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Technology development to explore the relationship between oral health and the oral microbial community.

Starke EM, Smoot JC, Smoot LM, Liu WT, Chandler DP, Lee HH, Stahl DA - BMC Oral Health (2006)

Bottom Line: Current estimates of bacterial diversity in the oral cavity range up to 700 species, although in any single individual this number is much lower.Microarrays are now being used to study oral microbiota in a systematic and robust manner.Although this technology is still relatively young, improvements have been made in all aspects of the technology, including advances that provide better discrimination between perfect-match hybridizations from non-specific (and closely-related) hybridizations.

View Article: PubMed Central - PubMed

Affiliation: Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA. micx@u.washington.edu

ABSTRACT
The human oral cavity contains a complex microbial community that, until recently, has not been well characterized. Studies using molecular tools have begun to enumerate and quantify the species residing in various niches of the oral cavity; yet, virtually every study has revealed additional new species, and little is known about the structural dynamics of the oral microbial community or how it changes with disease. Current estimates of bacterial diversity in the oral cavity range up to 700 species, although in any single individual this number is much lower. Oral microbes are responsible for common chronic diseases and are suggested to be sentinels of systemic human diseases. Microarrays are now being used to study oral microbiota in a systematic and robust manner. Although this technology is still relatively young, improvements have been made in all aspects of the technology, including advances that provide better discrimination between perfect-match hybridizations from non-specific (and closely-related) hybridizations. This review addresses a core technology using gel-based microarrays and the initial integration of this technology into a single device needed for system-wide studies of complex microbial community structure and for the development of oral diagnostic devices.

No MeSH data available.


Related in: MedlinePlus

Mean melting profiles of perfect-match and mismatch probes using Alexa 594-labeled rRNA from Streptococcus mutans of six replicates in three experiments. Perfect-match (PM) probe and mismatch (MM) probe have Td (50% of signal remaining during analysis) values of 41.7°C and 34.0°C, respectively. The 95% confidence intervals are shown as dashed lines and MAXDCSD is 0.36 and occurs at 40°C. All values were calculated using fANOVA, see text for details (Bugli, submitted).
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Figure 2: Mean melting profiles of perfect-match and mismatch probes using Alexa 594-labeled rRNA from Streptococcus mutans of six replicates in three experiments. Perfect-match (PM) probe and mismatch (MM) probe have Td (50% of signal remaining during analysis) values of 41.7°C and 34.0°C, respectively. The 95% confidence intervals are shown as dashed lines and MAXDCSD is 0.36 and occurs at 40°C. All values were calculated using fANOVA, see text for details (Bugli, submitted).

Mentions: The challenge of all microarray experiments, including our own, is confirming the identity of species within a sample with a high level of confidence. In order to detect non-specific hybridization, researchers typically employ the use of a mismatch probe that differs in sequence by one nucleotide relative to each perfect-match probe. Another tactic is to use multiple probes for each organism [31]. Our approach exploits the solution-phase nature of the gel elements and employs dissociation nonequilibrium analysis to resolve perfect and imperfect duplexes on the array. A reader (microscope and camera) in combination with a thermal platform is used to characterize the dissociation of the target from each probe by measuring residual signal as the temperature is incrementally increased. The resulting melting profile (signal versus temperature) is used as a measure of duplex composition (see Figure 2). This dissociation approach has been shown to help discriminate targets from closely related non-target sequences, since targets containing one or more mismatches disassociate earlier than perfect-match targets [33,39,41-45]. Discriminating perfect-match from mismatch hybridizations – a key step toward determining the presence or absence of a particular target (e.g. species) – is also influenced by such factors as the diffusivity of the gel array, the quality of the target material, and image analysis methods.


Technology development to explore the relationship between oral health and the oral microbial community.

Starke EM, Smoot JC, Smoot LM, Liu WT, Chandler DP, Lee HH, Stahl DA - BMC Oral Health (2006)

Mean melting profiles of perfect-match and mismatch probes using Alexa 594-labeled rRNA from Streptococcus mutans of six replicates in three experiments. Perfect-match (PM) probe and mismatch (MM) probe have Td (50% of signal remaining during analysis) values of 41.7°C and 34.0°C, respectively. The 95% confidence intervals are shown as dashed lines and MAXDCSD is 0.36 and occurs at 40°C. All values were calculated using fANOVA, see text for details (Bugli, submitted).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2147590&req=5

Figure 2: Mean melting profiles of perfect-match and mismatch probes using Alexa 594-labeled rRNA from Streptococcus mutans of six replicates in three experiments. Perfect-match (PM) probe and mismatch (MM) probe have Td (50% of signal remaining during analysis) values of 41.7°C and 34.0°C, respectively. The 95% confidence intervals are shown as dashed lines and MAXDCSD is 0.36 and occurs at 40°C. All values were calculated using fANOVA, see text for details (Bugli, submitted).
Mentions: The challenge of all microarray experiments, including our own, is confirming the identity of species within a sample with a high level of confidence. In order to detect non-specific hybridization, researchers typically employ the use of a mismatch probe that differs in sequence by one nucleotide relative to each perfect-match probe. Another tactic is to use multiple probes for each organism [31]. Our approach exploits the solution-phase nature of the gel elements and employs dissociation nonequilibrium analysis to resolve perfect and imperfect duplexes on the array. A reader (microscope and camera) in combination with a thermal platform is used to characterize the dissociation of the target from each probe by measuring residual signal as the temperature is incrementally increased. The resulting melting profile (signal versus temperature) is used as a measure of duplex composition (see Figure 2). This dissociation approach has been shown to help discriminate targets from closely related non-target sequences, since targets containing one or more mismatches disassociate earlier than perfect-match targets [33,39,41-45]. Discriminating perfect-match from mismatch hybridizations – a key step toward determining the presence or absence of a particular target (e.g. species) – is also influenced by such factors as the diffusivity of the gel array, the quality of the target material, and image analysis methods.

Bottom Line: Current estimates of bacterial diversity in the oral cavity range up to 700 species, although in any single individual this number is much lower.Microarrays are now being used to study oral microbiota in a systematic and robust manner.Although this technology is still relatively young, improvements have been made in all aspects of the technology, including advances that provide better discrimination between perfect-match hybridizations from non-specific (and closely-related) hybridizations.

View Article: PubMed Central - PubMed

Affiliation: Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA. micx@u.washington.edu

ABSTRACT
The human oral cavity contains a complex microbial community that, until recently, has not been well characterized. Studies using molecular tools have begun to enumerate and quantify the species residing in various niches of the oral cavity; yet, virtually every study has revealed additional new species, and little is known about the structural dynamics of the oral microbial community or how it changes with disease. Current estimates of bacterial diversity in the oral cavity range up to 700 species, although in any single individual this number is much lower. Oral microbes are responsible for common chronic diseases and are suggested to be sentinels of systemic human diseases. Microarrays are now being used to study oral microbiota in a systematic and robust manner. Although this technology is still relatively young, improvements have been made in all aspects of the technology, including advances that provide better discrimination between perfect-match hybridizations from non-specific (and closely-related) hybridizations. This review addresses a core technology using gel-based microarrays and the initial integration of this technology into a single device needed for system-wide studies of complex microbial community structure and for the development of oral diagnostic devices.

No MeSH data available.


Related in: MedlinePlus