In addition to organism-specific databases, PubMLST also hosts the following projects:
- Fish pathogen genome database
- This database has been set up for research on fish pathogens by the Sheppard Laboratory, University of Bath.
- Global Meningitis Genome Library
- Genome libraries for the four most common causes of bacterial meningitis: N. meningitidis, H. influenzae, S. agalactiae, and S. pneumoniae. Funding contributions to the GMGL have been provided by the Meningitis Research Foundation.
- Drakenstein Child Study genome database
- European Meningococcal Epidemiology in Real Time (EMERT) II
- Mycobacterium bovis ERADbTB project
- NIHR Mucosal Pathogens