Cost-Effective Microbiome Sequencing with 10x Genomics and Athena Assembler

If you missed Ami Bhatt’s talk at AGBT last month, a bioRxiv preprint is a great way to catch up on her team’s impressive work characterizing microbial communities — from the human gut to the sea floor. Bhatt and her colleagues developed Athena, a de novo assembler that can produce high-quality individual draft genomes from even very complex microbiomes without conflating species.

In “Culture-free generation of microbial genomes from human and marine microbiomes,” senior author Bhatt, lead author Alex Bishara, and colleagues from Stanford University and the University of California, San Diego, present experimental validation of Athena and the rest of the microbiome elucidation pipeline they created. The process can be conducted “at a price point that gives it relevance to the broader microbiome community,” the team notes. We’re proud that they chose the BluePippin platform for their size selection needs prior to analysis with the 10x Genomics Chromium system.

“Metagenomic shotgun sequencing has facilitated partial reconstruction of strain-level community structure and functional repertoire,” the authors write. “Unfortunately, it remains difficult to cost-effectively produce high quality genome drafts for individual microbes without isolation and culture.”

To address this challenge, they used 10x technology to produce read clouds, defined by the scientists as “short-read sequences containing long-range information.” Combined with the Athena assembler, this approach produces “the most complete individual genome drafts,” they report. They tested the method on a mock microbial community, and then validated it with real samples to analyze both the human intestinal tract and sediment from the sea floor. “We find that our approach combines the advantages of both short read and [synthetic long read] approaches, and is capable of producing many highly contiguous drafts (>200kb N50, <10 contigs) with as little as 20x raw short-read coverage,” the team writes. For the marine sample, their approach was the only of many tested that could produce useful, contiguous individual assemblies.

“We anticipate that our approach will be a significant step forward in enabling comparative genomics for bacteria, enabling fine-grained inspection of microbial evolution within complex communities,” the scientists conclude.

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