MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats
Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectroscopy (MALDI-TOF MS) has been used routinely over the past decade in clinical microbiology laboratories to rapidly characterize diverse microorganisms of medical importance both at the genus and species levels. Currently, there i...
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doaj-5d4b5db7bf8d4db4b245136e0f34b0a82020-11-24T23:06:00ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-10-01910.3389/fmicb.2018.02442377057MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm HabitatsJames M. Tuohy0Sabrina R. Mueller-Spitz1Sabrina R. Mueller-Spitz2Chad M. Albert3Chad M. Albert4Stacy E. Scholz-Ng5Stacy E. Scholz-Ng6Melinda E. Wall7Melinda E. Wall8George T. Noutsios9Anthony J. Gutierrez10Todd R. Sandrin11Todd R. Sandrin12Biology Department, Glendale Community College, Glendale, AZ, United StatesBiology Department, University of Wisconsin Oshkosh, Oshkosh, WI, United StatesSustainability Institute for Regional Transformations, University of Wisconsin Oshkosh, Oshkosh, WI, United StatesBiology Department, Glendale Community College, Glendale, AZ, United StatesDepartment of Natural Sciences, Western New Mexico University, Silver City, NM, United StatesBiology Department, Glendale Community College, Glendale, AZ, United StatesDepartment of Natural Sciences, Western New Mexico University, Silver City, NM, United StatesBiology Department, Glendale Community College, Glendale, AZ, United StatesDepartment of Natural Sciences, Western New Mexico University, Silver City, NM, United StatesSchool of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, United StatesSchool of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, United StatesSchool of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, United StatesJulie Ann Wrigley Global Institute of Sustainability, Arizona State University, Tempe, AZ, United StatesMatrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectroscopy (MALDI-TOF MS) has been used routinely over the past decade in clinical microbiology laboratories to rapidly characterize diverse microorganisms of medical importance both at the genus and species levels. Currently, there is keen interest in applying MALDI-TOF MS at taxonomic levels beyond species and to characterize environmental isolates. We constructed a model system consisting of 19 isolates of Deinococcus aquaticus obtained from biofilm communities indigenous to diverse substrates (concrete, leaf tissue, metal, and wood) in the Fox River – Lake Winnebago system of Wisconsin to: (1) develop rapid sample preparation methods that produce high quality, reproducible MALDI-TOF spectra and (2) compare the performance of MALDI-TOF MS-based profiling to common DNA-based approaches including 16S rRNA sequencing and genomic diversity by BOX-A1R fingerprinting. Our results suggest that MALDI-TOF MS can be used to rapidly and reproducibly characterize environmental isolates of D. aquaticus at the subpopulation level. MALDI-TOF MS provided higher taxonomic resolution than either 16S rRNA gene sequence analysis or BOX-A1R fingerprinting. Spectra contained features that appeared to permit characterization of isolates into two co-occurring subpopulations. However, reliable strain-level performance required rigorous and systematic standardization of culture conditions and sample preparation. Our work suggests that MALDI-TOF MS offers promise as a rapid, reproducible, and high-resolution approach to characterize environmental isolates of members of the genus Deinococcus. Future work will focus upon application of methods described here to additional members of this ecologically diverse and ubiquitous genus.https://www.frontiersin.org/article/10.3389/fmicb.2018.02442/fullmass spectroscopyfreshwater biofilmsBruker’s BiotypingBOX-A1R fingerprinting16S rRNA gene |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
James M. Tuohy Sabrina R. Mueller-Spitz Sabrina R. Mueller-Spitz Chad M. Albert Chad M. Albert Stacy E. Scholz-Ng Stacy E. Scholz-Ng Melinda E. Wall Melinda E. Wall George T. Noutsios Anthony J. Gutierrez Todd R. Sandrin Todd R. Sandrin |
spellingShingle |
James M. Tuohy Sabrina R. Mueller-Spitz Sabrina R. Mueller-Spitz Chad M. Albert Chad M. Albert Stacy E. Scholz-Ng Stacy E. Scholz-Ng Melinda E. Wall Melinda E. Wall George T. Noutsios Anthony J. Gutierrez Todd R. Sandrin Todd R. Sandrin MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats Frontiers in Microbiology mass spectroscopy freshwater biofilms Bruker’s Biotyping BOX-A1R fingerprinting 16S rRNA gene |
author_facet |
James M. Tuohy Sabrina R. Mueller-Spitz Sabrina R. Mueller-Spitz Chad M. Albert Chad M. Albert Stacy E. Scholz-Ng Stacy E. Scholz-Ng Melinda E. Wall Melinda E. Wall George T. Noutsios Anthony J. Gutierrez Todd R. Sandrin Todd R. Sandrin |
author_sort |
James M. Tuohy |
title |
MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats |
title_short |
MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats |
title_full |
MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats |
title_fullStr |
MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats |
title_full_unstemmed |
MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats |
title_sort |
maldi-tof ms affords discrimination of deinococcus aquaticus isolates obtained from diverse biofilm habitats |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2018-10-01 |
description |
Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectroscopy (MALDI-TOF MS) has been used routinely over the past decade in clinical microbiology laboratories to rapidly characterize diverse microorganisms of medical importance both at the genus and species levels. Currently, there is keen interest in applying MALDI-TOF MS at taxonomic levels beyond species and to characterize environmental isolates. We constructed a model system consisting of 19 isolates of Deinococcus aquaticus obtained from biofilm communities indigenous to diverse substrates (concrete, leaf tissue, metal, and wood) in the Fox River – Lake Winnebago system of Wisconsin to: (1) develop rapid sample preparation methods that produce high quality, reproducible MALDI-TOF spectra and (2) compare the performance of MALDI-TOF MS-based profiling to common DNA-based approaches including 16S rRNA sequencing and genomic diversity by BOX-A1R fingerprinting. Our results suggest that MALDI-TOF MS can be used to rapidly and reproducibly characterize environmental isolates of D. aquaticus at the subpopulation level. MALDI-TOF MS provided higher taxonomic resolution than either 16S rRNA gene sequence analysis or BOX-A1R fingerprinting. Spectra contained features that appeared to permit characterization of isolates into two co-occurring subpopulations. However, reliable strain-level performance required rigorous and systematic standardization of culture conditions and sample preparation. Our work suggests that MALDI-TOF MS offers promise as a rapid, reproducible, and high-resolution approach to characterize environmental isolates of members of the genus Deinococcus. Future work will focus upon application of methods described here to additional members of this ecologically diverse and ubiquitous genus. |
topic |
mass spectroscopy freshwater biofilms Bruker’s Biotyping BOX-A1R fingerprinting 16S rRNA gene |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2018.02442/full |
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