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The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus

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Title The Identification of Discriminating Patterns from 16S
rRNA Gene to Generate Signature for Bacillus Genus
 
Creator More, Ravi
Purohit, H J
 
Subject Microbiology
 
Description The 16S ribosomal RNA (16S rRNA) gene has been widely used for the taxonomic classi-
fication of bacteria. A molecular signature is a set of nucleotide patterns, which constitute a
regular expression that is specific to each particular taxon. Our main goal was to identify
discriminating nucleotide patterns in 16S rRNA gene and then to generate signatures for
taxonomic classification. To demonstrate our approach, we used the phylum Firmicutes as a
model using representative taxa Bacilli (class), Bacillales (order), Bacillaceae (family), and
Bacillus (genus), according to their dominance at each hierarchical taxonomic level. We
applied combined composite vector and multiple sequence alignment approaches to generate
gene-specific signatures. Further, we mapped all the patterns into the different hypervariable
regions of 16S rRNA gene and confirmed the most appropriate distinguishing region as
V3–V4 for targeted taxa. We also examined the evolution in discriminating patterns of
signatures across taxonomic levels. We assessed the comparative classification accuracy of
signatures with other methods (i.e., RDP Classifier, KNN, and SINA). Results revealed that
the signatures for taxa Bacilli, Bacillales, Bacillaceae, and Bacillus could correctly classify
isolate sequences with sensitivity of 0.99, 0.97, 0.94, and 0.89, respectively, and specificity
close to 0.99. We developed signature-based software DNA Barcode Identification (DNA
BarID) for taxonomic classification that is available at website http://www.neeri.res.in/
DNA_BarID.htm. This pattern-based study provides a deeper understanding of taxonspecific
discriminating patterns in 16S rRNA gene with respect to taxonomic classification.
 
Publisher Mary Ann Liebert, Inc
 
Date 2016-07-21
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://neeri.csircentral.net/808/1/04%20more2016_N.pdf
More, Ravi and Purohit, H J (2016) The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus. Journal of Computational Biology, 23 (8). pp. 1-11. ISSN 1066-5277, ESSN: 1557-8666
 
Relation http://www.liebertpub.com/overview/journal-of-computational-biology/31/
http://neeri.csircentral.net/808/