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 l...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Charles Dumolin, Maarten Aerts, Bart Verheyde, Simon Schellaert, Tim Vandamme, Felix Van der Jeugt, Evelien De Canck, Margo Cnockaert, Anneleen D. Wieme, Ilse Cleenwerck, Jindrich Peiren, Peter Dawyndt, Peter Vandamme, Aurélien Carlier
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	bioinformatics MALDI-TOF MS dereplication microbial ecology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e77ff3e9251f4d39ae16f6485fa97af1
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:e77ff3e9251f4d39ae16f6485fa97af1
record_format	dspace
spelling	oai:doaj.org-article:e77ff3e9251f4d39ae16f6485fa97af12021-12-02T19:46:17ZIntroducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data10.1128/mSystems.00437-192379-5077https://doaj.org/article/e77ff3e9251f4d39ae16f6485fa97af12019-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00437-19https://doaj.org/toc/2379-5077ABSTRACT 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.Charles DumolinMaarten AertsBart VerheydeSimon SchellaertTim VandammeFelix Van der JeugtEvelien De CanckMargo CnockaertAnneleen D. WiemeIlse CleenwerckJindrich PeirenPeter DawyndtPeter VandammeAurélien CarlierAmerican Society for MicrobiologyarticlebioinformaticsMALDI-TOF MSdereplicationmicrobial ecologyMicrobiologyQR1-502ENmSystems, Vol 4, Iss 5 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	bioinformatics MALDI-TOF MS dereplication microbial ecology Microbiology QR1-502
spellingShingle	bioinformatics MALDI-TOF MS dereplication microbial ecology Microbiology QR1-502 Charles Dumolin Maarten Aerts Bart Verheyde Simon Schellaert Tim Vandamme Felix Van der Jeugt Evelien De Canck Margo Cnockaert Anneleen D. Wieme Ilse Cleenwerck Jindrich Peiren Peter Dawyndt Peter Vandamme Aurélien Carlier Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data
description	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.
format	article
author	Charles Dumolin Maarten Aerts Bart Verheyde Simon Schellaert Tim Vandamme Felix Van der Jeugt Evelien De Canck Margo Cnockaert Anneleen D. Wieme Ilse Cleenwerck Jindrich Peiren Peter Dawyndt Peter Vandamme Aurélien Carlier
author_facet	Charles Dumolin Maarten Aerts Bart Verheyde Simon Schellaert Tim Vandamme Felix Van der Jeugt Evelien De Canck Margo Cnockaert Anneleen D. Wieme Ilse Cleenwerck Jindrich Peiren Peter Dawyndt Peter Vandamme Aurélien Carlier
author_sort	Charles Dumolin
title	Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data
title_short	Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data
title_full	Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data
title_fullStr	Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data
title_full_unstemmed	Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data
title_sort	introducing spede: high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption–ionization time of flight mass spectrometry data
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/e77ff3e9251f4d39ae16f6485fa97af1
work_keys_str_mv	AT charlesdumolin introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT maartenaerts introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT bartverheyde introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT simonschellaert introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT timvandamme introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT felixvanderjeugt introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT eveliendecanck introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT margocnockaert introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT anneleendwieme introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT ilsecleenwerck introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT jindrichpeiren introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT peterdawyndt introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT petervandamme introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata AT aureliencarlier introducingspedehighthroughputdereplicationandaccuratedeterminationofmicrobialdiversityfrommatrixassistedlaserdesorptionionizationtimeofflightmassspectrometrydata
_version_	1718376056986009600

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

Ejemplares similares