Miniaturization Leads to Significant Reduction in Time and Costs for Microbiome Research
The human microbiome plays a vital role in the immmunologic responses and metabolic homeostatis of the body. As researchers continue to explore and study the interaction of the body and the microbiome, Echo acoustic liquid handling leads the way by dramatically simplifying the library preparation workflow and reducing the amount of sample required. This ultimately reduces lab time and sample costs, significantly impacting the bottom-line.
Reduced operating costs through efficient assay miniaturization
Improved data quality with assay volumes as low as 250 nL
Elimination of cross-contamination for accurate species ID
Integrated systems and software tailored for genomic assays
Cost-effective, Miniaturized Next-Generation Sequencing for Microbiome and Metagenomics
Jefferson Lai and Dr. Nur A Hasan|Labcyte Inc and CosmosID
In this presentation, the speakers demonstrate a 10-fold reduction in reagent consumption and the associated costs using the miniaturized and time-efficient library preparation of 16S rRNA amplicons and Nextera XT whole genomes using the Labcyte Echo 525 Acoustic Liquid Handler in concert with CosmosID’s microbiome bioinformatics platform. They demonstrate that miniaturized reactions produce sufficient reads and high-quality data, while using typically one-tenth of the volumes described in standard protocols.
We Need a Google Maps for Metagenomics
On the Mendelspod podcast you can hear an interview with Labcyte customer Dr. Rob Knight about progress in understanding the microbiome. Dr. Knight, Professor and Founder of the Center for Microbiome Innovation at UC San Diego, is well known for his microbiome research, including work showing that the microbiome of lean mice differed from those of obese mice.
Streamline 16S and NGS Workflows for More Accurate Species ID
For many microbiome research studies, the cost of sample preparation is a limiting factor. Echo Liquid Handlers offer an opportunity to scale with confidence. By combining the Echo Liquid Handler's low-volume acoustic transfer capability with library preparation kits, researchers can drastically increase the number of libraries generated.
The Echo acoustic liquid handling technology provides additional benefits. The ability to reliably transfer volumes as low as 25 nanoliters allows for direct dilution of libraries for pooling so there is no sample loss or error propagation and pooling time is significantly reduced. It also allows for efficient usage of small sample quantities. And tipless liquid handling eliminate cross-contamination for more accurate species identification. Using the Echo Liquid Handler, you can miniaturize both 16s rRNA sequencing and whole genome shotgun sequencing, cutting costs and turnaround time for your metagenomics studies.
Marine Biology Research Division, Scripps Institution of Oceanography, UCSD
Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1.42 per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. We further validated the optimized method by sampling five body sites from 46 Pacific chub mackerel fish caught across 16 sampling events over seven months from the Scripps Institution of Oceanography pier in La Jolla, CA. Fish microbiome samples were processed with the miniaturized 5-µl reaction volume with 0.2 µl of genomic DNA (gDNA) and the standard 25-µl reaction volume with 1 µl of gDNA. Between the two methods, alpha diversity was highly correlated (R2 > 0.95), while distances of technical replicates were much lower than within-body-site variation (P < 0.0001), further validating the method. The cost savings of implementing the miniaturized library preparation (going from triplicate 25-µl reactions to triplicate 5-µl reactions) are large enough to cover a MiSeq sequencing run for 768 samples while preserving accurate microbiome measurements.