ZymoBIOMICS Microbial Community Standard II (Log Distribution)

D6310


ZymoBIOMICS Microbial Community Standard II (Log Distribution)

Cat # Name Size Price Quantity
D6310 ZymoBIOMICS Microbial Community Standard II (Log Distribution) 10 Preps $330.00
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Documents


Highlights
  • Log abundance distribution: assess detection limit over a broad range (102 to 108 cells)
  • Accurate composition: assess the accuracy of microbiome measurements
  • Microbiomics QC: ideal for quality control of microbiome measurements
Description

ZymoBIOMICS Microbial Community Standard II (Log Distribution) is a mock microbial community consisting of eight bacterial and two fungal strains. This microbial standard can be used to assess the performance of microbiomics workflows and can also be used as a positive control for routine sequencing. Cells of the ten microbes were mixed in a log-distributed abundance, which allows the user to easily assess the detection limit of their microbiomics workflow. 75 µl of the standard contains about ~100 cells of Staphylococcus aureus, the organism of lowest abundance. If needed, the standard can be spiked into a sample matrix (e.g. soil and blood) to mimic real samples of interest. Theoretical Composition Based on Genomic DNA: Listeria monocytogenes - 89.1%, Pseudomonas aeruginosa - 8.9%, Bacillus subtilis - 0.89%, Saccharomyces cerevisiae - 0.89%, Escherichia coli - 0.089%, Salmonella enterica - 0.089%, Lactobacillus fermentum - 0.0089%, Enterococcus faecalis - 0.00089%, Cryptococcus neoformans - 0.00089%, and Staphylococcus aureus - 0.000089%.

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Applicable For NGS, microbiomics, metagenomics.
Processing Volume 75 µl per preparation.
Purity Contains < 0.01% foreign microbial DNA.
Sample Source Eight bacteria (3 Gram-negative and 5 Gram-positive) and 2 yeasts.
Yield Approximately 220 ng DNA per preparation.

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.