Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data

Abstract

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption–ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.

Endophytic Bacteria From the Roots of the Medicinal Plant Alkanna tinctoria Tausch (Boraginaceae): Exploration of Plant Growth Promoting Properties and Potential Role in the Production of Plant Secondary Metabolites

“…To conduct the MALDI-TOF MS, pure 2nd generation cultures were grown. The proteins were then extracted, spotted in duplicate onto MALDI-TOF target plates and overlaid with matrix solution (10 mg/mL α-cyano-4-hydroxycinnamic acid in acetonitrile-water-trifluoroacetic acid) as previously described ( Dumolin et al, 2019 ). The protein profiles were read with the Bruker Microflex TM LT/SH system.…”

Editorial: MALDI-TOF MS Application in Microbial Ecology Studies

“…MALDI-TOF MS based identification becoming a must for the large-scale culturomics experiments, as it is a fast and cost-effective method to filter out multiple conspecific strains or genetically identical clones (Dumolin et al, 2019). Though, the limited database and bias of commercial databases toward microbes of clinical or food safety relevance restrict the application of MALDI-TOF MS. Methods based on similarity measures combined with the clustering of MALDI-TOF mass spectra have been developed to uncouple dereplication from database based identification.…”

“…Till recently, the identification of identical strains was done by visual interpretation of dendrograms or by using a distance cutoff value (Strejcek et al). Recently, an algorithm (SPeDE) has been introduced, which enables the rapid analysis and dereplication of isolates using comparison of MALDI-TOF MS profiles (Dumolin et al, 2019). This approach identifies unique spectral features between pairs of spectra and clusters them into operational isolation units (OIUs).…”

Novel acetic acid bacteria from cider fermentations: Acetobacter conturbans sp. nov. and Acetobacter fallax sp. nov

“…Finally, MALDI-TOF MS profiles of strains LMG 1627 T , LMG 1636 T and LMG 1637, and of the type strains of closely related neighbours were obtained by the method described by Dumolin et al [36]. All strains were cultivated on LMG agar medium 0404.…”