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. FAQs for MicrobeBridge™ Software
• What is MicrobeBridge™ software?
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.
MicrobeNet is a web-based reference database for the identification of microbial
pathogens through 16S rRNA gene sequence BLAST searches. MicrobeNet contains a
database of genetic and phenotypic properties for bacterial identification actively
curated by the CDC.
• What are the benefits of using the MicrobeBridge™ software?
Faster Turnaround Time and Lower Cost:
Current microbial identification workflows with Sanger sequencing data require manual
quality checks, assembly, manual examination of the assembled sequence, and finally a
manual alignment search against the National Institute of Health’s GenBank® genetic
sequence database to identify the bacterial species.
Using MicrobeBridge™ software, MicrobeNet users will be able to efficiently
assemble and QC their sequencing data using the CDC recommended primer set for
16S rRNA gene sequencing analysis. Users can connect to MicrobeNet via a single
click in the software or export the consensus contig.
Using MicrobeBridge™ software improves the bacterial identification workflows in
public health and microbiology laboratories using MicrobeNet. Users will be able to
get to their results quickly and accurately thereby saving money and time spent
assembling, interrogating, and identifying bacteria or pathogens in their data.
Connecting to CDC’s expertise:
Users are able to connect directly into the actively curated CDC MicrobeNet virtual
reference database for identifying rare and complex pathogens faster and more
accurately. Although any laboratory with an internet connection can access the
MicrobeNet database worldwide, MicrobeBridge™ software streamlines the CE data
and connects to MicrobeNet directly.
• Who can benefit from the MicrobeBridge™ software?
Public health, microbiology, and any other laboratories conducting disease surveillance
or bacterial identification with MicrobeNet can benefit from using the
MicrobeBridge™ software.

2. • Is MicrobeBridge™ software a replacement for the MicroSEQ™ ID software?
No. MicrobeBridge™ software is specifically designed for public health, microbiology,
and any other laboratories utilizing the MicrobeNet database. MicroSEQ™ ID software
is designed for use in pharmaceutical analytics laboratories who typically do not use the
MicrobeNet database but require other functionalities. However MicroSEQ™ ID users
can install and use MicrobeBridge™ software if they wish to do MicrobeNet searches.
• What is the difference between MicrobeBridge™ software and MicroSEQ™ ID
software?
Through a successful partnership with the Special Bacteriology Reference Laboratory
at the CDC, Thermo Fisher Scientific has developed MicrobeBridge™ software to
enable public health, microbiology, and any other laboratories worldwide to directly
access the CDC’s MicrobeNet virtual reference database using 16S rRNA sequencing
technology.
MicrobeBridge™ software provides a streamlined workflow for analyzing Sanger
sequencing data (.ab1 data files) generated on CE Sanger sequencing instruments or
genetic analyzers. MicrobeBridge™ performs contig assembly, contig editing, primer
trimming, data quality check, contig sequence copying, and one-click connection to
MicrobeNet for bacterial identification through 16S rRNA BLAST searches.
In contrast, MicroSEQ™ ID software is part of a complete system designed for
pharmaceutical analytics workflows. The system includes secondary analysis software,
validated reference libraries for bacterial and fungal identification, links to query public
domain databases, creation of custom reference databases, and SAE features that
enables 21 CFR Part 11 compliance.
• Can sequences generated using the MicroSEQ™ ID PCR and Sequencing kits be
analyzed by MicrobeBridge™ software?
Yes, data from the MicroSEQ™ 16S Full Gene Kit package can be analyzed by
MicrobeBridge™ software.
• Are there recommended protocols, reagents, and primers, to generate
MicrobeBridge™ software samples?
CDC MicrobeNet has recommended primers which have been configured into the
MicrobeBridge™ software. We recommend using MicroSEQ™ 16S Full Gene kit
package for a complete package solution.
• Do I need to sequence with a specific chemistry to use MicrobeBridge™ Software?
No. A specific chemistry is not needed as long as the 16S full gene is covered.

3. • Does MicrobeBridge™ software do basecalling?
Yes, MicrobeBridge™ software uses KB Basecaller v1.4.1.8 by default.
• Can I export the final contig so I can search other databases?
Yes, you can export the final contig sequence for other database searches.
• Can I manually override changes the software makes to the contig?
Yes, you can edit the contig sequence.
• Can I edit the MicrobeNet software search parameters in MicrobeBridge™
software?
No. MicrobeBridge™ software does not provide any search parameters which are used
by MicrobeNet software.
• Is there a list of organisms that can be identified with MicrobeBridge™ software?
MicrobeBridge™ software does not do bacterial identification. It provides a
connection to MicrobeNet which does the bacterial identification.
• Does MicrobeNet database provide species level identification?
Yes. MicrobeNet database provides species level identification.
• Do I need a MicrobeNet account?
To use MicrobeNet, you will need to register for a MicrobeNet account. You can
register at https://microbenet.cdc.gov/
• What instruments will the MicrobeBridge™ software support?
MicrobeBridge™ software supports data outputs from 3500, 3500xL, 310, 3130,
3130xl, 3730 and 3730xl systems.
• Which input file formats can I use with MicrobeBridge™ software?
Only .ab1 files can be used with the MicrobeBridge™ software.
• Do I lose any data if I upgrade from free trial version to full version?
No data is lost with the installation of the full version on top of the free trial version.

4. • What are the minimum system requirements for installing the MicrobeBridge™
software?
Recommended hardware requirements:
Minimum 1.8 GHz processor, 2 GB RAM and 20 GB of free hard disk space
The software has been tested on Window 7 32-bit SP1 and Window 7 64-bit SP1
operating systems with Intel®
Core™ i3-3220 CPU, i5-3380M and i3-3240 processors.
• Who do I contact for support for MicrobeBridge™ software and for MicrobeNet
database issues?
For MicrobeBridge™ software, please contact your local Thermo Fisher Technical
Support or email techsupport@lifetech.com.
In US:
Dial 1-800-955-6288, select menu option 4, or email abtechsupport@lifetech.com
For MicrobeNet, please contact the CDC directly at microbenet@cdc.gov. This
account is actively monitored by the CDC MicrobeNet staff.
• Where can I get a copy of the free trial version of the MicrobeBridge™ software?
Download a 60 day- free trial version at:
http://www.thermofisher.com/order/catalog/product/A29238