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

Overview

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

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, fungal and tick species identifications from user-submitted MALDI-TOF spectra and gene sequences
  • Genus and species clinical text descriptions
  • Photographs of colony morphologies, gram stains and tick morphology
  • 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 18,500 spectra covering more than 6,000 bacterial and fungal species and 300 spectra from ticks in eight MALDI-TOF databases from around the world, including:
    • Bruker
    • CDC
    • ReNaEM (Argentina)
    • National Microbiology Lab (Canada)
    • Robert Koch Institute (Germany)
    • Instituto Nacional de Salud (Colombia)
    • CDC Unidentified Bacteria
    • CDC tick database

How it works

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. To use it:

1. Visit the MicrobeNet homepage and click the "enter" tab.

2. Submit your 16S and ITS gene sequences for a BLAST query and/or MALDI-TOF spectra by placing files in the dropbox on the main dashboard.

3. Enter your email address.

4. MicrobeNet identifies the closest species matches within minutes and emails you your results.

Still have questions? Email us at microbenet@cdc.gov.


What's ahead

MicrobeNet staff continually update the site with new information and tools. Upcoming expansions and improvements include:

  • A whole genome sequence (WGS) module for raw sequencing identification
  • More frequent updates of MALDI-TOF databases
  • Access to more MALDI-TOF pathogen databases from around the world.
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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)