will beryllium peculiarly valuable for studying viruses, which dress up nan immense mostly of nan microbes successful nan water but travel successful a wide scope of sizes and tin often beryllium excessively mini to isolate pinch a travel cytometer.

Indeed, nan study highlights immoderate of nan advantages of nan caller attack compared to existing single-cell and metagenomic methods.

Though each of nan methods nan authors tested agreed successful position of nan wide creation of nan microbial organization - providing assurances that nan caller method useful - nan microcompartment attack generated immoderate unsocial insights. For example, nan methods that usage travel cytometry appeared to prime up much ample viruses, whereas nan caller attack captured viruses of each sizes coming successful nan sample. Likewise, nan microcompartment attack provided genome sequences that were much complete and of higher value than nan wide utilized metagenomic methods.

The scientists besides recovered that galore of nan viral genomes identified utilizing nan caller attack belonged to a family of viruses called Naomiviridae that person only been precocious cultured and person specified an different DNA building they tin beryllium excluded utilizing different methods.

"This group of viruses was nan astir abundant successful our dataset, and we recovered grounds that it whitethorn infect nan astir abundant germs successful nan ocean, but we would person missed it wholly pinch different methods," Weinheimer said. "We're showing that there's a batch that tin still beryllium discovered astir nan viral organization that's presently invisible to america that we're starting to unlock pinch these caller methods."

The activity was funded by nan National Science Foundation, Simons Foundation, and nan Research Council of Lithuania. Co-authors see scientists astatine Vilnius University and Atrandi Biosciences successful Lithuania, arsenic good arsenic respective Bigelow Laboratory researchers, including Brian Thompson, Julia Brown, Jacob Munson-McGee, Greg Gavelis, Corianna Mascena, and Nicole Poulton.