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Updated: Dec 24, 2025

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
Published on: May 15, 2019
Improving the usability and comprehensiveness of microbial databases
Caitlin Loeffler1,2, Aaron Karlsberg3, Lana S Martin3
1Department of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA. cloeffler@ucla.edu.
Abstract:
Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research.
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