Most Cited Extraction Methods Substantially Skew Microbial Profiles

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Does your extraction method misrepresent your microbiome data?

“We found that DNA extraction had the largest effect on the outcome of metagenomic analysis.

Published Data Shows More Than 10X Mischaracterization

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“Different DNA extraction protocols result in substantial technical variation , both in taxonomic and in functional space”

High Profile Studies Show Differing Results

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Is the difference technical or biological?

The two best-known human microbiome profiling efforts, the Human Microbiome Project (HMP) and Metagenomics of Human Intestinal Tract (MetaHIT) agree that Bacteroidetes and Firmicutes are in dominance, but the HMP profile indicates higher abundance of Bacteroidetes. Is the difference observed capturing a biological change? When these DNA extraction methods were replicated on the same samples, researchers found the HMP protocol yields a higher relative abundance of Bacteroidetes as compared to the MetaHIT DNA extraction protocol (Wesolowska-Andersen et al., 2014). This indicates the differences are at least in part technical and highlights the difficulty in comparing data generated using different, nonstandardized extraction methods.

Leaders are Calling for Standardized Methods

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“The interlab comparability of measurements on microbiomes is generally poor. Biases exist along every step of the measurement process, from sample collection, extraction techniques, measurement technology employed (e.g. NGS, mass spec, NMR), and, finally, to data analysis and interpretation. There is a need for the adoption of reference materials, reference data, and reference protocols in order to identify and eliminate measurement bias.”

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“Unfortunately, variations at each step in the pipeline is enormous from physical sample collection and processing to computational quantification of microbial communities.”

Zymo Research Sets the Standard for Complete Lysis

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Ensure Accurate Microbial Profiling

Zymo Research’s data supports what Costea, et. al reported. The most cited methods are consistently underrepresenting hard-to-lyse organisms due to inefficient lysis technologies. Benchmarking with mock microbial community standards helps identify bias and ensures reproducible, accurate data. Zymo Research’s ZymoBIOMICS DNA Extraction kits were designed and optimized with high quality standards to ensure complete lysis of organisms of varying hardiness.

Test the Limits of Your Protocol

Take the Microbial Extraction Challenge

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  • Implement standards to identify potential bias in your extraction method
  • Put Zymo Research’s lysis technology to the test
  • Free 16S Sequencing included - A $680 value!

Benchmark Your Extraction Protocol for Free!

Limited Availability

How the Challenge Works

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Extract DNA from our microbial standard and a sample of your choice with both:

• ZymoBIOMICS DNA Miniprep

• Method of your choice

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Ship the purified DNA to Zymo Research

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Zymo Research will handle 16S Sequencing and send a report to you

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