IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry
Abstract
Abstract The identification and analysis of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to achieve this, use of MALDI-TOF mass spectrometry (MS), particularly in clinical microbiology, can provide high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate isolate identification via spectral comparison. Further, most current MALDI MS data analysis platforms lack meaningful ways to compare properties from large numbers of bacterial isolates. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures spanning seven bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented.
Article Details
Authors (45)
Nyssa K. Krull
Michael Strobel
Julia Saulog
Liana Zaroubi
Bruno S. Paulo
Mandisa Timba
Douglas R. Braun
Gabrielle Mingolelli
Jessia Raherisoanjato
Robert A. Shepherd
Abigail F. Scott
Carlo De Silva
Claire Fergusson
Zachary Daniel
Shailaja K. Pokharel
Sean Romanowski
Antonio Hernandez
Mónica Monge-Loría
Claire E. Dylla
Manasi M. Natu
Valentina Z. Petukhova
Chase M. Clark
Neha Garg
Paul R. Jensen
Scripps Institution of Oceanography, University of California San Diego
Adriana Blachowicz
Chelsi D. Cassilly
Lisa Guan
D. Cole Stevens
Jaclyn M. Winter
Shaun M. K. McKinnie
Barbara I. Adaikpoh
Skylar Carlson
Erin P. McCauley
William W. Metcalf
Tim S. Bugni
Pharmaceutical Sciences Division
Michael W. Mullowney
Eric G. Pamer
Matthew T. Henke
Hazel Barton
David O. Carter
Laboratory of Forensic Taphonomy, Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu
Alessandra S. Eustáquio
Roger G. Linington
Laura M. Sanchez
Department of Chemistry and Biochemistry, University of California-Santa Cruz
Mingxun Wang
Brian T. Murphy