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ZymoBIOMICS Microbial Community Standard
ZymoBIOMICS Microbial Community Standard
- Accurate composition: composition cross-validated with multiple types of measurements.
- Assessing bias in DNA isolation: containing microbes of varying size and cell wall recalcitrance (8 bacteria and 2 yeasts).
- Microbiomics QC: ideal for microbiome profiling quality control.
Microbial composition profiling techniques powered by Next-Generation sequencing are becoming routine in microbiomics and metagenomics studies. However, these analytical techniques can suffer from significant bias from collection to analysis. The ZymoBIOMICS Microbial Community Standard is designed to assess bias and errors in the extraction methods of a microbiomics workflow. The Microbial Community Standard mimics a mixed microbial community of well-defined composition, containing three easy-to-lyse Gram-negative bacteria, five tough-to-lyse Gram-positive bacteria, and two tough-to-lyse yeasts. Acting as a defined input from the beginning, the Microbial Community Standard can guide construction and optimization of entire workflows and can also be used as a routine quality control.
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%.
|Purity||< 0.01% foreign microbial DNA|
|Sample Source||A mixture of ten inactivated microorganisms (bacterial and fungal).|
|Sample Storage||-80 °C|
Q1: Which standard should I use and how do I use it?
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.
Q2: Is the standard supposed to be spiked into a sample?
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.
Q3: Is the standard compatible with Qiagen kits?
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).
Q4: Where can I find your reference files for the genomes of your Standard strains (D6300, D6305, and D6306)?
You can find the reference genome and 16S/18S sequences here: ZymoBIOMICS.STD.refseq.v2.zip.
Q5: Why do my abundance results not match the theoretical composition?
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
Q6: What database was used to generate the data for the standards on the data sheet?
We use an in-house curated database to generate the data for the standards.
Q7: Is the raw sequencing data for the standards available?
Please contact Technical Support at firstname.lastname@example.org for raw sequencing data.
Q8: What is the expected DNA fragment length in the Microbial Community DNA Standard? (D6305/D6306)
The expected DNA fragment size is <15kb.
Q9: How come I am unable to detect certain organisms in the standard?
This could indicate bias in the workflow, such as inefficient lysis, library prep or bioinformatics analysis.