OMNIgene™•ORAL and OMNIgene™•VAGINAL devices are validated tools
for the collection and stabilization of nucleic acids from oral and vaginal
microbiome samples
Anne Bouevitch, Evgueni Doukhanine and Brice LeFrançois
DNA Genotek, Ottawa, Ontario, Canada
2023-04-12

Introduction
In recent years, we have gained better understandingof the critical role the human microbiome plays inhealth and disease.1-3 The oral and vaginal cavities
are highly distinct ecological niches and, as such,
harbour distinct microbial communities.4 Beyondsite-specific bacterial profiles, significant differences
can exist between donors and their microbialcommunity structures and individual profiles canchange over time.5,6 Having the appropriate tools
to collect and stabilize human microbiome samples
is critical for microbiome studies. These tools must
be able to capture unique microbial profiles that
represent the in vivo state as closely as possible.
DNA Genotek has developed and validated 3 swabbased microbial collection devices for the study ofthe gum/plaque, tongue or vaginal microbiome.
In this paper, we show that microbial nucleic acids(DNA and RNA) as well as microbial profiles ofsamples collected with OMNIgene™•ORAL orOMNIgene™•VAGINAL devices remain stable
during shipping or storage at room temperature.

Materials and methods
Sample collection and processing
Donors collected oral and vaginal microbiome
samples using OMNIgene devices (OMR-110,
OMR-120 or OMR-130) following the instructions
supplied with the products. When collecting paired
samples (i.e., multiple tubes), donors were instructedto collect from the right and left gums (OMR-110)
and the right and left sides of the tongue (OMR-120).
For OMR-130, donors were to collect two vaginal
samples. Upon collection, swabs were immediately
placed into OMNIgene collection tubes, except forneutrality testing purposes where collected swabs
were immersed in TES buffer (10 mM Tris-HCl
pH7.5, 1 mM EDTA, 100 mM NaCl) and extracted
immediately. Collected OMNIgene samples were
PD-WP-00076 Issue 1/2023-04© 2023 DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc., all rights reserved.

extracted at baseline (T0), after storage at room
temperature (23°C ± 3°C) or -80°C for 30 days orafter 3 freeze-thaw cycles (20°C to +30°C, with aminimum of 3 hours at each temperature). Prior to
nucleic acid extraction, samples were treated withProteinase K for 1 hour at 50°C.

DNA and RNA extraction, quantification and qPCR
DNA was extracted from a 250 µL aliquot using theMasterPure™ Complete DNA and RNA Purification
Kit (Lucigen®). Final DNA pellet was reconstituted
in 50 µL H2O. RNA was extracted from a 250 μL
aliquot using the RNeasy® PowerMicrobiome® Kit(QIAGEN®) and eluted in 100 µL H2O. DNA wasquantified with the Quant-iT™ PicoGreen™ dsDNA
Assay Kit (Thermo Fisher Scientific) and quality wasassessed by running samples on a 0.8% agarose gel.
RNA quality and concentration were determinedby running samples on RNA 6000 Pico Chips on
a 2100 Bioanalyzer system (Agilent Technologies).
Relative bacterial DNA content in oral and vaginal
microbiome samples was determined by qPCR using
universal bacterial primers targeting the 16S rDNA
gene (BacrRNA173‐F 5’-ATTACCGCGGCTGCTGG;
BacrRNA173‐R 5’-CCTACGGGAGGCAGCAG 3’).
Serial dilutions of E. coli gDNA were used to generatea standard curve and as a control (pure bacterial DNA).

Sequencing and analysis
Library preparation was conducted by amplificationof the 16S V3-V4 hypervariable regions(Fwd: 5’- CCTACGGGNGGCWGCAG-3’; Rev: 5’GACTACHVGGGTATCTAATCC-3’). For RNA
profile analysis, an aliquot of total RNA (7 µL)
was reverse transcribed into cDNA using random
hexamers and MMLV-RT. 2.5 µL cDNA and 12.5 ng
DNA were used as an input into the V3-V4 16S PCR
reaction, respectively. Final libraries were pooled, andpaired-end sequencing was performed using PE-300
V3 kit (2 x 300 bp) on a MiSeq® System (Illumina®).
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For whole genome sequencing (WGS), samples
were sequenced using Diversigen’s proprietary
BoosterShot™ pipeline on an Illumina NovaSeq
platform, and downstream sequence processing
and taxonomic annotation were performed within
Diversigen’s Core Analysis™ pipeline. Jensen-Shannon
divergence was calculated on species-level taxonomic
annotation after subsetting samples to a read depthof 14,000 reads. Principal coordinate analysis (PCoA)
plots were generated in R using the phyloseq package.
Taxonomic bar plots showing the percentage
abundance at genus level were calculated fromthe total read depth per sample.

Results
Oral and vaginal microbiome samples havevarying amounts of host DNA
OMNIgene•ORAL and OMNIgene•VAGINAL areswab-based collection devices that were specificallydeveloped to collect gum/plaque (OMR-110), tongue(OMR-120) and vaginal (OMR-130) microbiome
samples. Unlike stool microbial communities,
oral and vaginal microbial communities are tightly
associated with host epithelial tissue, and as such asignificant amount of host material can be harvested
during the collection process. We collected oral andvaginal microbiome samples from 10 healthy donors
using OMR-110, OMR-120 or OMR-130 kits.

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Total DNA was extracted and the relative abundanceof bacterial DNA was determined using a qPCR
assay targeting 16S rDNA. We found that tongue
microbiome samples had a significantly higher
proportion of bacterial DNA (44% on average) than
did gum/plaque or vaginal samples (4% and 1.8%
on average, respectively) (Figure 1). We determinedthat tongue samples were the most challenging
sample to stabilize in the OMNIgene kits, as therelative abundance of bacteria was 10x-20x higher
than in the other sample types. As a result, weused tongue microbiome samples as a paradigm
in subsequent experiments (i.e., neutrality testing
and 30-day room temperature stability).
100

Bacterial DNA content (%)

For 16S V3-V4 hypervariable regions sequencing,
the FLASH algorithm7 was used for read merging
and automated rejection of low-quality sequences;quality screening for length and ambiguous bases was
performed in mothur.8 A closed-reference taxonomic
classification was performed where each sequence
was aligned to the Greengenes version 13.8 reference
database. Sequences were aligned at 97% sequence
identity using the NINJA-OPS tool, version 1.2(Knights Lab, unpublished data). A genus-level
table was calculated by summarizing the absoluteabundance before rarefaction. All samples wererarefied to an even sampling depth of 31,261 reads
per sample after taxonomic classification at theoperational taxonomic unit (OTU) level. Alpha
diversity metrics (Shannon index (SI), Chao1)
were obtained by measuring the proportion ofeach OTU relative to the total number of OTUs.
Bray-Curtis dissimilarity was calculated on therarefied OTU-level table with the beta_diversity.py
workflow in QIIME 1.9.1.

80

60

40

20

0
Gum/plaque(OMR-110)

Tongue(OMR-120)

Vaginal(OMR-130)

Figure 1: Tongue microbiome samples have higher relative
bacterial content than gum/plaque or vaginal microbiome
samples. Oral (tongue vs. gum/plaque) and vaginal microbiome
samples were collected by 10 donors in OMNIgene devices and
DNA was extracted. The relative proportion of bacterial DNA wasestimated based on 16S rDNA qPCR yields versus total concentrationof DNA determined through PicoGreen. Average bacterial DNA
content was 4% for gum, 44% for tongue and 1.8% for vaginal
samples. (*** p < 0.001 One-way ANOVA)OMNIgene•ORAL devices are neutral and do not
impact bacterial profiles upon sample collection
We first assessed if collection of a tongue microbiome
sample in OMNIgene•ORAL preservation buffer
would introduce a bias in the microbial profile.
Paired tongue microbiome samples (left side vs. rightside of the tongue) were collected by 8 donors witheither OMNIgene•ORAL (OMR-120) or Puritan
flocked swabs returned in 1 mL TES buffer (10 mM
Tris-HCl pH7.5, 1 mM EDTA, 100 mM NaCl).
DNA was extracted immediately after collection.

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B

5

600

4
400

3
2

200

Shannon index

Chao1 diversity

A

1
0

Donor todonor***
Fresh vs.
OMR-1200
OMR-120Fresh

OMR-120

Fresh

0.0

0.2

0.4

0.6

0.8

1.0

Bray-Curtis distance

Figure 2: Sample collection in OMNIgene•ORAL is neutral and has no detectable impact on tongue DNA microbial profiles.
(A) Alpha diversity metrics (Chao1 and Shannon index) are similar in fresh tongue samples compared to a sample collected in OMNIgene•ORAL
kits (OMR-120). n.s., non-significant Mann-Whitney test. (B) Beta diversity measure (Bray-Curtis dissimilarity) between paired tongue samples
from the same donor (fresh vs. OMR-120) as compared to donor-to-donor dissimilarity. (*** p < 0.001 Mann-Whitney test). Paired tongue
samples were collected (fresh vs. OMR-120) by 8 donors and DNA was extracted at baseline. Alpha and beta diversity metrics were generated
following 16S sequencing (V3-V4).

Bacterial profiles were generated by 16S ampliconsequencing and analyzed by donor. Alpha diversity
metrics (Shannon index, Chao1) (Figure 2A) weresimilar for samples collected with OMNIgene•ORAL
versus those in TES buffer (fresh), indicating thatspecies richness and evenness were not affected by
the use of preservation buffer in OMR-120. Similarly,
Bray-Curtis distance between paired samples
from the same donor (fresh vs. OMR-120) waslow (median = 0.28) and was significantly lower
than the dissimilarity seen when comparing
samples from different donors (Figure 2B).
This result demonstrates that collection in
OMNIgene kits has no detectable impact on
microbial profiles.

OMNIgene•ORAL devices preserve tongue andgum/plaque microbial nucleic acids and profiles
To assess nucleic acid stability during storage atroom temperature or during shipping at ambient
temperature, paired gum/plaque and tongue samples
were collected by 20 healthy individuals withOMNIgene•ORAL devices (OMR-110 and OMR-120).
DNA and RNA were extracted from each kit at baseline(T0) and following storage at room temperature/-80°C
for 30 days or 3 freeze-thaw cycles (-20°C to +30°C).
Freeze-thaw cycles were used to simulate harshconditions that can be encountered during shippingat ambient temperature. DNA and RNA yields werehighly donor- and site-dependent and were notimpacted by storage and/or freeze-thaw cycles (Table 1).

Table 1: Average DNA and RNA yields for samples collected in OMNIgene•ORAL devices (OMR-110 and OMR-120). DNA and RNA
were extracted from a 250 μL aliquot at baseline (T0), following storage at room temperature/-80°C for 30 days or for 3 freeze-thaw cycles.
DNA was quantified with the PicoGreen assay while RNA concentration was determined by running the samples on the RNA PicoChip.
Data are presented as mean ± standard deviation. Median yields are shown in brackets.

Gum/plaque(OMR-110)

Tongue(OMR-120)

AnalyteT0 (baseline)

3 freeze-thaw cycles

30 days at room
temperature

30 days at -80°C

DNA

1.6 ± 0.83 µg/kit(1.56 µg)1.68 ± 0.80 µg/kit(1.70 µg)

N/A

2.74 ± 1.02 µg/kit(2.31 µg)

RNA577 ± 571 ng/kit(428 ng)523 ± 713 ng/kit(258 ng)

N/A

N/A

DNA

2.54 ± 1.32 µg/kit(2.39 µg)2.81 ± 1.36 µg/kit(2.66 µg)3.52 ± 1.91 µg/kit(2.94 µg)3.65 ± 1.71 µg/kit(3.82 µg)

RNA490 ± 376 ng/kit(440 ng)929 ± 1062 ng/kit(566 ng)581.7 ± 377 ng/kit(424 ng)

N/A

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A

Donor A
T0

3x
F/T

Tube A

T0

Donor B-80
30d

Tube B

C

T0

3x
F/T

T0

Donor C-80
30d

Tube A

Tube B

RT
30d

Tube A

T0

3x
F/T

T0

3x
F/T

Tube A

Donor A
T0

T0

T0

B
-80
30d

Tube B

RT
30d

Tube A

T0

Donor B Donor C

T0

T0

3x
F/T

3x
F/T

T0

3x
F/T

Tube B

Donor B-80
30d

Donor A

D
3x
F/T

-80
30d

Donor A
T0

RT
30d

3x
F/T

Donor B
T0

RT
30d

3x
F/T

Tube B

Figure 3: OMNIgene•ORAL devices maintain DNA and RNA quality of collected oral microbiome samples (gum/plaque and tongue)
during extended storage at room temperature or following multiple freeze-thaw cycles. (A and B) DNA and RNA quality of gum/plaquesamples collected in OMNIgene•ORAL (OMR-110) and extracted at baseline (T0), after 3 freeze-thaw cycles (3x F/T) or storage at -80°C for 30 days(-80 30d). (C and D) DNA and RNA quality of tongue samples collected in OMNIgene•ORAL (OMR-120) and extracted at baseline (T0), after
storage at room temperature for 30 days (RT 30d), after 3 freeze-thaw cycles (3x F/T) or storage at -80°C for 30 days (-80 30d). Samples from
2-3 representative donors are shown.

For both OMNIgene•ORAL devices (OMR-110 and
OMR-120), DNA integrity was maintained whensamples were kept at room temperature for up to 30 daysor subjected to 3 freeze-thaw cycles (Figure 3A and 3C).
DNA quality was comparable to the quality of a sample
stored at -80°C, a control storage condition for nucleic
acids. Similarly, gum/plaque and tongue RNA quality
was largely unaffected by storage at room temperaturefor up to 30 days or following multiple freeze-thaw
cycles (Figure 3B and 3D). No significant differenceswere seen between samples stored 30 days at room
temperature and those put through 3 freeze-thaw cycles.
To assess sample stability in collected devices,
bacterial profiles across different post-collection time
points were generated from the extracted nucleic
acids using 16S amplicon sequencing targeting theV3-V4 region. Bray-Curtis dissimilarity between
OMNIgene•ORAL (OMR-110) samples extracted atbaseline (T0) and samples extracted after 3 freezethaw cycles was relatively small and comparable tothe dissimilarity between samples extracted at

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baseline (T0) and samples stored at -80°C for 30 days
(control) for both DNA and RNA (Figure 4A); in
contrast, comparisons between biological replicates(left gum line vs. right gum line) or across donors
showed greater distances (Figure 4A), as expected.
Taxonomic bar plots (genus level) further
demonstrate the stability of both DNA and RNA in
OMNIgene•ORAL devices with highly consistent
gum/plaque bacterial taxonomic profiles between
samples extracted at baseline (T0), subjected to
3 freeze-thaw cycles or stored at -80°C for 30 days
(Figure 4B and 4C). Similar DNA and RNA profile
stability was seen for tongue microbiome samples,
including following extended storage at room
temperature (Figure 5). Our results demonstrate thatOMNIgene•ORAL captures and maintains gum andtongue microbial profiles, during 30-day storage atroom temperature or following multiple freeze-thaw
cycles (Figure 4 and 5). Taken together, our data clearly
indicates that OMNIgene•ORAL is a highly effective
at-home collection tool for oral microbiome studies.

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A

A

-80°C 30 days
3x F/T
Biological variability
Donor to donor

DNA

DNA

-80°C 30 days
3x F/T
Biological variability
Donor to donor

RNA

RNA
0.0

0.2

0.4

0.6

0.8

-80°C 30 days
3x F/T
RT 30 days
Biological variability
Donor to donor-80°C 30 days
3x F/T
RT 30 days
Biological variability
Donor to donor

1.0

0.0

0.2

Bray-Curtis distance

Donor A

Donor B

80
60
40
20

T0

-80

T0

F/T

C

T0

-80

T0

Donor A

Donor B

Relative abundance (%)

40
20

T0

80
60
40
20

T0

C

60

-80

F/T

Veillonella
RothiaOther
Streptococcus
Actinomyce
Corynebacterium
Haemophilus

T0

-80

Donor BRT

T0 F/T

-80

T0

RT

Prevotella

Leptotrichia

Veillonella

Other

Neisseria

Actinomyces

RothiaStreptococcus

Porphyromonas

Oribacterium

Haemophilus

Bulleida

T0 F/T-80

Fusobacterium80

T0

Donor A

0

F/T

100

0

0.8

100

Actinomyces
Corynebacterium
Haemophilus
Capnocytophaga
Selenomosa
Leptotrichia
Campylobacter

Prevotella
Veillonella
RothiaOther
Fusobacterium
GemellaStreptococcus

Relative abundance (%)

B

100

0

0.6

Bray-Curtis distance

Relative abundance (%)

Relative abundance (%)

B

0.4

T0

F/T

Prevotella
Fusobacterium
Capnocytophaga
Selenomosa
Leptotrichia
Campylobacter
Cardiobacterium

Figure 4: OMNIgene•ORAL (OMR-110) stabilizes gum/plaquemicrobial profiles through multiple freeze-thaw cycles.
(A) Bray-Curtis dissimilarity for DNA and RNA samples extracted
following 3 freeze-thaw cycles or storage at -80°C for 30 days ascompared to baseline (T0). Donor-to-donor dissimilarity andbiological variability (difference between tube A and B at baseline)
are also shown for reference. (* p < 0.05, ** p < 0.01 and *** p < 0.001
Kruskal-Wallis test) (B and C) 16S taxonomic profiles (V3-V4 - genus
level) for paired DNA (B) or RNA (C) samples collected in OMR-110
devices and extracted at baseline (T0) after 3 freeze-thaw cycles orstorage at -80°C for 30 days. Bar plots from 2 representative donors
are shown.

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Donor A

Donor B

100
80
60
40
20
0
T0

RT

T0 F/T

-80

T0

RT

Prevotella

Actinomyces

Veillonella

Streptococcus

Neisseria

Oribacterium

RothiaCampylobacter

Fusobacterium

Porphyromonas

T0 F/T-80

Other

Figure 5: OMNIgene•ORAL (OMR-120) captures and stabilizes
tongue microbial profiles during extended storage atroom temperature or through multiple freeze-thaw cycles.
(A) Bray-Curtis dissimilarity for DNA and RNA samples extracted
following 3 freeze-thaw cycles, storage at room temperature for
30 days or storage at -80°C for 30 days as compared to baseline (T0).
Donor-to-donor dissimilarity and biological variability (difference
between tube A and B at baseline) are also shown for reference.
(* p < 0.05 and *** p < 0.001 Kruskal-Wallis test) (B and C) 16S
taxonomic profiles (V3-V4 - genus level) for paired DNA (B) or RNA (C)samples collected in OMR-120 devices and extracted at baseline andafter 3 freeze-thaw cycles or storage at -80°C and at room
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Table 2: Average DNA and RNA yields for samples collected in OMNIgene•VAGINAL devices (OMR-130). DNA and RNA were extracted
from a 250 μL aliquot at baseline (T0), following storage at -80°C for 30 days or for 3 freeze-thaw cycles. DNA was quantified with the
PicoGreen assay while RNA concentration was determined by running the samples on the RNA PicoChip. Data are presented as mean ±standard deviation. Median yields are shown in brackets.

Vaginal(OMR-130)

AnalyteT0 (baseline)

3 freeze-thaw cycles

30 days at room
temperature

30 days at -80°C

DNA

15.1 ± 6.5 µg/kit(13.4 µg)14.5 ± 7.1 µg/kit(15.3 µg)

N/A

17.3 ± 7.1 µg/kit(18.33 µg)

RNA

942 ± 521 ng/kit(823 ng)

820 ± 400 ng/kit(668 ng)

N/A

N/A

shown.

AOMNIgene•VAGINAL devices preserve vaginal
microbial nucleic acids and profiles
Paired vaginal microbiome samples were collectedby 20 healthy individuals with OMNIgene•VAGINAL(OMR-130) devices. Stability was assessed following
multiple freeze-thaw cycles, a treatment known tobe highly detrimental to nucleic acid stability. Briefly,
DNA and RNA were extracted from each sample atbaseline (T0) or following 3 freeze-thaw cycles(-20°C to +30°C with a minimum of 3 hours at
each temperature). As a control, samples were also
stored for 30 days at -80°C before DNA and RNA
were extracted. Freeze-thaw cycles had no detectable
impact on nucleic acid yields (Table 2) or on thequality/integrity of the extracted DNA and RNA(Figure 6A and 6B). High molecular weight DNA
and high-quality total RNA (as demonstrated by
the presence of intact 16S and 23S rRNA bands)
were recovered for all donors and conditions.

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Donor A
T0

-80
30d

Tube A

B

Donor B
3x
F/T

T0

Tube B

T0

-80
30d

T0

Tube A

Donor C
3x
F/T

Tube B

T0

Tube A

Donor A Donor B

Donor C

T0

T0

3x
F/T

T0

3x
F/T

-80
30d

T0

3x
F/T

Tube B

3x
F/T

Figure 6: OMNIgene•VAGINAL devices maintain DNA and RNA
quality of vaginal microbiome samples following multiple
freeze-thaw cycles. DNA (A) and RNA (B) quality of vaginal
microbiome samples collected using OMNIgene•VAGINAL (OMR-130)
devices and extracted at baseline (T0), after 3 freeze-thaw cycles (3x F/T)or storage at -80°C for 30 days (-80 30d). DNA and RNA samples from
3 representative donors are shown.

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Rela

20
0

A
-80°C 30 days
3x F/T
Biological variability
Donor to donor

DNA

0.0

0.2

0.4

0.6

0.8

1.0

Bray-Curtis distance

Donor A

Relative abundance (%)

B

RNA

DNA

RNA

T0 -80 T0 F/T

T0 -80 T0 F/T

T0 -80 T0 F/T

T0 -80 T0 F/T

80
60
40
20

C

Other

Prevotella

Ureaplasma
Lactobacillus

Dialister
Streptococcus

Bifidobacterium

Anaerococcus

Donor ADNA

tive abundance (%)

Donor B

DNA
100

0

T0 -80 T0 F/T

T0 -80 T0 F/T

Other

Prevotella

Ureaplasma
Lactobacillus

Dialister
Streptococcus

Bifidobacterium

Anaerococcus

Donor AT0 -80 T0 F/T

Donor B

DNA

RNA

DNA

RNA

T0 -80 T0 F/T

T0 -80 T0 F/T

T0 -80 T0 F/T

T0 -80 T0 F/T

100
80
60
40
20
0

Other
Ureaplasms
Lactobacillus
Prevotella

Streptococcus
Gardnerella
Atobopium

Figure 7: OMNIgene•VAGINAL (OMR-130) devices stabilize
vaginal microbial profiles through multiple freeze-thaw cycles.
(A) Bray-Curtis dissimilarity for DNA and RNA samples extracted
following 3 freeze-thaw cycles or storage at -80°C for 30 days ascompared to baseline (T0). Donor-to-donor dissimilarity andbiological variability (difference between paired replicate tube A
and B at baseline) are also shown for reference. (*** p < 0.001
Kruskal-Wallis test) (B and C) 16S taxonomic profiles (V3-V4 - genus
level) for Lactobacillus-dominated (B) and non-Lactobacillusdominated (C) dominated samples collected in OMR-130 devices
with DNA and RNA extracted at baseline (T0) after 3 freeze-thaw
cycles or storage at -80°C for 30 days. Bar plots from 2 representative
donors are shown.

OMNIgene•ORAL and OMNIgene•VAGINAL
devices stabilize bacterial profiles under real-life
conditions-80°C 30 days
3x F/T
Biological variability
Donor to donor

RNA

C
Relative abundance (%)

To further assess profile stability, bacterial profiles
were generated from the extracted nucleic acids using
16S amplicon sequencing, targeting the V3-V4
region. Bray-Curtis dissimilarity between DNA andRNA samples extracted at baseline (T0) and samples
extracted after 3 freeze-thaw cycles was relatively
small and comparable to the biological variability(2 samples collected side by side by the same donorin 2 different tubes). In contrast, Bray-Curtis
dissimilarity was significantly higher when DNA
and RNA profiles were compared across donors.
This result indicates that each donor’s uniquemicrobial profile is captured and stabilized in
OMNIgene•VAGINAL devices. Moreover, taxonomic
profiles between samples extracted at baseline (T0)and those subjected to freeze-thaw cycles or tocontrols (-80°C for 30 days) were highly similar —this was observed for both DNA and RNA derived
profiles (Figure 7B and 7C). Importantly, both
Lactobacillus-dominated vaginal samples (Figure 7B)
and non-Lactobacillus-dominated samples (Figure 7C)
were preserved in OMNIgene•VAGINAL devices.

T0 -80 T0 F/T

Lastly, we tested the performance of our OMNIgene
devices in a real-life sample shipping and lab
processing scenario. OMNIgene•ORAL (tongue
and gum/plaque) and OMNIgene•VAGINAL samples
were collected by 10-15 healthy individuals in Ottawa,
Canada, and shipped at ambient temperature (nocold-chain transport) to Diversigen in Minneapolis,USA. Upon receipt, samples were stored for a few
days at room temperature before DNA was extractedusing DNeasy® PowerSoil® Pro HT Kit (QIAGEN®).
Metagenomic sequencing of the samples was thenperformed with BoosterShot, and taxonomic profiles
were generated with Diversigen’s Core Analysis
pipeline. Representative vaginal and oral profiles
were obtained from these samples (Figure 8A and 8B).
WGS data identified both Lactobacillus (donors 1 and
2 — Figure 8A) and non-Lactobacillus vaginal samples(donors 3 and 4 — Figure 8A). Oral samples, on theother hand, were dominated by Streptococcus,

Donor B
RNA

DNA

RNA

100

80
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40

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A

B

100

80

Relative abundance (%)

Neisseira and Rothia, with discrete differences
between tongue and gum/plaque samples. Principal
coordinate analysis revealed that each site had aunique microbial profile (Figure 8C), echoing theresults of the Human Microbiome Project.4 Taken
together, these data indicate that OMNIgene devices
capture and maintain site- and donor-specificbacterial profiles from point of collection to pointof extraction/processing.

60

40

20

100
0

D2

D1

60

D2

Actinomyces

Neisseria
VibrioRemainder
Haemophilus
Paeniglutamicibacter
Veillonella
Rothia80

Relative abundance (%)

D1

Streptococcus
Lactobacillus
Capnocytophaga
GemellaPrevotella

40

C
Jensen-Shannon divergence20
Gum/plaque(OMR-110)

D1

D2

D3

D4

Prevotella

Arthrobacter

Atopobium

Aerococcus

Leptospira

Peptoniphilus

Gardnerella

Colwellia

Streptococcus

Streptococcus

Paeniglutamicibacter

Rhizobacter

VibrioRemainder

PCo2 (16.5% of variance)0

Tongue(OMR-120)

Vaginal(OMR-130)

Lactobacillus

PCo1 (60.6% of variance)

Figure 8: OMNIgene•ORAL and OMNIgene•VAGINAL devices capture and stabilize site-specific microbiome profiles at pointof collection. (A and B) Taxonomic profiles (genus level) of vaginal (A) or oral (B) microbiome samples collected in OMNIgene devices(OMR‑110, 120 or 130) and sequenced by whole genome sequencing. (C) Principal coordinate analysis (PCoA) based on Jensen-Shannon
divergence between oral and vaginal samples. Samples were collected in Ottawa (Ontario, Canada) and shipped at ambient temperature
to Diversigen (Minnesota, USA), where they were extracted and processed. Samples were sequenced with BoosterShot and taxonomic
assignment was performed with the Core Analysis™ workflow. Ellipses represent the 95% confidence interval for each sample type: gum/plaque (red), tongue (green) and vaginal (blue).

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Conclusions•

OMNIgene•ORAL and OMNIgene•VAGINAL
devices:•••utilize intuitive designs and instructions to enablehighly compliant at-home collection of oral andvaginal microbiomes
preserve high-quality microbial DNA and RNA
during shipping at ambient temperature andextended storage at room temperature•

maintain neutral microbial profile of samples
without introduction of any detectable bias
maintain oral and vaginal DNA and RNA
bacterial profile stability during shippingat ambient temperature and during storage
at room temperature for up to 30 days
are validated tools for microbiome studies withthe ability to accurately capture and stabilize
complex microbial profiles from point ofcollection onward

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AEM.01541-09

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OMNIgene and DNA Genotek are trademarks 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.

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