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Comparative Study
. 2009 Jun;24(3):197-203.
doi: 10.1111/j.1399-302X.2008.00495.x.

Comparative whole-genome analysis of Streptococcus mutans isolates within and among individuals of different caries status

L Zhang  1 , B Foxman, D R Drake, U Srinivasan, J Henderson, B Olson, C F Marrs, J J Warren, M L Marazita
Affiliations
Comparative Study

Comparative whole-genome analysis of Streptococcus mutans isolates within and among individuals of different caries status

L Zhang et al. Oral Microbiol Immunol. 2009 Jun.

Abstract

Introduction: Genotypic analyses of Streptococcus mutans using fingerprinting methods depend on a few genetic loci being different but do not reveal the underlying genome-wide differences between strains.

Methods: We used comparative genomic hybridization (CGH) with 70-mer oligonucleotide microarrays containing open reading frames (ORFs) from S. mutans strain UA159 to examine the genetic diversity of 44 isolates from nine children selected from a local study population in Eastern Iowa.

Results: Unique strains (clones) within each child initially identified by arbitrary-priming polymerase chain reaction were confirmed by CGH. There was a wide range of variation in the hybridization patterns of the 1948 ORFs among the test isolates examined. Between 87 and 237 ORFs failed to give a positive signal among individual isolates. A total of 323 of the UA159 ORFs were absent from one or more of the test strains. These 323 variable genes seemed to be distributed across the entire UA159 genome and across all the predicted functional categories.

Conclusion: This set of very close geographically and temporally collected S. mutans isolates had a degree of gene content variation as high as a previously examined global set of strains. Comparing the frequency of these variable genes, the majority of which have unknown function, among strains of different origins (i.e. different caries status) could help to determine their relevance in S. mutans cariogenicity.

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Figures

Figure 1
Figure 1
S. mutans genome feature and the distribution of dispensable genes (identified by CGH) along the circular genome. Going outward, circle 1: variable genes represented by green areas and conserved gene by red; circle 2: percentage GC content; circle 3: predicted genes in positive (violet) and negative (orange) DNA strands; circle 5: genome coordinates. The diagram was created using the Microbial Genome Viewer 1.0 (16).
Figure 2
Figure 2
Number of all (blue) and dispensable (red) genes in S. mutans strain UA159 classified in each of the clusters of orthologous genes (COG) category plus those not classified in COG database. Dispensable genes are defined as those deleted in at least one test genome. There are 615 genes within the UA159 genome classified as not in COGs and the bar for the corresponding category in the figure is truncated.
See this image and copyright information in PMC

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