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Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Lin IH, Liu TT, Teng YT, Wu HL, Liu YM, Wu KM, Chang CH, Hsu MT - PLoS ONE (2011)

Bottom Line: We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans.This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced.The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

View Article: PubMed Central - PubMed

Affiliation: Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan.

ABSTRACT
Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

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Related in: MedlinePlus

Phylogenetic relationship of S. gallolyticus to other sequenced streptococci.The multiple sequence alignment of 16S rRNA was constructed using MAFFT. The evolutionary history was inferred using the UPGMA method and the bootstrap consensus tree inferred from 1000 replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches. The evolutionary distances were computed using the Jukes-Cantor method. All positions containing gaps and missing data were eliminated from the dataset, and a total of 1240 positions in the final dataset. Bacillus subtilis strain 168 was included as an outgroup. Phylogenetic analyses were conducted in MEGA4.
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pone-0020519-g002: Phylogenetic relationship of S. gallolyticus to other sequenced streptococci.The multiple sequence alignment of 16S rRNA was constructed using MAFFT. The evolutionary history was inferred using the UPGMA method and the bootstrap consensus tree inferred from 1000 replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches. The evolutionary distances were computed using the Jukes-Cantor method. All positions containing gaps and missing data were eliminated from the dataset, and a total of 1240 positions in the final dataset. Bacillus subtilis strain 168 was included as an outgroup. Phylogenetic analyses were conducted in MEGA4.

Mentions: Streptococci phylogeny was constructed based on the 16S rRNA sequences of all sequenced bacteria of the Streptococcus genus. The result was shown in Figure 2. The traditional Lancefield grouping on streptococci matched the modern-day 16S rRNA analysis very well. The S. gallolyticus ATCC 43143, S. gallolyticus UCN34 and S. pasteurianus ATCC 43144 were of the Bovis group with ATCC 43143 phylogenetically more related to UCN34 (both biotype I) than to ATCC 43144 (biotype II.2) of the different subspecies.


Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Lin IH, Liu TT, Teng YT, Wu HL, Liu YM, Wu KM, Chang CH, Hsu MT - PLoS ONE (2011)

Phylogenetic relationship of S. gallolyticus to other sequenced streptococci.The multiple sequence alignment of 16S rRNA was constructed using MAFFT. The evolutionary history was inferred using the UPGMA method and the bootstrap consensus tree inferred from 1000 replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches. The evolutionary distances were computed using the Jukes-Cantor method. All positions containing gaps and missing data were eliminated from the dataset, and a total of 1240 positions in the final dataset. Bacillus subtilis strain 168 was included as an outgroup. Phylogenetic analyses were conducted in MEGA4.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102119&req=5

pone-0020519-g002: Phylogenetic relationship of S. gallolyticus to other sequenced streptococci.The multiple sequence alignment of 16S rRNA was constructed using MAFFT. The evolutionary history was inferred using the UPGMA method and the bootstrap consensus tree inferred from 1000 replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches. The evolutionary distances were computed using the Jukes-Cantor method. All positions containing gaps and missing data were eliminated from the dataset, and a total of 1240 positions in the final dataset. Bacillus subtilis strain 168 was included as an outgroup. Phylogenetic analyses were conducted in MEGA4.
Mentions: Streptococci phylogeny was constructed based on the 16S rRNA sequences of all sequenced bacteria of the Streptococcus genus. The result was shown in Figure 2. The traditional Lancefield grouping on streptococci matched the modern-day 16S rRNA analysis very well. The S. gallolyticus ATCC 43143, S. gallolyticus UCN34 and S. pasteurianus ATCC 43144 were of the Bovis group with ATCC 43143 phylogenetically more related to UCN34 (both biotype I) than to ATCC 43144 (biotype II.2) of the different subspecies.

Bottom Line: We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans.This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced.The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

View Article: PubMed Central - PubMed

Affiliation: Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan.

ABSTRACT
Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

Show MeSH
Related in: MedlinePlus