About MicrobeNet

Key points

  • MicrobeNet is a free virtual microbiology laboratory.
  • It assists clinical laboratory personnel in identifying pathogens.
  • Scientists outside clinical settings can use this tool to identify bacteria and fungi.
Image of the branded logo for MicrobeNet


MicrobeNet is an online resource designed to assist microbiologists with identifying bacterial and fungal pathogens and its free to use. MicrobeNet users can submit MALDI-TOF spectra, 16S and ITS gene sequences, and biochemical testing data to query against CDC and collaborator pathogen databases to obtain bacterial or fungal species identification.

MicrobeNet aims to identify rare and unusual pathogens online, saving clinical labs time and money by eliminating the need to send specimens to specialized labs for identification.

Why it's important

This tool is crucial as it enables medical and public health personnel to identify rare and unusual pathogens much faster than traditional hierarchical workflow structures typically allow.

MicrobeNet users can access the following information when using the tool:

  • Bacterial and Fungal identifications from user-submitted MALDI-TOF spectra and gene sequences
  • Genus and species clinical text descriptions
  • Photographs of colony morphologies and gram stains
  • CDC testing procedures
  • Gene sequences and biochemical testing results
  • CDC contacts and support information

MicrobeNet currently contains:

  • Over 6,500 16S and ITS gene sequences from bacterial and fungal species
  • Over 17,500 spectra from over 6,000 bacterial and fungal species
  • Bruker, CDC, ReNaEM (Argentina), National Microbiology Lab (Canada), Robert Koch Institute (Germany), and CDC Tick databases
  • Biochemical testing results from 239 curated bacterial pathogens.

How it works

New users can request a free account by completing the registration form. Internet access and an email address is needed to create an account.

Registered users can access MicrobeNet by signing in at microbenet.cdc.gov. To use MicrobeNet:

1. Please submit your 16S and ITS gene sequences, MALDI-TOF spectra, and/or results from biochemical test panels.

2. MicrobeNet then returns the closest identified matches within minutes.

3. Click on the results for more information about the identified pathogen.

Still have questions? Contact a CDC subject matter expert specific to the identified pathogen by using the contact information listed in MicrobeNet (see link above).

MicrobeNet can help medical and public health personnel save time and resources by not creating redundant databases and avoiding unnecessary shipment of samples to CDC laboratories for identification.

What's ahead

MicrobeNet is continually updated with new information and tools. Upcoming expansions and improvements include:

  • A whole genome sequence module for raw sequencing identification
  • A new "Epi Tools" module that could help predict when an outbreak might occur
  • MicrobeNet en español, for Spanish speaker access
  • New pathogens, including more select agents
  • Access to MALDI-TOF pathogen databases from around the world