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ZymoBIOMICS Microbial Community Standard II

The ZymoBIOMICS™ Microbial Community Standard II is a well-defined, mock microbial community ideal for assessing the detection limit of microbiomics workflows and as a positive control for routine sequencing. Consisting of eight bacterial and two fungal strains mixed to create a log-distributed abundance, this standard is accurately characterised and contains negligible impurities. 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.

Benefits of using this log distribution standard
• Well defined & characterised
• Less than 0.01% impurities
• Ideal for QC of microbiome measurements
• Assess the accuracy of microbiome measurements

Also available is the ZymoBIOMICS™ Microbial Community DNA Standard II, which consists of a mixture of genomic DNA of eight bacterial and two fungal strains and is ideal for assessing the performance of microbiomics workflows or as a positive control for routine QC. The microbiobial standard is accurately characterised and contains negligible impurity (<0.01%).

ZymoBIOMICS Microbial Community Standard II (Log Distribution)

The microbial composition of the standard measured by NGS shotgun sequencing as compared to the defined composition. After mixing, the microbial composition of the standard was confirmed using deep Illumina® shotgun sequencing. Briefly, the genomic DNA was extracted using the ZymoBIOMICS™ DNA Miniprep. Library preparation was performed using an in-house protocol. Shotgun sequencing was performed using Illumina HiSeq™ or MiSeq™. Microbial abundance was estimated based on the number of reads that were mapped to references genomes of the organisms.

Microbial composition

Species Defined composition (%)
Genomic DNA 16S only1 16S & 18S1 Genome copy2 Cell number2
Listeria monocytogenes 89.1 95.9 91.9 94.8 94.9
Pseudomonas aeruginosa 8.9 2.8 2.7 4.2 4.2
Bacillus subtilis 0.89 1.2 1.1 0.7 0.7
Saccharomyces cerevisiae 0.89 NA 4.1 0.23 0.12
Escherichia coli 0.089 0.069 0.066 0.058 0.058
Salmonella enterica 0.0089 0.07 0.067 0.059 0.059
Lactobacilus fermentum 0.0089 0.012 0.012 0.015 0.015
Enterococcus faecalis 0.00089 0.00067 0.00064 0.001 0.001
Cryptococcus neoformans 0.00089 NA 0.0014 0.00015 0.00007
Staphylococcus aureus 0.000089 0.0001 0.0001 0.0001 0.0001


1 The theoretical composition in terms of 16S (or 16S and 18S) rRNA gene abundance was calculated from theoretical genomic DNA composition with the following formula: 16S/18S copy number = total genomic DNA (g) × unit conversion constant (bp/g) / genome size (bp) × 16S/18S copy number per genome. Use this as reference when performing 16S targeted sequencing.
2 The theoretical composition in terms of genome copy number was calculated from theoretical genomic DNA composition with the following formula: genome copy number = total genomic DNA (g) × unit conversion constant (bp/g) / genome size (bp). Use this as reference when inferring microbial abundance from shotgun sequencing data based on read depth.
3 The theoretical composition in terms of cell number was calculated from theoretical genomic DNA composition with the following formula: cell number = total genomic DNA (g) × unit conversion constant (bp/g) / genome size (bp)/ploidy.

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Material available for download
ZymoBIOMICS™ Microbial Community Standard II (Log Distribution) protocol
ZymoBIOMICS™ Microbial Community Standard II (Log Distribution) SDS
ZymoBIOMICS™Microbial Community DNA Standard II (Log Distribution) protocol
ZymoBIOMICS™ Microbial Community DNA Standard II (Log Distribution) SDS

Products

Note: product availability depends on country - see product detail page.

Details Cat number & supplier Size Price
ZymoBIOMICS Microbial Community Standard II D6310 · Zymo Research
D6310
Zymo Research
10 preparations £351.00
10 preparations
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ZymoBIOMICS Microbial Community DNA Standard II D6311 · Zymo Research
D6311
Zymo Research
220 ng £180.00
220 ng
view