Olwen Paterson - s43931558 Bench A 18/10/2017 
Higher order taxa
‘’Fusobacterium periodonticum’’ The type strain for ‘’F. periodonticum’’ is EK1-15 (ATCC 33693)
Description and significance
‘’F. periodonticum’’ was first described by J. Slots and colleagues in 1983. The species was isolated from an advanced periodontitis lesion from a 17 year old patient suffering from insulin-dependent diabetes mellitus. In this study ‘’F. periodonticum’’ was cultured on blood agar plates. The average cell size was reported as 0.5-7.0µm. The cells were situated separately or in filaments which were observed to reach over 100um. Moreover, ‘‘F. periodonticum’’ were described as gram-negative, non-motile, non-spore forming bacterium with a rod shape. These characteristics are typical of the Fusobacterium genus.
‘‘F. periodonticum’’ is commonly found in the human oral cavity and is typically commensal but can become pathogenic although the cause for this change is not known . While it was initially described in the human oral cavity more recent studies have detected ‘‘F. periodonticum’’ in the human gut microbiome . Of particular interest is the association of ‘‘F. periodonticum’’ in the gut microbiome with neurological diseases. It is because of this pathogenic potential in both periodontitis and other disease that it is important to study ‘’F. periodonticum’’. Through investigating this bacterium greater understanding of and new treatments for diseases may be discovered.
Four genomes have been assembled using whole genome shotgun sequencing for ‘’F. periodonticum’’. Among them is the type strain ATCC 33693. The ATCC 33693 genome is 2,615,003 bp in length, has a GC content of 27.4% and contains 2,601 genes in total. The genes they are annotated as follows: 2,352 coding genes, 58 RNA genes, 10 rRNA genes, 45 tRNA genes, 3 ncRNA genes, 191 pseudo genes, and 1 CRISPR array. While no plasmids have been characterised for ATCC 33693 two genes, a plasmid mobilisation protein  and a plasmid recombination enzyme, are annotated in the genome. Therefore, ATCC 33693 may have the ability to take up plasmids.
Cell structure and metabolism
When ‘‘F. periodonticum’’ was first documented it was determined to be gram-negative and non-motile. Further investigation into this species has determined that it has extensive ability to co-aggregate with other microbes in the oral microbiome to form biofilms. In addition, an adhesive protein, Fusobacterium adhesin A, has been found on ‘‘F. periodonticum’’ cells that allow them to bind to proteins on the surface of oral mucosal cells. This ability likely assists in the initial stages of biofilm formation. Using the online resource metacyc.org the metabolic capabilities of strain ATCC 33693 were characterised. ‘‘F. periodonticum’’ can perform two versions of glycolysis. By using glucose or glucose 6-phosphate under stress conditions the bacteria can produce a small quantity of ATP, pyruvate and precursors to essential metabolic molecules. The bacterium is also capable of an alternative for glucose oxidation; the non-oxidative branch of the pentose phosphate pathway. The pathway allows for the synthesis of NADH and the production of essential precursor metabolites, such as those for aromatic acid synthesis. ‘‘F. periodonticum’’ does not perform the TCA cycle or oxidative phosphorylation but instead relies upon the less efficient substrate level phosphorylation to generate energy. ‘‘F. periodonticum’’ is capable of pyruvate fermentation to lactate, acetate and ethanol to fulfil their energy requirements. However, ‘‘F. periodonticum’’ is an auxotroph; it cannot synthesise all required amino acids. Therefore, it will have to take up amino acids from the environment to survive.
‘‘F. periodonticum’’ is an obligate anaerobe, meaning that it can only survive in environments without oxygen. The bacterium is typically commensal and in the human oral microbiome resides in the gingival sulcus or periodontal pockets. ‘‘F. periodonticum’’ has also been detected in other sites within the mouth. Using checkerboard DNA-DNA hybridisation ‘‘F. periodonticum’’ was detected in the highest proportions on the dorsum and lateral tongue and in saliva. It was also detected on the vestibule lip, attached gingiva, floor of the mouth, buccal, ventral tongue, hard plaque, and the supra and sub gingival regions of the teeth. In addition, ‘‘F. periodonticum’’ has been detected in gut biopsy specimens, indicating it is not restricted to the oral microbiome. The ability to detect ‘‘F. periodonticum’’ in other body sites or environments is hampered by aspects of their biology. Firstly, within the ‘’Fusobacterium’’ genus there is high similarity in the 16S rDNA sequences so they cannot be used to identify samples down to the species level. For example there is 99.4–99.8% similarity between ‘’F. nucleatum’’ and ‘‘F. periodonticum’’ in their 16S rDNA sequence. It has also been noted that standard biochemical and phenotypic markers used for identification are unreliable when applied to ‘’F. periodonticum’’. However, ‘‘F. periodonticum’’ specific PCR primers have been developed for the type strain ATCC 33693, termed F3/Fp-R2 and Fp-F1/Fp-R2, which will aid in the accurate detection of this species in the future. Overall members of the genus ‘’Fusobacteria’’ have extensive abilities to coaggregate and thus form biofilms/plaque with other bacteria in the mouth. For ‘‘F. periodonticum’’ it has been established that it can coaggregate with ‘’H. pylori’’ and ‘’F. nucleatum’’ . By forming biofilms ‘‘F. periodonticum’’ is able to interact with other microbes in the oral microbiome. Consequently it will have access to nutrients and molecules, like amino acids, that it requires for survival and protection from the environment. Moreover, ‘‘F. periodonticum’’ can bind to human cells directly or via extracellular macromolecules. This adherence ability allows ‘‘F. periodonticum’’ to securely anchor itself onto cellular surfaces to avoid being dislodged and removed from its habitat. An interesting genetic interaction between ‘‘F. periodonticum’’ and its human hosts has been documented. Individuals with a least one copy of allele-2 [T] at two specific polymorphisms in the cluster of Interleukin-1 (IL-1) genes on chromosome 2 have greater mean counts of ‘‘F. periodonticum’’ and other microorganisms associated with periodontal inflammation.
As can be surmised from its name ‘‘F. periodonticum’’ is associated with periodontal disease. ‘‘F. periodonticum’’ has been detected in samples of periodontitis from European adults and samples of gingivitis and necrotising ulcerative gingivitis from Chinese adults. In addition, a microbial survey of root canals in children with pulp necrosis and periradicular lesions found ‘‘F. periodonticum’’ in all samples. These findings were corroborated by another study where ‘‘F. periodonticum’’ was detected in 18.5% of pus samples from periradicular lesions. However, the role of ‘‘F. periodonticum’’ in these diseases has not yet been determined. Both periodontal and gingivitis disease involve a change in the composition of the microflora of the oral microbiome that leads to tissue damage and inflammation of the gum around the base of teeth. Environmental factors such as smoking and a compromised immune system can predispose individuals to these diseases. Severe forms of these diseases can compromise teeth structure and lead to damage to the bone. Therefore, while understanding ‘‘F. periodonticum’’ will help to comprehend periodontal and gingivitis disease it is not the only aspect of these diseases that needs investigation. Due to ‘’F. periodonticum’s’’ association with disease in the oral microbiome it should be investigated whether its presence in the gut microbiome is also associated with disease. Especially since it coaggregates with ‘’H. pylori’’ which is a known factor in gastric ulcers and possibly gastric cancers. A possibility strengthened by the association of ‘‘F. periodonticum’’ in the gut with neurological diseases.
Application to biotechnology
‘‘F. periodonticum’’ has not been used in any biotechnology efforts to date but several approaches could be possible. Because of its natural fermentation abilities, ‘‘F. periodonticum’’ could be metabolically engineered to produce ethanol. A new ethanol producing pathway could be engineered into the bacteria by introducing new enzymes that facilitate ethanol production which has been successfully in lactic acid bacteria. Firstly, a pyruvate decarboxylase will be needed to produce Acctaldehyde from pyruvate. Secondly, an alcohol dehydrogenase is need to produce ethanol from Acctaldehyde. This pathway also produces CO2 and consumes NADH. The nisin-controlled gene expression system should be used to overexpress the two new enzymes to enhance ethanol yield. Moreover, to ensure that pyruvate is being channelled into this pathway and not consumed by other fermentation pathways; lactate dehydrogenase should be removed via gene knock-out. However, because ‘‘F. periodonticum’’ is an auxotroph the molecules it cannot synthesise itself will have to be provided to it in culture. Another possibility for biotechnology in ‘‘F. periodonticum’’ is drug targeting. A possible drug target are the adhesive molecules that allow them to interact with other bacteria to form biofilms. Antibody like proteins could be designed to bind to and thus block the action of these proteins. Moreover, this concept can be extended to the Fusobacterium adhesin A to prevent ‘‘F. periodonticum’’ from binding to mucosal cells and possibly prevent it from colonizing new sites in the mouth.
There is still much to learn about ‘’F. periodonticum’’, especially how it contributes to disease. A recent study on the microbiome of children with the tooth decay disease Caries found that ‘‘F. periodonticum’’ was significantly more abundant in children without Caries when compared with children without Caries. Consequently, the abundance of ‘‘F. periodonticum’’ could be used to screen children for risk of developing Caries. A study on the treatment of inflammation and decay of the tissues around dental implants looked at how cytokine levels and bacteria counts changed due to treatment. After 6 months of treatment the abundance of ‘‘F. periodonticum’’ had decreased along with a reduction in cytokines and bacterial counts of key pathogens. These findings are consistent with previous studies on the species role in pathology in the oral microbiome. Several recent studies have shown that the use of blue light in phototherapy may prove to be an effective tool in reducing the relative abundances of bacteria associated with periodontal diseases, including ‘’F. periodonticum’’. There is still a great deal to learn about this species in relation to how it contributes to disease and how these diseases can be successfully treated.
5. Strauss, J., White, A., Ambrose, C., McDonald, J., & Allen-Vercoe, E. (2008). Phenotypic and genotypic analyses of clinical Fusobacterium nucleatum and Fusobacterium periodonticum isolates from the human gut. Anaerobe, 14(6), 301-309.
6. Alifirova, V. M., Saltykova, I., V, Zhukova, I. A., Zhukova, N. G., Petrov, V A, Alifirova, V M, . . . Sazonov, A E. (2016). Comparison study of gut microbiota in case of Parkinson’s disease and other neurological disorders. Bûlleten' Sibirskoj Mediciny, 15(5) , 113-125.
12. Kolenbrander, P., Parrish, K., Andersen, R., & Greenberg, E. (1995). Intergeneric coaggregation of oral Treponema spp. with Fusobacterium spp. and intrageneric coaggregation among Fusobacterium spp. Infection and Immunity : IAI., 63(12), 4584-4588.
13. Han, Y., Ikegami, A., Rajanna, C., Kawsar, H., Zhou, Y., Li, M., . . . Deng, C. (n.d.). Identification and characterization of a novel adhesin unique to oral fusobacteria. Journal of Bacteriology., 187(15), 5330-5340.
15. Park, Soon-Nang, Park, Jae-Yoon, & Kook, Joong-Ki. (2010). Development of species-specific polymerase chain reaction primers for detection of Fusobacterium periodonticum. Microbiology and Immunology., 54(12), 750-753.
17. Moore, W. E. C., Moore, L. H., Ranney, R. R., Smibert, R. M., Burmeister, J. A., & Schenkein, H. A. (1991). The microflora of periodontal sites showing active destructive progression. Journal of Clinical Periodontology, 18(10), 729-739.
18. Gmür, R., Munson, M., & Wade, W. (n.d.). Genotypic and phenotypic characterization of fusobacteria from Chinese and European patients with inflammatory periodontal diseases. Systematic and Applied Microbiology., 29(2), 120-130.
19. Gmür, R., Wyss, C., Xue, Y., Thurnheer, T., & Guggenheim, B. (n.d.). Gingival crevice microbiota from Chinese patients with gingivitis or necrotizing ulcerative gingivitis. European Journal of Oral Sciences, 112(1), 33-41.
20. Triches, T., De Figueiredo, L., Feres, M., De Freitas, S., Zimmermann, G., & Cordeiro, M. (n.d.). Microbial profile of root canals of primary teeth with pulp necrosis and periradicular lesion. Journal of Dentistry for Children., 81(1), 14-19.
21. Siqueira, J., Rôças, I., Souto, R., Uzeda, M., & Colombo, A. (2001). Microbiological evaluation of acute periradicular abscesses by DNA-DNA hybridization. Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology and Endodontics., 92(4), 451-457.
22. Hugenholtz, J., & Kleerebezem, M. (1999). Metabolic engineering of lactic acid bacteria: Overview of the approaches and results of pathway rerouting involved in food fermentations. Current Opinion in Biotechnology., 10(5), 492-497.
23. Jiang, S., Gao, X., Jin, L., & Lo, E. (2016). Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children. International Journal of Molecular Sciences., 17(12), International journal of molecular sciences. , 2016, Vol.17(12).
24. Renvert, S., Widén, C., & Persson, R. (n.d.). Cytokine and microbial profiles in relation to the clinical outcome following treatment of peri-implantitis. Clinical Oral Implants Research, 28(9), 1127-1132.
This page is written by Olwen Paterson for the MICR3004 course, Semester 2, 2017