ZymoBIOMICS Microbial Community DNA Standard

D6305 / D6306


ZymoBIOMICS Microbial Community DNA Standard

Cat # Name Size Price Quantity
D6305 ZymoBIOMICS Microbial Community DNA Standard 200ng $114.40
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D6306 ZymoBIOMICS Microbial Community DNA Standard 2000ng $228.80
- +

Documents

ZymoBIOMICS Microbial Community DNA Standard

Highlights
  • Accurate composition: composition cross-validated with multiple types of measurements.
  • Negligible impurity: guaranteed to contain < 0.01% foreign microbial DNA.
  • Wide range of GC content: 15%-85%, for assessing bias caused by GC content variation.
Description

One of the major challenges in the emerging field of microbiomics is the bias and errors introduced in the complex workflows. Besides nucleic acid purification, bias also arises from sequencing library preparation and subsequent processes. The ZymoBIOMICS Microbial Community DNA Standard is designed to assess bias, errors and other artifacts after the step of nucleic acid purification. This DNA standard is created by pooling DNA extracted from pure cultures. It has an accurately defined composition, negligible impurities (0.01%), and contains genomes of a wide range of GC content (15% - 85%). This DNA standard is designed to have the same microbial composition with the cellular version, the ZymoBIOMICS Microbial Community Standard, so that they can be more powerful when working in tandem. Theoretical Composition Based on Genomic DNA: Listeria monocytogenes - 12%, Pseudomonas aeruginosa - 12%, Bacillus subtilis - 12%, Escherichia coli - 12%, Salmonella enterica - 12%, Lactobacillus fermentum - 12%, Enterococcus faecalis - 12%, Staphylococcus aureus - 12%, Saccharomyces cerevisiae - 2%, and Cryptococcus neoformans - 2%.

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Purity < 0.01% foreign microbial DNA
Sample Source A mixture of genomic DNA of ten microbial strains.
Sample Storage -20 °C
Supplemental Info

We recommend working backwards from the analysis. First optimize your library prep with the ZymoBIOMICS Microbial Community DNA Standard (D6305, D6311) to assess bias in PCR, sequencing, bioinformatics, etc. Once your results have low/no bias when compared to the theoretical composition, then use the whole cell ZymoBIOMICS Microbial Community Standard (D6300, D6310) to assess bias in lysis efficiency.

No, the Microbial Community Standard is designed to assess the efficiency of the lysis method and is intended to be run in parallel with your samples. If all the organisms can be detected at/near the theoretical abundance, you can be confident your extraction method is unbiased.

The chemistry of the Qiagen Kits (QIAamp Powerfecal, DNeasy Powersoil) and the storage solution the Microbial Community Standard is stored in (DNA/RNA Shield) are not completely compatible. Instead, less input volume should be used (25 ul).

You can find the reference genome and 16S/18S sequences here: ZymoBIOMICS.STD.refseq.v2.zip.

This may indicate an issue with the lysis method, which can be biased toward gram negative bacteria. See the Optimized Lysis Protocols under Documents for a table of bead beating devices and protocols validated by Zymo Research.

Devices found to underrepresent tough-to-lyse organisms under all tested conditions:

  • Retsch Mixer Mills
  • Tissues Lyzers
  • MP Fast Prep 96

We use an in-house curated database to generate the data for the standards.

Please contact Technical Support at tech@zymoresearch.com for raw sequencing data.

The expected DNA fragment size is <15kb.

This could indicate bias in the workflow, such as inefficient lysis, library prep or bioinformatics analysis.