OMNIgene®•SKIN (OMR-140): an optimized collection device
for the capture and stabilization of the human skin microbiome
Anne Bouevitch, Jean Macklaim and Brice Le François
DNA Genotek, Ottawa, Ontario, Canada
2020-09-22

Introduction
The human skin is a vast and diverse environmentthat harbours hundreds of bacterial species as well
as fungal and viral taxa in lower relative abundance.
The discrete regions of the human skin can bedivided into three main subgroups: sebaceous, wet
and dry, all of which exhibit different physical andchemical properties and tend to harbour different
microbial populations. As the skin surface isgenerally poor in nutrients, has exposure to external
environments, and lacks a mucosal surface, it cannot
sustain microbial biomass associated with morecommonly studied internal body sites, such as thegut or oral cavity. Low average microbial abundanceand significant variability between potential
collection sites make skin microbiome sampling
notoriously difficult, and warrant the developmentof a standardized and fit-for-purpose collection
method. To this end, DNA Genotek™ has developed
OMNIgene®•SKIN (OMR-140), a swab-based skinmicrobiome collection device that effectively capturesand stabilizes the human skin microbiome across all
major sampling sites.

Material and methods
Sample collection
Healthy donors self-collected microbial samples
from a variety of skin sites using OMNIgene•SKIN
following the device Instructions For Use (IFU).
Briefly, the swab was immersed in the provided
wetting solution and used to collect microbial
cells from the skin surface of interest: face, scalp,
toe web, axilla or forearm. An area approximately
2.5 in × 2.5 in (6.35 cm × 6.35 cm) (if applicable)
was rubbed for a total of 60 seconds. The swab wasthen stored in the stabilization solution (OMNIgene®
collection tube) until extraction.

PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

For skin collection performance experiments, paired
samples were collected using two devices: eNAT™
specimen collection device (Copan Diagnostics,
Murrieta, CA, USA) and the Swab collection andDNA preservation system (Norgen Biotek Corp.,
Thorold, ON, Canada). Collection instructions fromthe Human Microbiome Project (HMP)1 were used
for both these devices as IFUs for the collection ofskin samples were not provided by the manufacturers.
For simulated collections, 2N puncture resistantartificial skin (SynDaver®, Tampa, FL, USA) was used.
To assess collection performance, decreasing amountsof an overnight culture of Francisella philomiragia(ATCC 25017) were spread on a 2.5 in × 2.5 in(6.35 cm × 6.35 cm) piece of artificial human skinand allowed to dry for 5 minutes. Samples werethen collected using OMNIgene•SKIN devices as
per the IFU.

Extractions and qPCROMNIgene•SKIN-collected samples were extractedusing QIAamp® PowerFecal® Pro DNA Kit(QIAGEN®, Germantown, MD, USA) or our
optimized extraction workflow, an in-house protocol
specifically developed for low biomass samples.
A high-throughput version of this optimized
extraction method is also available for Diversigen®
customers. DNA was quantified using PicoGreen™
and used as a template in qPCR assays and/or next
generation sequencing (NGS) applications. Samples
collected with Copan’s eNAT device were extractedwith PowerFecal Pro DNA Kit while samples collectedusing the Norgen device were extracted using
Norgen’s saliva DNA isolation kit. Recovery of
F. philomiragia from artificial skin was determined
by qPCR using primers targeting iglC3(Fwd 5’-AGCCAACAGAACTTATGGGTGT-3’
and Rev 5’-ACTTGCAGCACCGCATACA-3’).
Serial dilutions of F. philomiragia gDNA wereused as a standard curve.

www.dnagenotek.com • support@dnagenotek.com

16S copy number in extracted DNA was also
determined by qPCR using universal bacterial
primers (Fwd 5’-ATTACCGCGGCTGCTGG-3’;
Rev 5’- CCTACGGGAGGCAGCAG-3’).
Serial dilutions of E. coli gDNA were used
as a standard curve.

Sequencing and analysis
Library preparation and sequencing were conductedby amplification of the 16s rRNA gene V3-V4
hypervariable regions (bacterial) and the internaltranscribed spacer 2 (ITS2) (fungal). Paired-end
sequencing was performed using PE-300 V3 kit (2x300)
on an Illumina MiSeq® platform. Raw sequence data
were processed using a DADA2 (v 1.14.1) workflow2.
Briefly, primers were removed (Cutadapt 2.1)3,
and reads were quality filtered and trimmed.
Using DADA2’s error estimation model, reads
were dereplicated, merged into full-length amplicons,and chimeras were removed before generating
the amplicon sequence variants (ASVs) used fordownstream analyses. ASVs were assigned taxonomy
via DADA2 using the SILVA v132 database4(for 16S amplicons) or the UNITE (10.10.2017)
database5 (for ITS2 amplicons). Only ASVs having
at least 100 reads total, and at least 1% abundancein any one sample were retained for downstream
analyses. The filtered 16S dataset had a medianof 91780 reads per sample (IQR: 41574, 107120)
and for ITS2 a median of 37811 reads per sample(IQR: 17511, 68479). For whole genome sequencing(WGS), samples were sequenced using BoosterShot™
methodology (Diversigen, New Brighton, MN, USA)on Illumina’s NovaSeq™ platform, and downstreamA

OMNIgene•SKIN sample

B

Add Proteinase K andincubate for 1 hour at 50°C

Results
An optimized workflow to maximize yields
from OMNIgene•SKIN collected samples
Skin samples tend to yield particularly low amountsof microbial DNA which can lead to significant issues
in downstream processing such as poor or lack ofamplification in PCR assays or amplification of
background DNA contamination stemming fromprocessing steps or inappropriate collection means.
To maximize yields from OMNIgene•SKIN devices,
we developed two optimized extraction workflows
where the entire sample can be processed in a single
extraction. Using both approaches, presented in
Figure 1A, we were consistently able to recover

PFP (with upfront SpeedVac)

DNAG (in-house bead beating extraction)

800

Transfer andconcentrate down to250 µL using SpeedVac(recommended)

600
DNA yields (ng/kit)

Discard swab

Extract entire sample (1 mL)
with DNA Genotek’s in-housebead beating protocol

sequence processing and taxonomic annotation
were performed within Diversigen’s CoreAnalysis™
pipeline. The feature counts table was filtered to keeptaxa that were present in at least 2 samples and witha total of 10 reads or more, resulting in a median of
3412298 reads per sample (IQR: 1436762, 6552988).
Further data analyses and raw figure generation were
performed in R6 using the ggplot27 and MicrobeR8
packages. For statistical analysis, taxonomic tablewere filtered to an appropriate level for each analysis,
and transformed to centre log-ratios (CLR). Changes
in the total microbial profile between pairs of samples
were measured with Aitchison’s distance, and bydifferential analysis of each taxonomic component
using ALDEx29; differences were only reported
if statistically significant. Taxonomic barplots are
represented as percent abundance per taxonomic
group out of total filtered reads.

Extract 250 µL (concentrated)with PowerFecal Pro

400
200
20
15
10
5
0

Face
Scalp
(sebaceous) (sebaceous)

Forearm(dry)

Toe web(wet)

Axilla(wet)

Environmental
controls

Figure 1: Processing steps for optimal DNA recovery from OMNIgene•SKIN samples. (A) Schematic of the optimized workflows allowing
processing of the entire sample: PowerFecal Pro DNA Kit (PFP) vs. DNA Genotek’s in-house bead beating extraction protocol (DNAG). (B) Total DNA
yields (ng) extracted from samples collected in OMNIgene•SKIN from the 5 commonly studied sites which together represent three major types ofskin sites (sebaceous, dry and wet). Paired samples collected by 8 donors were extracted using either PFP or DNAG protocol and quantified using
the PicoGreen assay. Mean DNA yield from each site is presented here.

PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

www.dnagenotek.com • support@dnagenotek.com

2

detectable levels of DNA from all skin sites sampledwith OMNIgene•SKIN, including particularly
low biomass regions such as forearm (dry skin).
As expected, yields were highest for sebaceous skin(151 ng/kit ± 79 ng for face and 110 ng/kit ± 104 ng
for scalp), lowest for dry skin (11.4 ng/kit ± 8.6 ng
for forearm), while wet skin sites were highly variable(146 ng/kit ± 231 ng for toe webs and 4.9 ng/kit ±3.6 ng for scalp) (Figure 1B). Importantly, theamount of DNA extracted from environmental
control samples was quite low and represented on
average less than 5% of the total DNA extracted fromtoe web, scalp and face samples and approximately
30% of the total DNA extracted from forearm
samples. This is indicative of an overall low
bioburden in the OMNIgene•SKIN device.

A

OMNIgene•SKIN accurately captures site-specificbacterial and fungal profiles
We next assessed the performance of DNA samples
extracted from OMNIgene•SKIN samples in highthroughput sequencing assays. Samples collectedfrom all skin sites showed robust amplification in
16S and ITS2 amplicon sequencing applications.
Final library concentrations from collected samples
were at least 5× higher than those of corresponding
environmental controls, which confirms the low
overall bioburden of the device.
16S taxonomic profiles revealed thatOMNIgene•SKIN captures bacterial taxa known
to be associated with discrete skin sites (Figure 2A).
For instance, Cutibacterium (formally known

C

Bacterial relative abundances
100

Compositional PCA plot
Skin site

Genus level

Face

Other

Toe web

Anaerococcus
Dermacoccus
Clostridium sensu stricto 13

50

Streptococcus

PC2: 12.8%% Abundance

Scalp

0.04

Facklamia

75

0.00

Neisseriaceae (family)
Lawsonella

25

−0.04

Corynebacterium 1
Staphylococcus
Cutibacterium0
Forearm

B

Face

Scalp

Toe web

−0.08
−0.03

0.00

0.03

0.06

PC1: 26.9%

Fungal relative abundances
100

Genus level
Other
Malasseziales (order)% Abundance

75

Trichophyton
Debaryomyces
Mrakiella

50

Saccharomyces
MrakiaAscomycota (phylum)

25

CandidaCyberlindnera
Malassezia

0
Forearm

Face

Scalp

Toe web

Figure 2: Bacterial and fungal taxonomic profiles of skin microbial samples collected from the forearm (dry), face and scalp (sebaceous)and toe webs (wet) using OMNIgene•SKIN. (A) 16S rRNA gene was amplified using primers targeting V3-V4. Relative abundance plot was
generated from the filtered amplicon sequence variant (ASV) data classified using the SILVA database and aggregated to genus-level, or lowest
assignable taxonomic level as denoted in brackets. (B) For fungal analysis the ITS2 region was amplified by PCR and the relative abundance plot
was generated from the filtered ASV data classified using the UNITE database and aggregated to genus-level, or lowest assignable taxonomic level
as denoted in brackets. In both (A) and (B), the top 10 most abundant taxa from 4 representative donors are shown with the remaining reads
grouped as “other”. (C) Principal component analysis (PCA) plot of samples collected from the scalp, face and toe web using OMNIgene•SKIN.
Samples were sequenced by WGS and taxonomic assignment was performed within Diversigen’s BoosterShot and CoreAnalysis workflows.
Aitchison distance was calculated between samples, and the first two components explaining the most variation between samples (PC1: 26.9%
and PC2: 12.8%) are shown. Ellipses represent the 95% confidence interval for each sample group (face, scalp, and toe web).
PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

www.dnagenotek.com • support@dnagenotek.com

3Given the relatively high concentrations of DNA
recovered from several skin sites, we also performed
WGS on OMNIgene•SKIN samples collected fromthe face, scalp and toe webs. Samples collected fromthe face and scalp consistently yielded high enoughconcentrations of DNA for WGS, compared to
40% of samples collected from the toe web (Table 1).
In WGS, the proportion of reads mapping to bacterial
genomes was highly site and donor dependent, withsebaceous skin sites averaging 30% bacterial reads.
Overall, taxonomic profiles were similar to the ones
observed with 16S amplicon sequencing (data notshown). WGS increased our ability to detect thediscrete taxonomic profile differences between thethree different sites (Figure 2C), especially between
toe web samples (wet) and sebaceous skin sites(face/scalp). Moreover, we were able to detect up
to 20 unique Cutibacterium acnes strains in our
WGS dataset, with face and scalp samples having
the highest prevalence of detectible C. acnes, andtoe web having little to none (Table 1).
Proportion of
Average
Number ofsamples compatible proportion of Cutibacteriumwith WGS
bacterial reads acnes strain([DNA] > 0.5 ng/µL)(Range)detectedFace(sebaceous)

100%

Scalp
(sebaceous)

100%

Forearm(dry)0%

Toe web
(wet)

40%

27%
(8 to 63%)20

38%
(6 to 63%)

20

N/A
96%
(93 to 99%)

OMNIgene•SKIN stabilizes the skin microbial
profile at room temperature and during transportand storage without introducing a bias
To assess stability of the skin microbial samples
collected in OMNIgene•SKIN, paired half-facesamples (left vs. right) were collected from 20 donors.
One sample from each pair was extracted at baseline
while the matching sample was stored at room
temperature (20°C to 26°C / 68°F to 79°F) for up to
30 days then extracted. Bacterial profiles were thengenerated using 16S rRNA gene (V3-V4) ampliconsequencing and analyzed for each sample pair. The
difference in total microbial profile following storage
at room temperature for 30 days was not significantly
different from normal biological sampling variability
seen between replicate samples (left vs. right) extracted
at baseline (control group), and much lower than the
differences observed between donors (Figure 3A).

A

Difference in microbiome profile (Aitchison distance)
****

50






40

Aitchison distanceas Propionibacterium) was primarily associatedwith sebaceous skin sites (face and scalp) while
Corynebacterium and Staphylococcus were the twodominant genera on toe webs (wet skin site),as previously reported10. Similarly, ITS2 taxonomic
profiles showed that Malassezia was found at highrelative abundance on sebaceous and dry skin of the
majority of donors while a greater diversity of fungal
genera was detected on toe webs (Figure 2B).




















30



20
Medianbiologicalvariablity
10










N/A

Table 1: Overview of WGS outcome for OMNIgene•SKIN samples.
The proportion of samples meeting library prep input requirement([DNA]>0.5 ng/µL) as well as the average proportion of reads mapping
to bacterial genomes are shown and expressed as percentages.
The number of unique Cutibacterium acnes strains detected following
WGS is also shown for the two sebaceous sites sampled in our study(face and scalp).


























































































50°C

N/A

























ns

37°C

F/T

Simulated shippingRT
30 days

Biological Donorvariability to-donor

Figure 3A: Microbial profile stability in OMNIgene•SKIN samples.
Groupwise comparison of Aitchison distance as a measure of stability
in microbial profile. Each point represents the difference between
a baseline sample (T0) and a paired sample from the same donor
extracted after simulated shipping (37°C for 3 days, 50°C for 1 day, or
3× cycles of freeze-thaw) or storage at room temperature for 30 days.
Significance testing was performed against T0 replicate variability(T0 paired left and right sample replicates) and donor-to-donor
variability. None of the condition tested exceeded the baseline (T0)variability, and therefore no significant changes were detected(Kruskal-Wallis non-parametric test, and two-group comparisonsusing a t-test).
Continued on next page.

PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

www.dnagenotek.com • support@dnagenotek.com

4

B

C

Bacterial relative abundances (30 days at room temperature)
100

Bacterial relative abundances (3 days at 37°C)
100

Genus level

Genus level

Other

75

Dietzia
Finegoldia

50

RothiaLawsonella
Streptococcus

25

Gemella75

Haemophilus% Abundance% Abundance

Other

Lactobacillus

Neisseria
Lawsonella
Rothia50

Chloroplast (order)
Streptococcus
Corynebacterium 1

25

Staphylococcus

Neisseriaceae (family)

Corynebacterium 10

Staphylococcus

Cutibacterium

T0

T30
A

T0

T30

T0

B

T30
C

T0

0

T30

Cutibacterium

T0

T3

T0

A

D

T3

T0

B

T3

T0

C

T3
D

Donor

Donor

Figure 3A and 3B: Microbial profile stability in OMNIgene•SKIN samples. (B, C) Taxonomic profile stability in OMNIgene•SKIN samples stored
at room temperature for 30 days (B) or 37°C for 3 days. (C) The 16S rRNA gene from T0 and T30 extracted samples was amplified using primers
targeting V3-V4 and the relative abundance plot was generated from the filtered amplicon sequence variant (ASV) data classified using the SILVA
database and aggregated to genus-level, or lowest assignable taxonomic level as denoted in brackets.

We also assessed if collection of a sample in an
OMNIgene•SKIN device could introduce a bias in
the microbial profile. Paired samples from each sideof a donor’s face (left vs. right) were collected from20 donors and placed in either OMNIgene•SKIN
stabilization solution or PBS (phosphate-bufferedsaline) and extracted within 30 minutes of collection.
Bacterial profiles were then generated using
16S amplicon sequencing and analyzed for each

PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

sample pair. Biological variability (left vs. right) was
similar between OMNIgene•SKIN and PBS collected
samples and again significantly lower than donor-todonor variability (Figure 4). Similarly, no detectablechanges in M. globosa levels (qPCR) were detected
when comparing OMNIgene•SKIN and PBS collected
samples (data not shown). Taken together, our datashows that sample collection with OMNIgene•SKIN
captures the donor’s unique microbiome signature
at the point-of-collection without impacting its
taxonomic composition.
Difference in microbiome profile (Aitchison distance)
****

50









40
Aitchison distance

A similar comparison was used to assess stabilityof samples during simulated shipping conditions(3× freeze/thaw cycles, 1 day at 50°C (122°F) or
3 days at 37°C (98.6°F)). Data showed that no
significant changes in the overall variability wereintroduced by any of these conditions (Figure 3A).
Importantly, no taxa were found to be differentiallyexpressed in paired samples for any of the groups(ALDEx2: effect size <1, p-adj >0.05), and thetaxonomic profiles from individual donors weremaintained after storage at room temperature for
30 days (Figure 3B) or simulated shipping conditions
such as incubation at 37°C for 3 days (Figure 3C),
incubation at 50°C for 1 day or 3 cycles of freezethaw (data not shown). Fungal profile stability was
also assessed, by spiking live Malassezia globosa cells
in OMNIgene•SKIN samples collected from the face.
qPCR analysis showed that fungal levels remained
stable during simulated shipping and storage at room
temperature for 30 days (data not shown). This
demonstrates that OMNIgene•SKIN maintains thestability of the microbial profile from the point-ofcollection to point-of-extraction even when subjected
to harsh shipping conditions or storage at room
temperature for up to 30 days.














30












ns











20






















10

















PBS

OMR-140

Donorto-donor

Figure 4: Sample collection in OMNIgene•SKIN is neutral anddoes not introduce a bias in the microbial profile. Groupwise
comparison of Aitchison distance as a measure of change in the
microbial profile. Each point represents the difference in paired
samples (left vs. right side of the face) collected either in PBS or
OMNIgene•SKIN (OMR-140) and extracted at baseline (T0). There wasno difference in sampling variability for either collection method at T0,
and the differences between sample replicates in both PBS andOMNIgene•SKIN was significantly lower than the donor-to-donor
differences. Significance tested with Kruskal-Wallis non-parametrictest, and two-group comparisons using a t-test.

www.dnagenotek.com • support@dnagenotek.com

5

OMNIgene•SKIN collects superior
skin microbiome samples

Futhermore, we assessed the effectiveness of our IFUs
for skin microbiome sampling. Paired skin face(left and right) samples were collected in our device
using either our optimized IFUs or the standard skincollection instructions from the Human Microbiome
Project (HMP protocol) and DNA was extracted with
our optimized workflow. DNA yields for samples
collected following our IFUs were significantly higher
than for samples collected with HMP instructions(Figure 5C). This illustrates the effectivenessof our device’s IFU in ensuring better collection
performance which is paramount for successful
sampling of low biomass sites.

We compared the collection performance ofOMNIgene•SKIN to commonly used skinmicrobiome collection devices (Copan’s eNAT
specimen collection device and Norgen’s swab
collection and DNA preservation system) by collecting
paired cheek (sebaceous skin) or forearm (dry skin)samples from healthy adults. Our data shows thatDNA concentrations were consistently higher for
OMNIgene•SKIN collected samples than samples
collected with the other devices (Figure 5A). This wasparticularly pronounced for forearm samples where
yields were 3 to 4-fold higher on average when collectedwith OMNIgene•SKIN. In fact, DNA concentrations
collected from forearm were indistinguishable
from environmental controls for >50% of donors
when using the other swab-based devices.

Qualitative performance of theOMNIgene•SKIN device
The human skin has a highly variable microbial
density11,12 with dry skin harboring approximately
103 microbial cells/cm2 of skin, while richer sites suchas sebaceous skin can harbor as many as 109 cells/cm2.
To better assess the qualitative performance andcollection efficiency of OMNIgene•SKIN devices,
we designed an experiment where decreasing (log10)
amounts of a bacterial culture were spiked on artificial
skin and collected with OMNIgene•SKIN. Using aqPCR assay, we were able to demonstrate that theWe also quantified the average number of 16S copies/μL
recovered from cheek samples, and inferred thatOMNIgene•SKIN collects more bacterial cells thanother kits tested (Figure 5B). Moreover, the relatively
high concentrations of 16S copies recovered fromOMNIgene•SKIN samples is indicative of consistent
performance across multiple donors.

OMR-140

Norgen

2.0

1.5
1.0
0.5

1.5
1.0
0.5
0.0

0.0
Cheek

0.2
0.1

0.12
0.08

0.0
Cheek

B

Forearm

Environmental
controls

OMR-140
IFU

HMP
protocolForearm

Environmental
controls

C
1 × 106

100

1 × 105

DNA yields/kit (ng)

16S copy number/µL

0.16

0.3
[DNA] (ng/µL)[DNA] (ng/µL)

2.0[DNA] (ng/µL)

Copan[DNA] (ng/µL)

A

1 × 104
1 × 103
1 × 1021 × 101

75
50
25
0

Cheek

Figure 5: OMNIgene•SKIN offers superior collection performance and improved usability. (A) Paired cheek and forearm samples were collectedusing either OMNIgene•SKIN (OMR-140) or other swab-based collection devices (Norgen and Copan) from a total of 9 or 10 donors. DNA was extractedusing the QIAamp PowerFecal Pro DNA Kit (for OMR-140 vs. Copan) or Norgen Saliva DNA isolation kit (for Norgen vs. OMNIgene•SKIN) and quantified
using PicoGreen. DNA concentration is shown for each donor and each sampled body site. (B) Average 16S copy number per µL of eluate (geometricmean ± geometric SD) in cheek samples collected with OMNIgene•SKIN vs. other swab-based collection device. 16S copy number was measured by qPCR
using universal bacterial primers. (C) Impact of the end-user performance on OMNIgene•SKIN DNA yields. Paired face samples were collected using
OMNIgene•SKIN following our optimized IFUs (OMR-140 IFU) or standard collection instructions from the Human Microbiome Project (HMP protocol).

PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

www.dnagenotek.com • support@dnagenotek.com

6

recovery rate of the spiked bacteria (F. philomiragia)
with OMNIgene•SKIN was consistent across several
logs, with an average recovery around 38% (Figure 6).
Notably, we were able to efficiently recover and detect
as low as 104 bacterial cells spread on a 6.25 in2
surface (40 cm2). This indicates that our collection
methodology and processing workflow efficiently
recover very low bioloads. This confirms the device’s
excellent performance with dry skin where total
number of bacteria on a 6 in2 surface is expected
to be <105 cells.

CFUs recovered (%)

100

75

Conclusions•

OMNIgene•SKIN efficiently captures andstabilizes the microbiome profiles (bacterial
and fungal) of commonly studied skin sites(sebaceous, wet and dry), for downstream
high-throughput sequencing and qPCR
applications.

•

The collected skin microbial profile is stable
during shipping at ambient temperature and up
to 30 days during storage at room temperature.

•

OMNIgene•SKIN’s enhanced IFUs are optimized
for collection of low biomass samples, ensuring
superior performance.

50

25

0

109

108

107

106

105

104

Spiked amount of F. philomiragia (CFUs)

Figure 6: Collection performance of OMNIgene•SKIN. Increasing
amounts of a F. philomiragia culture were spread on artificial skin
(SynDaver) and allowed to dry. The spiked bacteria were then collectedusing our device following our standard IFUs and DNA was extracted using
our optimized workflow (bead beating). Recovery of F. philomiragia wasassessed using a qPCR assay targeting the iglC3 gene and was calculated
as a percentage of the total CFUs spiked on the artificial skin surface.
References
1
2
3
4
5
6
7
8
9
10
11
12

Manual of Procedures for Human Microbiome Project Core Microbiome Sampling Protocol A, HMP Protocol # 07-001 Version
Number 12.0, 29 Jul 2010.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina
amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038/nmeth.3869
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17(1):10-12.
doi:https://doi.org/10.14806/ej.17.1.200.
Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Nucleic Acids Res. 2013;41(Database issue):D590-D596. doi:10.1093/nar/gks1219
Nilsson RH, Larsson KH, Taylor AFS, et al. The UNITE database for molecular identification of fungi: handling dark taxa andparallel taxonomic classifications. Nucleic Acids Res. 2019;47(D1):D259-D264. doi:10.1093/nar/gky1022
R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna,
Austria. URL https://www.R-project.org/.
Wickham H. Ggplot2: Elegant Graphics for Data Analysis. Springer. 2016. doi: 10.1007/978-0-387-98141-3
MicrobeR: Handy functions for microbiome analysis in R. R package version 0.3.2. URL https://github.com/jbisanz/MicrobeR
Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB. Unifying the analysis of high-throughput sequencing
datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.
Microbiome. 2014;2:15. Published 2014 May 5. doi:10.1186/2049-2618-2-15
Kong HH, Segre JA. Skin microbiome: looking back to move forward. J Invest Dermatol. 2012;132(3 Pt 2):933-939. doi:10.1038/jid.2011.417
Ross AA, Rodrigues Hoffmann A, Neufeld JD. The skin microbiome of vertebrates. Microbiome. 2019;7(1):79. Published 2019
May 23. doi:10.1186/s40168-019-0694-6
Leyden JJ, McGinley KJ, Nordstrom KM, Webster GF. Skin microflora. J Invest Dermatol. 1987;88(3 Suppl):65s-72s.
doi:10.1111/1523‑1747.ep12468965

OMNIgene®•SKIN (OMR-140) is for Research Use Only, not for use in diagnostic procedures.
Some DNA Genotek™ products may not be available in all geographic regions.
®OMNIgene is a registered trademark and DNA Genotek is a trademark of DNA Genotek Inc. All other brands and names contained herein are the property of their respective owners.
All DNA Genotek protocols, white papers and application notes, are available in the support section of our website at www.dnagenotek.com..

PD-WP-00067 Issue 1/2020-09© 2020 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

www.dnagenotek.com • support@dnagenotek.com

7