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A Comprehensive Solution for Microbiomics and Metagenomics

crobiomic
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Standardizing Microbiomics
crobiomic
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Optimizing Microbiomics Workflows

Advances in DNA sequencing and other genome-enabled
technologies have lowered the cost and time requirements
needed to sequence any organism. Next-Generation
Sequencing of microbial communities has supercharged
our ability to research and explore both human and
environmental microbial ecosystems. This advancement in
technology has allowed, for the first time, large-scale, multilab studies of microbial communites1.
Early quality control studies of microbiomic research suggest
that this vast new frontier of research is littered with potential
sources for error and bias. From collection to sequencing,
the potential for variation at each step in the microbiomic
workflow is enormous.
During the collection and transportation phase, depending
on the quality of the method, microbes can continue to grow
and decay. Nucleic acids can also degrade during this phase.
These two factors can lead to overall misrepresentation of
the original community profile, causing downstream bias. In
the extraction phase, inferior forms of lysis can fail to extract
DNA from tough-to-lyse microbes (e.g. Gram-positive
bacteria and yeast), leading to the underrepresentation of
tough-to-lyse microbes and overrepresentation of easyto-lyse microbes (e.g. Gram-negative bacteria). During
sequencing, different library preparation methods can
cause biased coverage depending on the GC content of the
organisms.
As multi-lab, longitudinal microbiomic studies become more
common, there is an urgent need for standards to establish
validated methods for reproducible data2.

Zymo Research has endeavored to develop standards for the

advancement and optimization of microbiomic workflows
to allow researchers to have increased confidence in their
microbiomics data. ZymoBIOMICS Microbial Community
Standards are groundbreaking community standards,
containing a well-defined and characterized community of
Gram-positive bacteria, Gram-negative bacteria and yeast.
They are ideal for validating and optimizing microbiomics
and metagenomic workflows from extraction to analysis.
At collection, DNA/RNA Shield stabilizes nucleic acids and
inactivates all organisms including pathogens in your
sample, allowing for accurate community profiling. There is
no degradation of nucleic acids, creating a perfect molecular
snapshot of your sample at the time of collection.
Our ZymoBIOMICS DNA Mini Kit ensures accurate
community profiling by enabling unbiased lysis from any
sample, including feces, soil, water, biofilms, swabs, body
fluid, etc. DNA extracted from this kit is ultra-pure, inhibitorfree, and ready for all downstream applications, including
PCR 16S rRNA gene sequencing and shotgun sequencing.
If you would prefer to leave the work to us, we offer a
comprehensive list of ZymoBIOMICS Services covering
all steps of a microbiomics workflow from collection to
analysis. Simply send us your sample and we will handle
the rest. All workflows are validated to be non-biased using
the ZymoBIOMICS Microbial Community Standards and
provide publication-ready data.
ZymoBIOMICS- Standardizing Microbiomics

At Zymo Research, we have made it our goal to eliminate

bias across the entire microbiomic workflow. Our new
product line, ZymoBIOMICS, is a complete workflow, from
collection to analysis, which offers streamlined collection,
purification, and the first microbial community standards.

1. Sinha, Rashmi, et al. The microbiome quality control project: baseline study design and future directions.Genome biology16.1 (2015)
2. Stulberg, Elizabeth, et al. An assessment of US microbiome research. Nature Microbiology1 (2016): 15015.

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ZymoBIOMICS Microbial Community Standards

Cat No. D6300, D6305, D6306

crobiomic
Mi

Highlights

Mock microbial community of well-defined composition for workflow validation optimization

DNA standard of the same mock community for sequencing validation and optimization
Perfect for assessing bias of DNA extraction methods along with the quality control of
microbiome profiling and metagenomic analyses

Standards

Standards for Optimizing Microbiomics Workflows

Bacillus subtilis (G+)

Listeria monocytogenes (G+)
Staphylococcus aureus (G+)
Enterococcus faecalis (G+)
Lactobacillus fermentum (G+)
Salmonella enterica (G-)
Escherichia coli (G-)
Peudomonas aeruginosa (G-)

ZymoBIOMICS
DNA Mini Kit

Species

Avg. GC
(%)

Gram
Stain

gDNA
Abun. (%)

Pseudomonas aeruinosa

66.2

12

Escherichia coli

56.8

12

Salmonella enterica

52.2

12

Lactobacillus fermentum

52.8

12

Enterococcus faecalis

37.5

12

Syaphylococcus aureus

32.7

12

Listeria monocytogenes

38.0

12

Bacillus subtilis

43.8

12

Saccharomyces cerevisiae

38.4

Yeast

Cryptococcus neoformans

48.2

Yeast

Find Your Bias & Eliminate It

Accurate Characterization

ZymoBIOMICS Microbial Community Standard was used to compare

different DNA extraction protocols. DNA samples were profiled by 16S
rRNA gene targeted sequencing.

Containing three easy-to-lyse Gram-negative bacteria, five tough-to-lyse

Gram-positive bacteria, and two tough-to-lyse yeasts, the ZymoBIOMICS
Microbial Community Standards are perfect for assessing bias in various DNA
extraction methods. The microbial standards are accurately characterized,
with a wide GC range (15%-85%) and contain negligible impurities (<0.01%),
enabling easy exposure of artifacts, errors, and bias in microbiomics or
metagenomic workflows.

Reduce Noise in Your 16S rRNA Gene

Seq. with the ZymoBIOMICS Microbial
Community DNA Standard
Controlling noise/rare biosphere in 16S rRNA gene targeted sequencing
with ZymoBIOMICS Microbial Community DNA Standard. The pie
chart on the left is the microbial composition profile of the standard
determined by a regular workflow of 16S sequencing using primers
targeting v3-4 region. The pie chart on the right is the profile of the same
standard determined using the same primer sets but with an optimized
in-house workflow of 16S sequencing. Noise observed on the left panel
were mainly caused by PCR chimera, process contamination and reagent
contamination, which were controlled in the optimized workflow.

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Before

Optimized
Workflow

Noise and bias

After

True composition of
the standard

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Sample

DNA/RNA Shield
Collection

Nucleic Acid Stabilization at Ambient Temperature

saliva

30

Saliva

30

40

35
RNA

20

DNA
RNA

30

DNA

25

Ct

Average Ct

20

Ct
10

20

RNA

20

DNA

DNA

15

RNA

10

10

5
0
0 0
Day

Day14 14

Day 30

Day 0

Actin detection - 2x Shield 1.5:1 to Saliva

28

14

Day 7

Day 14

Day28
Days

DNA and RNA in saliva and stool is effectively stabilized in DNA/RNA Shield at ambient temperature. Graphs show: spike-in DNA and RNA controls
from saliva and stool purified at the indicated time points and analyzed by (RT)qPCR. Controls: HSV-1 and HIV (AcroMetrix, Life Technologies).

Without Shield Composition Changes

DNA/RNA Shield Preserves Microbial

Composition at Ambient Temperature

With Shield Accurate Composition

Microbial composition of stool is unchanged after one month

at ambient temperature with DNA/RNA Shield. Stool samples
suspended in DNA/RNA Shield and stored at room temperature
were compared to stool without preservative for one month.
They were sampled at the indicated time points and processed
with ZymoBIOMICS DNA Mini Kit. The extracted DNA was then
subjected to microbial composition profiling via 16S rRNA gene
targeted sequencing. Samples stored with DNA/RNA Shield had
a constant microbial composition while the samples stored without
shifted dramatically.

Microbial Inactivation
Virus

Bacteria

Yeast

C. neoformans
C. albiicans
S. cerevisiae *

E. coli *
B. subtilis
L. fermentum
E. faecalis
M. tuberculosis
L. monocytogenes
P. aeruginosa
S. enterica
S. aureus

HSV

Ebola

Influenza

bacteria/yeast: log cfu

virus: log pfu/ml

Ct - value

30

10

fecal

Stool

40

Complete
Inactivation

Complete Inactivation

DNA/RNA Shield

PBS

Viruses, bacteria and yeast are effectively inactivated by DNA/RNA Shield. Samples containing the infectious
agent (virus, bacteria, yeast) were treated with DNA/RNA Shield or mock (PBS) treated for 5 minutes. Titer (PFU) was
subsequently determined by plaque assay. Validated by: Influenza A - D. Poole and Prof. A. Mehle, Department of
Medical Microbiology and Immunology, University of Wisconsin, Madison; Ebola (Kikwit) - L. Avena and Dr. A. Griffiths,
Department of Virology and Immunology, Texas Biomedical Research Institute; HSV-1/2 - H. Oh, F. Diaz and Prof. D. Knipe,
Virology Program, Harvard Medical School; E. coli, L. fermentum, B. subtilis, S. cerevisiae Zymo Research Corporation).

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DNA/RNA Shield Collection Devices

Highlights

DNA/RNA Shield Collection Devices provide an unbiased molecular snapshot of the sample (feces, soil,
saliva, cells, tissue, etc.) at the time of collection by preserving nucleic acids at ambient temperature.
Inactivates pathogens (bacteria, fungus, parasites, and viruses) preventing microbial growth after collection.
DNA and RNA can be isolated directly without precipitation or reagent removal (directly compatible with the
ZymoBIOMICS DNA Mini Kit).

Fecal Collection Tube

15 ml container (prefilled with 9 mL DNA/RNA

Shield) for the direct collection of up to 1 gram
and/or 1 ml stool. Collection spoon is included in
the container screwcap.
DNA/RNA Shield - Fecal Collection Tube

R1100-9-T

Microbial/Tissue Lysis Tube

2 ml collection tube (prefilled with 1 mL DNA/RNA

Shield) and Bashing Beads for the collection and
homogenization of microbial or tissue samples.
Lysis Tube (Microbe)

R1100-1-B15

Lysis Tube (Tissue)

R1100-1-B2

Swab and Collection Tube

5 ml screwcap container (12x80mm) filled with 1

mL DNA/RNA Shield and a sterile HydraFlock
swab for specimen collection.

HydraFlock is a registered trademark of Puritan

DNA/RNA Shield - Swab & Collection

Tube

R1100-1ST-50

DNA/RNA Shield Reagent

All-purpose reagent for sample lysis and

stabilization of DNA/RNA in tissues (e.g.,
mammalian biopsy, whole insect), cells (animal,
microbial) and biological liquids.
Reagent concentrate (2X) for use with biological
liquids at 1:1 ratio.

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DNA/RNA Shield

R1100-50

DNA/RNA Shield

R1100-250

DNA/RNA Shield (2x concentrate)

R1200-25

DNA/RNA Shield (2x concentrate)

R1200-125

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ZymoBIOMICS DNA Kits

A/RNA
DN

Highlights

Isolation

Ultra-pure, inhibitor-free DNA from any sample (feces, soil, water, biofilms, swabs, body fluid, etc.)
that is ideal for all downstream applications including PCR, arrays, 16S rRNA gene sequencing,
and shotgun sequencing
Innovative lysis system enables efficient and unbiased lysis of microbes including Gram-positive/
negative bacteria, fungus, protozoans, and algae for accurate microbial community profiling

Accurate Community Profiling

Bacillus subtilis (G+)
Listeria monocytogenes (G+)
Staphylococcus aureus (G+)
Enterococcus faecalis (G+)
Lactobacillus fermentum (G+)
Salmonella enterica (G-)
Escherichia coli (G-)
Peudomonas aeruginosa (G-)

Validated, Unbiased DNA Isolation

The ZymoBIOMICS DNA Mini Kit provides
unbiased representation of the organisms
extracted from the ZymoBIOMICS Microbial
Community Standard.

ZymoBIOMICS
DNA Mini Kit

Innovation. Pure & Simple.

Ultra-pure DNA from Inhibitor Rich Samples
40.00

CT

17.57 17.48

17.63

15.00
10.00
5.00

17.82

No Amplification

20.00

No Amplification

25.00

No Amplification

30.00

No Amplification

35.00

Superior Yields
Zymo- Supplier

L L BIOMICS M P Q
ZymoBIOMICSTM
M
P

Q

10% Eluate
35% Eluate

0.00
ZymoBIOMICSTM
ZymoBIOMICS

Supplier M

Supplier P

Supplier Q

Kit

The ZymoBIOMICS DNA Mini Kit provides superior yields when compared to
Suppliers M, P, and Q.

The ZymoBIOMICS DNA Mini Kit provides inhibitor-free DNA even when
challenged with extremely inhibitor-rich samples.

Available Formats

Miniprep
D4300
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Microprep
D4301

Spin Plate
D4303, D4304

Magnetic Beads
D4302
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Highlights

ZymoBIOMICS RNA Mini Kit

Cat No. R2001

Rapid, robust, and simple purification of high quality, inhibitor-free total RNA (including small/micro RNAs) from
any sample including feces, soil, water, biofilms, swabs, saliva, and body fluids, etc.
ZymoBIOMICS innovative lysis system enables efficient and unbiased lysis of microbes including gram positive/
negative bacteria, fungus, protozoans, algae, viruses, etc.
DNA-free RNA is ready for use in any downstream application. DNase I included.

Reliable RNA Isolation

Total RNA isolated from human stool with or

without inclusion of the Zymo-Spin IV-HRC
Spin Filter during the ZymoBIOMICS RNA
Mini Kit protocol. Earlier amplification cycles
indicate complete removal of PCR inhibitors.

ZymoBIOMICS DNA/RNA Mini Kit

Cat No. R2002

Highlights

Rapid, robust, and simple purification of high quality, inhibitor-free DNA and total RNA (including small/micro
RNAs) from any sample including feces, soil, plant, water, biofilms, swabs, saliva, body fluids, etc.
ZymoBIOMICS innovative lysis system enables efficient and unbiased lysis of microbes including gram positive/
negative bacteria, fungus, protozoans, algae, viruses, etc.
High quality DNA and DNA-free RNA is ready for use in any downstream application. DNase I included.

DNA & RNA from the Same Sample

Human stool genomic DNA and total RNA

isolated with the ZymoBIOMICS DNA/RNA
Mini Kit is highly intact. Quality assessed by
Agilent 2200 TapeStation.

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DNA & RNA in One Fraction

DNA & RNA in Separate Fractions

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Lib

ZymoBIOMICS PCR Pre-Mix and

Femto DNA Quantification Kits

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Cat No. E2056, E2057, E2006, E2007, E2005

Use the low-bioburden, ZymoBIOMICS PCR Pre-Mix to ensure non-biased quantification

and microbiomic analysis
The Femto DNA Quantification Kits can reliably detect and quantify bacterial, fungal, and
human DNA with high sensitivity and specificity to as little as 20 fg of DNA in 1 l of eluate

Low-Bioburden DNA Polymerase

A. Milli-Q Water B. ZymoBIOMICS

DNase/RNase Free
Water

Figure 1 (left). A tenfold serial dilution of Lactobacillus fermentum genomic DNA was quantified via real-time PCR, after the addition of 2.5 M SYTO 9 to a 20
l reaction volume. Amplification of the 16S rRNA gene can be quantified down to 2 femtograms of bacterial genomic DNA in a 45 cycle qPCR. Figure 2 (right).
Quantification of no template controls (NTCs) via real-time PCR was determined by amplification of the 16S rRNA gene, after the addition of 2.5 M SYTO 9
to a 20 l reaction volume. Real-time PCR was performed for 45 cycles to determine the amount of bacterial contamination. NTCs include (A) Millipore filtered
water and (B) DEPC treated Millipore filtered water.

Accurately Quantify Bacterial, Fungal, or Human DNA

Reliable standards for the quantification of bacterial DNA: Bacterial DNA Standards (measured in duplicates) comprise a 10-fold
dilution series ranging from 20 ng to 20 fg.

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oin
Bi

ZymoBIOMICS Services

formatic
s

Highlights

Zymo Research offers the most comprehensive services for 16S rRNA and shotgun sequencing
from any sample type
ZymoBIOMICS Services are validated using the ZymoBIOMICS Microbial Community
Standards for unbiased, publication-quality data
Services include low-bioburden processing and accurate DNA/RNA isolation using the
ZymoBIOMICS product line for the most accurate taxonomic profiling

and

s
Analysi

Validated, Non-Biased Workflows from Collection to Analysis

Bacillus subtilis (G+)
Listeria monocytogenes (G+)
Staphylococcus aureus (G+)
Enterococcus faecalis (G+)
Lactobacillus fermentum (G+)
Salmonella enterica (G-)

ZymoBIOMICS Services are validated using the

ZymoBIOMICS Microbial Community Standards
for unbiased, accurate community profiling

Escherichia coli (G-)

Peudomonas aeruginosa (G-)

ZymoBIOMICS
Services

Comprehensive, Customizable Bioinformatics & Data Analysis

Composition Barplots

Beta-Diversity

LEfSe Cladogram

Inquire Today!
Our qualified service professionals are happy to help accelerate
your research with services custom-tailored to meet your needs.
To learn more, please give us a call or send us an email at
services@zymoresearch.com or visit at
www.zymoresearch.com/zymobiomics
Services are powered by the latest Next-Gen sequencing technologies.

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Related Products
From TRIzol to high-quality RNA in 7 minutes
without phase separation

Direct-zol RNA Kits

Product
Sample in TRIzol

Bind RNA directly

Elute RNA

Direct-zol RNA MiniPrep Plus

Direct-zol RNA MiniPrep

Direct-zol RNA MacroPrep

Add binding agent

to a spin-column

ready to use

Direct-zol-96 RNA MiniPrep Plus

Size

Cat. No.

50 preps

R2070; R2071*

200 preps

R2072; R2073*

50 preps

R2050; R2051*

200 preps

R2052; R2053*

50 preps

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200 preps

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2 x 96 preps

R2054; R2055*

4 x 96 preps

R2056; R2057*

*Supplied with TRI Reagent

Select-a-Size DNA Clean & Concentrator Kits

Select for DNA species 50 bp, 150 bp,
200 bp, 300 bp, 700 bp or perform double
size selection
Product
Select-a-Size DNA Clean and Concentrator allows for selection at 300 bp,
200 bp, 150 bp, 100 bp and 50 bp.

Select-a-Size DNA Clean &

Concentrator

Zymoclean DNA Gel Recovery

Size

Cat. No.

25 preps

D4080

Boost recoveries from agarose

gels to > 80%

Product

Size

Cat. No.

23 kb 9 kb -

Zymoclean Gel DNA Recovery Kit

(uncapped)

50 preps

D4001

200 preps

D4002

Zymoclean Gel DNA Recovery Kit

(capped)

50 preps

D4007

2 kb -

200 preps

D4008

2 x 96 preps

D4021

4 x 96 preps

D4022

25 preps

D4045

100 preps

D4046

500 bp DNA fragments recovered from an agarose gel using the

Zymoclean Gel DNA Recovery Kit. Lanes: M: DNA Ladder; 1-5:
individual ladder DNA fragments.

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ZR-96 Zymoclean Gel DNA Recovery

Kit
Zymoclean Large Fragment DNA
Recovery Kit

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ZymoBIOMICS Products
crobiomic
Mi

Standards
Sample

Product

Size

Cat. No.

ZymoBIOMICS Microbial Community Standards

10 preps.

D6300

200 ng

D6305

2,000 ng

D6306

Size

Cat. No.

50 ml

R1100-50

250 ml

R1100-250

25 ml

R1200-25

125 ml

R1200-125

DNA/RNA Shield - Fecal Collection Tube

10 pack

R1100-9-T

DNA/RNA Shield - Swab & Collection Tube

50 pack

R1100-1-ST-50

50 pack

R1100-1-B15 (Microbe)

50 pack

R1100-1-B2 (Tissue)

ZymoBIOMICS DNA Standards

Product
DNA/RNA Shield Reagent

Collection

DNA/RNA Shield Reagent (2X concentrate)

DNA/RNA Shield - Lysis Tube

A/RNA
DN

Isolation

Product

Size

Cat. No.

ZymoBIOMICS DNA Mini Kit

50 preps.

D4300

ZymoBIOMICS DNA Micro Kit

50 preps.

D4301

ZymoBIOMICS-96 Magbead DNA Kit

2 x 96 preps.

D4302

2 x 96 preps.

D4303

4 x 96 preps.

D4304

ZymoBIOMICS RNA Mini Kit

50 preps.

R2001

ZymoBIOMICS DNA/RNA Mini Kit

50 preps.

R2002

Product

Size

Cat. No.

50 rxns.

E2056

200 rxns.

E2057

Femto Bacterial DNA Quantification

100 rxns.

E2006

Femto Human DNA Quantification

100 rxns.

E2005

Femto Fungal DNA Quantification

100 rxns.

E2007

ZymoBIOMICS-96 DNA Kit

Lib

rary Prep

ZymoBIOMICS PCR Premix

an
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Innovation. Pure & Simple.

Since its inception in 1994, Zymo Research has been proudly serving the scientific
community by providing innovative, reliable, and high quality research tools at
affordable prices. Our vision... The Beauty of Science is to Make Things Simple
is now truer than ever. Whether its epigenetics, DNA, RNA, E. coli, or yeast based
research, our philosophy remains the same: To provide the highest quality products
in the industry while ensuring they are both simple to use and reliable in their
performance.
Zymo Research stands on three pillars which form the foundation of our company:
Innovation, Quality, and Customer Service. These pillars are fundamental to our
culture and ensure our products meet your needs.
Innovation
Zymo Research is historically recognized for its innovation of high quality nucleic
acid purification technologies. Under the branding DNA Purification Made Simple
and RNA Purification Made Simple, our technologies are pushing the limits of
what is possible with nucleic acid isolation. As The Epigenetics Company, Zymo
Research has also received much attention for its rapidly expanding portfolio of
epigenetics products and services. It is our objective to develop and provide the
most comprehensive set of tools for DNA, RNA, and epigenetic research and
analysis available today. Thousands of peer-reviewed scientific publications from
researchers around the world feature our technologies. Through innovation, our
scientists have made streamlined DNA methylation detection possible, pioneered
the micro-elution column for DNA and RNA purification, developed the simplest
and the most sophisticated methods for high-quality plasmid DNA purification, and
patented the first RNA purification directly from Trizol without phase separation
among many other leading technologies in the industry.
Quality
We are committed to quality and guarantee that all of our products and service
will meet and exceed your expectations. Our products are constantly evaluated by
scientists like you to help ensure their reliability and the highest standard of quality.
Customer Service
We strive for excellence in how we support your scientific endeavors. We pledge to
be honest and responsible for everything we do with you. We will treat you as we
would like to be treated. Together, we will build a brighter future.

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