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Chapter 6 : Insights into Genus in the Genomics Era

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Abstract:

The recent availability of genome sequences for species provides an exceptional opportunity to probe their biology and role in the microbial ecology of the mouth. The recent genome-scale stoichiometric model of metabolic networks is an exceptional example of such an approach and illustrates the potential of advancements in genome sequencing and bioinformatic tools in studies of bacterial metabolism and ecology. Fifteen complete genomes, three metagenomes of , and 38 genome surveys of oral isolates are available at the human oral microbiome database (HOMD). Seven genomes are currently available as genome surveys at the HOMD. Almost 10% of the total cultivable biota from the tongue consists of . lack hexokinase activity but have other glycolytic enzymes. are also unable to incorporate radiolabeled glucose into bacterial cell compounds and seem to lack a glucose phosphotransferase system. The observations on the physiology can now be confirmed and visualized in the carbohydrate metabolism glycolysis-gluconeogenesis pathway constructed with ATCC 10790 genome data. This chapter presents the genomic evidence for the presence of both nitrate reduction enzymes and membrane-bound proton-translocating ATPases. Interactions between spp. and spp. naturally occur in vivo and emphasize the natural relationship of species in the development of biofilms. The availability of complete genome sequences provides a unique opportunity for developing genetic systems for .

Citation: Chalmers N, Chen T, Hughes C. 2011. Insights into Genus in the Genomics Era, p 79-90. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch6

Key Concept Ranking

Microbial Ecology
0.6103097
Streptococcus gordonii
0.5157998
Veillonella parvula
0.49337378
Veillonella atypica
0.4837626
0.6103097
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Figures

Image of FIGURE 1
FIGURE 1

Evolutionary relationships of taxa of the genus and uncultured clones from the PubMed database. The evolutionary history was inferred using the neighbor-joining method ( ). The optimal tree with the sum of branch length (0.24542862) is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the maximum composite likelihood method ( ) and are in the units of the number of base substitutions per site. The analysis involved 21 nucleotide sequences. Codon positions included were first plus second plus third plus noncoding. All positions containing gaps and missing data were eliminated. There were a total of 409 positions in the final data set. Evolutionary analyses were conducted in MEGA5 ( ).

Citation: Chalmers N, Chen T, Hughes C. 2011. Insights into Genus in the Genomics Era, p 79-90. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch6
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Image of FIGURE 2
FIGURE 2

In silico reconstruction of ATCC 10790 pyruvate metabolism showing the presence of genes involved in taking lactic acid to phosphoenolpyruvate for gluconeogenesis and formation of cellular material. Bold rectangles identify the presence of a gene or enzyme homolog. (© 2010 Kanehisa Laboratories, used with permission.)

Citation: Chalmers N, Chen T, Hughes C. 2011. Insights into Genus in the Genomics Era, p 79-90. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch6
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Image of FIGURE 3
FIGURE 3

In silico reconstruction of ATCC 10790 of nitrate reduction enzymes (A) and membrane-bound proton-translocating ATPases (B) with KAAS, an automatic genome annotation and pathway reconstruction server ( ). Bold rectangles identify the presence of a gene or enzyme homolog.

Citation: Chalmers N, Chen T, Hughes C. 2011. Insights into Genus in the Genomics Era, p 79-90. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch6
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Tables

Generic image for table
TABLE 1

Genomic information for several

Citation: Chalmers N, Chen T, Hughes C. 2011. Insights into Genus in the Genomics Era, p 79-90. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch6
Generic image for table
TABLE 2

Comparative metabolism of the three species based on the genomic annotations

Citation: Chalmers N, Chen T, Hughes C. 2011. Insights into Genus in the Genomics Era, p 79-90. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch6

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