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Muhammad Irfan Zulkifle Bench E 1/9/2016 [1]
Classification
Higher order taxa
Bacteria (Kingdom) – FCB Group (Domain) – Bacteroidetes (Phylum) – Bacteroidia (Class) – Bacteroidales (Order) – Porphyromonadaceae (Family) – Porphyromonas (Genus)
Species
- Porphyromonas gingivalis
- Type strain: strain 2561 = ATCC 33277= CCUG 25893 = CCUG 25928 = CIP 103683 = DSM 20709 = JCM 12257 = NCTC 11834 [1]
Species name and type strain (consult LPSN http://www.bacterio.net/index.html for this information)
Description and significance
Give a general description of the species (e.g. where/when was it first discovered, where is it commonly found, has it been cultured, functional role, type of bacterium [Gram+/-], morphology, etc.) and explain why it is important to study this microorganism. Examples of citations [2], [3]
Genome structure
Select a strain for which genome information (e.g. size, plasmids, distinct genes, etc.) is available.
strain: ATCC33277 (less virulent strain)
The size of genome ATCC 33277 (GenBank: AP009380.1) is 2 354 886 bp, consisted of a single circular chromosome containing 2090 CDSs (average size 970bp which covered 86.1% of the complete sequence) and having an average G + C content of 48.4%. The strain has 4 RNA operons (rrn, 5S rRNA-23S rRNA-tRNAAla-tRNAIle-16S rRNA) and 53 specific amino-acid tRNA genes.
Some of the encoded genes:
GenBank (dpp11 gene): BR000944.1 Size: 2,163 bp Topology: Linear
GenBank (mfa2 gene): AB360435.1 Size: 975 bp Topology: Linear
GenBank (fimA(I) gene): AB261608.1 Size: 8,048 bp Topology: Linear
GenBank (ustA gene): AB188568.1 Size: 487bp Topology: Linear
GenBank (fimX gene): AY656999.1 Size: 943 bp Topology: Linear
GenBank (pgmA gene): AY633704.1 Size: 1,473bp Topology: Linear
GenBank (htpG gene): AF176245.1 Size: 2,076 bp Topology: Linear
GenBank (dnaK operon genes): AB015879.1 Size: 9,878 bp Topology: Linear
GenBank (mfa1 gene): AB016284.1 Size: 1,769 bp Topology: Linear
GenBank (pga67 gene): AB006481.1 Size: 2,100 bp Topology: Linear
strain: W38 (virulent strain)
The genome size of strain W83 (GenBank: AE015924.1) is 2,343,479 bp containing 4 ribosomal operons (5S-23S-tRNAAla-tRNAIle-16S), 2 structural RNA genes and 53 specific amino acid tRNA genes, with an average G+C content of 48.3% and having a total ORF of 1990 (covered the complete genome by 85%) (1-2). 54% of ORF consisted of biological role categories, 10.5 % of those have an unknown function, 9.2% were conserved hypothetical proteins/domain proteins while 26.3 were hypothetical proteins (2).
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. List of prokaryotic names with standing in nomenculture
- ↑ MICR3004
This page is written by Muhammad Irfan Zulkifle for the MICR3004 course, Semester 2, 2016