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(Description and significance)
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==Genome structure==
 
==Genome structure==
  
Select a strain for which genome information (e.g. size, plasmids, distinct genes, etc.) is available.  
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The genome of strain ATCC 33277 is comprised of a single circular chromosome with 2 354 886 bp (3). On average the guanine (G) and cytosine (C) content makes up approximately 48.4% of the genome (3). Covering 86.1% of the whole chromosome sequence is 2090 CDSs (coding DNA sequence) with an average size of 970 bp (3,9).  The circular chromosome encodes 65 RNA genes (9).  Strain ATCC 33277 contains 93 IS elements and 48 miniature inverted repeat transposable elements (MITEs) (3). 4 RNA operons (rrn, 5S rRNA-23S rRNA-tRNAAla-tRNAIle-16S rRNA), including 53 tRNA genes have also been documented (3). Interestingly the number of rrn operons and tRNA genes in strain ATCC 33277 were identical to those of a virulent strain counterpart W83 (3,10).  Nonetheless the extensive rearrangement between the two strains through the introduction of mobile elements inevitably altered the virulence of the bacterium.
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Further more it has been revealed a host of bacterial species such as Bacteroides fragilis exhibit a high gene similarity to those of the ATCC 33277 strain (3). Theories suggest these genes were introduced to ATCC 33277 by a horizontal gene transfer event (3).
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The genome of strain W88 is comprised of a circular chromosome made up of  2 343 479 bp’s. On average the guanine and cytosine content make up approximately 48.3 % of the genome. The circular chromosome encodes 1909 protein genes 65 RNA genes.  4 ribosomal operons (rrn, 5S rRNA-23S rRNA-tRNAAla-tRNAIle-16S rRNA) including 53 tRNA genes showing specificity for all 20 amino acids have been documented. Interestingly the number of rrn operons and tRNA genes in strain W83 were identical to those of an avirulent strain counterpart ATCC 33277. Nonetheless the extensive rearrangement between the two strains through the introduction of mobile elements inevitably altered the virulence of the bacterium.
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The genome of W83 is composed predominately (85%) of ORF. Encoding a total of 1,990 ORF, 1075 presented detectable biological roles. Of the remaining ORF, 184 were categorised as a conserved hypothetical protein or conserved domain protein, 208 had to known function, and 523 encoded hypothetical proteins.
  
 
==Cell structure and metabolism==
 
==Cell structure and metabolism==

Revision as of 09:33, 14 September 2016

Name Bench ID Date [1]

Classification

Higher order taxa

Bacteria – Bacteroidetes – Bacteroidia – Bacteroidales – Porphyromonadaceae - Porphyromonas - P. gingivalis

Species

Species name and type strain (consult LPSN http://www.bacterio.net/index.html for this information)

Description and significance

Porphyromonas gingivalis is an obligately aerobic, gram-negative bacterium belonging to the phylum Bacteroidetes (2). Characterised by its rod shaped morphology, it is a non-spore bearing and non-motile bacterium most commonly inhabiting the oral cavity (2). Recognised as an opportunistic pathogen, P. gingivalis is capable of living in commensal harmony with the host (5). Termed as a pathobiont, the bacterium can cause episodes of diseases when a change in the ecological balance of the periodontal microenvironment transpires (5,14). Although the bacterium is capable of existing as a commensal organism, certain strains are known to be more virulent and pathogenic than others (5). Virulent strains have found to include, W83, W50, ATCC 49417 and A7A1 (6,7). Avirulent strains include ATCC 381, 33277 and 23A4 (6,7). In vitro studies of the bacterium have found cells cultured in broth with a size range from 0.5 by 1 to 2 μm (2). Cells grown on a solid media showed coccobacilli or very short rod structures (2). On blood agar plates, the bacterium forms black-pigmented colonies, predominately smooth, shiny and convex with a diameter between 1 to 2 mm (2, 12).

Typically found in the oral cavity of individuals, P. gingivalis has been implicated with periodontal diseases, most commonly associated with chronic periodontitis. A report from the Centres for Disease Control and Prevention (CDC) recorded 47. 2 % of adults in the United Stated aged 30 years or older have experienced some form of periodontal disease (8). In light of this information, recent studies have also reported that P. gingivalis is associated with systematic diseases, including cardiovascular diseases, rheumatoid arthritis and decreased kidney function (4). Studies underlying the molecular mechanisms behind the bacterial pathogenesis are key to design effective treatments. Consequently reducing the potential development of inflammatory diseases that arise as a secondary consequence of periodontitis.



Examples of citations [1], [2]

Genome structure

The genome of strain ATCC 33277 is comprised of a single circular chromosome with 2 354 886 bp (3). On average the guanine (G) and cytosine (C) content makes up approximately 48.4% of the genome (3). Covering 86.1% of the whole chromosome sequence is 2090 CDSs (coding DNA sequence) with an average size of 970 bp (3,9). The circular chromosome encodes 65 RNA genes (9). Strain ATCC 33277 contains 93 IS elements and 48 miniature inverted repeat transposable elements (MITEs) (3). 4 RNA operons (rrn, 5S rRNA-23S rRNA-tRNAAla-tRNAIle-16S rRNA), including 53 tRNA genes have also been documented (3). Interestingly the number of rrn operons and tRNA genes in strain ATCC 33277 were identical to those of a virulent strain counterpart W83 (3,10). Nonetheless the extensive rearrangement between the two strains through the introduction of mobile elements inevitably altered the virulence of the bacterium.

Further more it has been revealed a host of bacterial species such as Bacteroides fragilis exhibit a high gene similarity to those of the ATCC 33277 strain (3). Theories suggest these genes were introduced to ATCC 33277 by a horizontal gene transfer event (3).

The genome of strain W88 is comprised of a circular chromosome made up of 2 343 479 bp’s. On average the guanine and cytosine content make up approximately 48.3 % of the genome. The circular chromosome encodes 1909 protein genes 65 RNA genes. 4 ribosomal operons (rrn, 5S rRNA-23S rRNA-tRNAAla-tRNAIle-16S rRNA) including 53 tRNA genes showing specificity for all 20 amino acids have been documented. Interestingly the number of rrn operons and tRNA genes in strain W83 were identical to those of an avirulent strain counterpart ATCC 33277. Nonetheless the extensive rearrangement between the two strains through the introduction of mobile elements inevitably altered the virulence of the bacterium.

The genome of W83 is composed predominately (85%) of ORF. Encoding a total of 1,990 ORF, 1075 presented detectable biological roles. Of the remaining ORF, 184 were categorised as a conserved hypothetical protein or conserved domain protein, 208 had to known function, and 523 encoded hypothetical proteins.

Cell structure and metabolism

Cell wall, biofilm formation, motility, metabolic functions.

Ecology

Aerobe/anaerobe, habitat (location in the oral cavity, potential other environments) and microbe/host interactions.

Pathology

Do these microorganisms cause disease in the oral cavity or elsewhere?

Application to biotechnology

Bioengineering, biotechnologically relevant enzyme/compound production, drug targets,…

Current research

Summarise some of the most recent discoveries regarding this species.

References

References examples

1. Sahm, K., MacGregor, B.J., Jørgensen, B.B., and Stahl, D.A. (1999) Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slotblot hybridization in a coastal marine sediment. Environ Microbiol 1: 65-74.

2. Human Oral Microbiome

  1. MICR3004

This page is written by Amy Pham for the MICR3004 course, Semester 2, 2016