The Thermo Fisher Scientific MicrobeBridge™ software is a desktop application which connects .ab1 data files generated on Applied Biosystems™ 3500 and 3130 Genetic Analyzers and 3730 DNA Analyzers with the Centers for Disease Control and Prevention (CDC)’s MicrobeNet virtual reference database via internet connection for bacterial identification using 16S rRNA gene sequencing analysis.

1. The world leader in serving science
Jing Zhai
Dennis Nagtalon
Karen Cormier
MicrobeBridge™Software
Bridging CE/Sanger instrumentation to the CDC MicrobeNet database
Oct 15, 2015

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What is MicrobeBridge™ Software?
Bridging your CE instrument to MicrobeNet database
• Unmet needs for current MicrobeNet users:
• Too many manual steps for current MicrobeNet
users to obtain assembled fasta from CE
instruments to MicrobeNet
• Only process 1 file at a time
De novo
Assembly
Consensus
Calling
User
Perform QC
and Edits
Send out
sequence
(~1500bp)
AB Sequencer
MicrobeBridge™ – Simple to Learn, Easy to Use

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What is MicrobeBridge™ Software ?
Bridging your CE instrument to MicrobeNet database
• MicrobeBridge™ software provides:
• Install on win7 based instrument computer to
boost instrument replacement or Computer
system upgrade
• Batch pre-processing of ab1 files
• QC and assemble to contigs
• Export to fasta OR One-click to MicrobeNet
database

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Simple to Learn, Easy to Use
• Create project
• Import samples and organize
• Review quality, delete low quality data if needed
• Review and edit Contig sequence
• One button click to MicrobeNet database and log in
• Search in MicrobeNet database using BLAST search
MicrobeBridge™software
MicrobeNet database

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What is MicrobeNet ?
CDC curated database using 16S rRNA sequencing
• A system that
can help diagnostic capabilities from the
highest tech public health laboratories to
the lowest tech capable to land on the
same page – microbenet.cdc.gov
• A that can increase PHL
capabilities for identifying and reporting
diseases, including genotypic method
based on DNA sequencing of 16S rDNA
• in real time by increasing the
critical information from Public Health Labs

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Key Features of MicrobeBridge™ Software
Overview of
read coverage
Shows the range of
sequences in a
specimen.
Contig review
Identify discrepancies
in the assembled contig
and allow editing
Quality status
Displays color-coded
trace files based on
user-settable quality
ranges
One-click access
to MicrobeNet
Provides one-click
access to
MicrobeNet

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Press Release
• Announced on July 16, 2015:
Thermo Fisher Collaborates with
CDC MicrobeNet for MicrobeBridge
software development
• Link:
• https://www.genomeweb.com/informatics/the
rmo-fisher-partners-cdc-develop-software-
microbenet-database

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Software Licensing and Deployment
• Perpetual Licensing
• Commercial software will be a physical CD package, with
printed license code inside package
• 60-day free trial software is available to download from
product page http://www.thermofisher.com/order/catalog/product/A29238
• Internal Employee can request training license here:
https://licensing.appliedbiosystems.com/training/wicket/bookmarkable/com.apldbi
o.licensing.register.web.training.page.TrainingLoginPage?0

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Public Health Labs will benefit from MicrobeBridge™ Software
Public Health Labs like to follow CDC
Guidance
• Inexperienced lab technicians
• SOP could be provided by CDC
• All phenotypic information is also available
• MicrobeNet™ software provides UI rich functionalities
to encourage PHL well plan their experiments
CDC surveillance all submitted
sequences
• Prevent outbreaks in advance by surveillance of all
submitted sequences
• SMEs continue to curate incoming sequences to
expand existing database
• BLAST against more known species in database

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MicrobeBridge™ Software provides standalone or complete
solution for customers’ needs
• Standalone
software for all
CE platform
• Consumable
Boost: Co-sell
MicroSEQ™ ID
16S Full Gene
Kit
• Instrument
Boost: Place
new 3500
• Instrument
Boost:
replacement of
3130 with 3500
3130
trade-in
Increase
new
instrument
sales
Works on
windows7
for CE
instruments
: 3130, 3730,
3500 series
Company
Pre-package
solution
Softwar
e boosts
sales for
Inst/Con

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MicrobeBridge™ software vs. MicroSEQ™ ID system
MicrobeBridge™ MicroSEQ™ ID
Integration with Data
Collection software
✖ ✔
Has validated database for
microbial identification
✖ ✔
Supports custom libraries
and sharing
✖* ✔
Pre-packaged kit available
✖ ✔
Reporting
✖ ✔
IQ / OQ
✖ ✔
SAE (CFR Part 11)
✖ ✔
Supports BDTv3.1 ✔ ✖ **
Supports Pop™ 7 Polymer
✔ ✖ **
* CDC provide external database MicrobeNet™
** Do not support BDTv3 chemistry, Do not support Pop7 polymer runs from MSID run
setup with Data Collection software, but analyzes POP7/BDTv1.1 data.

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Product Information (SKU: A29238)
• Marketing Page: www.thermofisher/microbebridge
• Contact your sales rep for more price information
Customer
needs
Kit Option with
SKUs/pricing
Software External Libraries
Homebrew
Only
Home-brewed kit MicrobeBridge™
(SKU: A29238)
MicrobeNet
Need a
Prepackaged
Solution
MicroSEQ™ 16S
Full Gene Kits Package
(SKUs: 4318930, 4349155,
4347484, 4408228, 4408227,
4415506, 4427807)
MicrobeBridge™
(SKU: A29238) MicrobeNet
Need a
Validated
Turnkey
Solution
MicroSEQ™ 16S
Full Gene Kits Package
(SKUs: 4318930, 4349155,
4347484, 4408228, 4408227,
4415506, 4427807)
MicroSEQ™ ID SW
(SKU: 4371431)
MicroSEQ™ ID 16S
rDNA Full Gene Library
(SKU: 4371295)

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Appendix

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Sample Prep Sequencing
Cycle
SequencingPCRSample
Data
Analyses
Heated lysis
10 min
Amplification
of full 16S
gene in 3
overlapping
fragments
Culture
plate with
single
colonies
CATCGAT
C
CA
CAT
CATC
CATCG
CATCGA
Cycle
sequencing
product
through 3
overlapping
regions
BDT v1.1, Pop
6 based
sequencing
on 3500/Xl
Analyses using
MicrobeBridge
and MicrobeNet
1.
PrepMan
Ultra
2.
MicroSEQ
Full Gene
PCR kit
3.
MicroSEQ
Full Gene
Sequencing
kit
4 – 7.
MicroSEQ
PCR and
Sequencing
clean-up kits
MicroSEQ™ ID Kit Workflow With MicrobeBridge™

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Part Number Description
1. 4318930 PrepMan™ Ultra Sample Preparation Reagent
2. 4349155 MicroSEQ™ Full Gene 16S rDNA PCR Kit
3. 4347484 MicroSEQ™ Full Gene 16S rDNA Sequencing Kit
4. 4408228 MicroSEQ™ ID Sequencing Cleanup Cartridges
5. 4408227 For MicroSEQ™ID sequencing clean-up
6. 4415506 MicroSEQ™ ID Purification Combo Kit, with clean-up plates
7.
4427807
MicroSEQ™ ID Purification Combo Kit, with clean-up
cartridges
• Software
• Kits
Part Number Description
1. 4371295 MicroSEQ™ ID 16S rDNA Full Gene Library
2. 4371431 MicroSEQ™ ID Software
MicroSEQ™ ID Product co-sell With MicrobeBridge™ Software

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