Microbial identification by mass cataloging

BMC Bioinformatics
Zhengdong ZhangRichard C Willson

Abstract

The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample.Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms. Ribonuclease T1 and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T1 of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individ...Continue Reading

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Citations

Jun 10, 2008·Nature Biotechnology·Adam M Feist, Bernhard Ø Palsson
Jun 27, 2006·BMC Bioinformatics·George W JacksonRichard C Willson
Jun 10, 2010·European Journal of Mass Spectrometry·Herbert Oberacher
Feb 18, 2011·Mass Spectrometry Reviews·Hiroshi NakayamaToshiaki Isobe

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Methods Mentioned

BETA
PCR
electrophoresis
restriction digest
in vitro transcription
nucleic

Software Mentioned

MathType
Epicenter

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