User:Rotifer218/Fusobacterium polymorphum

Fusobacterium polymorphum is a gram negative, spindle shaped, obligate anaerobic bacterium that has been isolated from the gingival crevice in humans. It has now been classified as a subspecies of F. nucleatum. F. polymorphum is a dominant species responsible for plaque formation, gingivitis, and periodontal disease in humans. This bacteria utilizes glucose as an energy source through fermentation, but the fermentation pathway is lost under various conditions. F. polymorphum is being looked at on an industrial level because it creates a tannase enzyme that is stable at high heat.

Discovery
F. polymorphum was first described by Knorr in 1922 and later published by Michael G. Newman of UCLA School of Dentistry in 1979 in a paper titled, “The Role of Bacteroides melaninogenicus and Other Anaerobes in Periodontal Infections”. Newman’s study found F. polymorphum to be reactive with serum antibodies and was identified as a main contributor to periodontal disease. The microorganism was grown at 37℃ via an anaerobic jar Gas-pak system with a mixed media. The liquid modified tryptone media with a pH of 7.2 was made up of 10g (per mL of distilled water) tryptone, 10g yeast extract, 1.25g K2HPO4, 1.25g MgSO4 4H2O, 2g glucose, and 5g sodium thioglycolate.

Characterization
This bacteria has been shown to ferment glucose during exponential growth, however, it loses the ability to metabolize glucose when in a resting state. The fermentation ability is also lost when washed with saline, but is partially restored when NAD, AMP, and Mg+ are added to the culture. F. polymorphum is a subspecies of F. nucleatum which has been studied in greater depth. It has been found to grow between pH 5.8 and 7.7 with an optimum growth rate at 7.4. During optimal growth conditions, it has a generation time of 3.5 hours. Another species, F. necrophorum, has been shown to remain viable between temperatures of -10 - 59 degrees Celsius. Although viable, no growth occurred under 21 degrees and above 43 degrees. Optimal growth temperature was at 37 degrees— human body temperature. Other studies have shown that outer membrane binding proteins RadD and CmpA form a tight bond with Streptococcus gordonii to form a strong biofilm in the human mouth.

Taxonomy and Phylogeny
The closest neighbors to the Fusobacteria phylum are Bacteroidetes and Proteobacteria. Bacteroidetes is a large phylum containing some of the most prominent bacteria found within the human oral cavity. The phylum Proteobacteria is most closely related to Fusobacteria by a phylogenetic mapping of the 37 most common oral tract bacteria. Fusobacterium has fourteen other species alongside F. polymorphum. Of these, the two most prominent are F. necrophorum which colonizes human and animal gastrointestinal tracts and causes Lemierre's syndrome and F. nucleatum which plays a role in periodontal disease, preterm births, and colon cancer.

Genomics
The F. polymorphum strain ATCC 1095 was first fully sequenced in 2007. The DNA was sheared using a nebulizer into 2-6 kb fragments. It was purified on an agarose gel, and cloned into a cloning vector of a puC18 derivative. PHRED was used for quality control over each base of sequencing reads, and Atlas genome tools were used for assembly of the reads. The genome’s coordinate system was selected based on relationship to the other Fusobacterium subspecies: Fusobacterium nucleatum and Fusobacterium vincentii. Annotation of the genome was entirely completed either through GeneMark or Glimmer.

It was discovered to have a genome consisting of a single circular chromosome and a single circular plasmid. Its chromosome is derived from 2,429,698 base pairs (bp) and has a Guanine/Cytosine (G/C) content of 26.84%, while its plasmid has 11,934 bp and a GC content of 24.53%. The bacterium has a predicted 2,433 open reading frames (ORFs). It is also predicted to contain 45 transfer RNA (tRNA) in one of seven clusters, 15 ribosomal RNA (rRNA), 11 non-coding RNA (ncRNA), and 42 pseudogenes. It was noted that most of the intergenic regions (IGR) were annotated as pseudogenes.

Annotation suggests that 38 ORFs function as transporters; 27 ORFs are related to transcriptional regulation. There are also some unique genes that code for unique proteins involved in DNA modification such as methylation, histone acetylation, and recombination. Genes for topoisomerase, integration, and type I restriction/modification are also present.

A cluster of genes found in F. polymorphum is homologous to propanediol utilization in Salmonella enterica. Propanediol is a byproduct from fructose fermentation, and yet the genome of F. polymorphum appears to lack the fructose catabolism operon (fuc). But because of the environment the bacterium is generally found in, researchers believe that F. polymorphum may be able to use propanediol without needing to produce it as a byproduct of fermentation, and that neighboring bacteria such as Escherichia coli can provide it.

Many different virulence and iron sequestering proteins have been identified genetically in F. polymorphum although their exact functions have only been suggested, not yet observed, at this point.

Ecology
F. nucleatum subsp. polymorphum is widespread throughout the world and is primarily found within the oral cavities of humans. It is associated with periodontitis. Periodontitis is classified as one of the most common infections in humans .F. polymorphum plays a primary role in the biofilm formation on human teeth. Genes have been found in F. polymorphum that suggest the bacteria use the signaling molecule AI-2 for communication with other bacteria within the biofilm on human teeth, also called plaque. In dental plaque, F. polymorphum form a complex biofilm that also contains numerous other bacterial species. These bacteria are key in interactions between Gram-negative and Gram-positive bacteria in dental biofilms.

F.polymorphum is one of five subspecies of F. nucleatum and it can be separated from the other subspecies by metagenomics and by phenotypic studies that suggested a different metabolism and different physical interactions with immune cells. A study in 2017, used next generation sequencing to identify the F. polymorphum bacteria from a large sample of other bacteria, by the 16s gene rRNA sequences at a species level. Overall, the ecology of F. polymorphum can be further assessed by swabbing of human oral cavities or OSCC lesions and 16s rRNA gene sequencing of the bacterial swab. A study done in 2017 found that F. polymorphum is one of the most abundant bacterial species found in swabs of OSCC lesions, along with P. aeruginosa and differing Campylobacter species.

Human Health
F. nucleatum subsp. polymorphum is associated with gingivitis, periodontitis and oral squamous cell carcinoma (OSCC) and has been obtained from the gingival crevice in humans. F. polymorphum is a key bacterium involved in the biofilm formation on human teeth, called plaque. Therefore, the environment in which F. polymorphum are found are the oral cavities within humans. While F. polymorphum have also been found in the mouth of healthy individuals that do not have gingivitis, periodontitis or OSCC, it is more abundant in the mouths of those with these diseases. Gingivitis is the early and reversible stage of periodontal disease in which the gums are inflamed, red and sore due to the immune response to the bacterial infection. Gingivitis can progress into chronic periodontitis which can cause the gums to pull away from the teeth and bone as well as teeth can be lost of become loose. According to the CDC, nearly half of Americans over the age of 30 have a form of periodontal disease and this increases to nearly 2/3 of Americans over the age of 65. The CDC has also started a periodontal disease surveillance project with the American Academy of Periodontology to survey and track the prominence and progression of periodontitis since 2003. Periodontitis also affects individuals across other countries as well.

While the prominent cause of gingivitis and periodontitis are bacterial infection, underlying immune deficiencies can contribute to the risk of developing these diseases. The current prevention method for gingivitis and periodontitis are good oral hygiene but research is being conducted to develop a possible probiotic or prebiotic method for prevention and treatment. Researchers believe that F. polymorphum may act as a mid-point between the Gram-positive bacteria that are present early in the dental plaque formation and the Gram-negative bacteria present later in plaque formation.

Industrial and Medical Use
F. polymorphum has been found to contain a highly active tannase enzyme TanBFnp which is used as an adaptive mechanism for bacteria during stressful conditions in their environment. This tannase was the first to be identified in an oral pathogen. This tannase has potential for industrial use because it has high thermal stability as well as a high specificty of function. This tannase could also have medical application because its specific biochemical properties suggest it plays a key role in the bacteria's ability to survive in the human mouth.