User:S4355889

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Name: Callum Le Lay
Bench ID: C
Date: 31/08/2016
[1]

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Classification

Higher order taxa

Bacteria - Terrabacteria group - Firmicutes - Negativicutes - Veillonellales - Veillonellaceae - Veillonella

Species

Veillonella parvula
Type strain: Prevot Te 3 = ATCC 10790 = DSM 2008 = JCM 12972

Description and significance

Named after french biologist Adrien Veillon who first discovered the species in 1898[2][3], Veillonella parvula is a gram negative bacteria found in many of the microenvironments of the human body. It is most common and well described in the oral cavity and the gastrointestinal tract[4] [REF]. Veillonella is part of the Negativicutes class which are known for their perculiar gram negative cell wall despite being a part of the Firmicutes phyla, in which the majority of species are gram positive. V. parvula is obligately anaerobic, auxotrophic, lactate fermenting and cocci shaped [5][6][KEGG, genome paper and other REFs]. The species is small at 0.3-0.5um[5].

Veillonella make close physical associations with all Streptococcus species[7]. Veillonella cannot metabolise carbohydrates and will ferment other sources of energy [REF]. As V. parvula ferments lactate, a common byproduct of anaerobic respiration in bacteria, it has a commensual relationship with the Streptococcus spp. which are the major producer of the metabolite. It will bind to the surface of the cells and metabolise the lactate as it is produced. This benefits V. parvula as it does not have to compete for resources. Coaggregation of Veillonella spp. with certain Streptococcus spp. (each species has preferences) is also shown to promote biofilm formation[7] and the two species are known early colonisers in oral plaque communities [REF].

It the importance of research on this microbe is its pathogenesis. It has been shown to produce biofilm and contribute to plaque formation[7]; is present in dental caries[REF] and in chronic peridontitis[8][9][REF]; and is less commonly associated with other types of diseaes such as endodontitus[REF], vaginosis[10] and even osteomyetitis[11].

Genome structure

Veillonella parvula, specifically the type strian DSM 2008, was sequenced and analysed in 2009 by Gronow et. al.. The genome is circular and is 2.13Mbp. It contains 1920 genes, 96.82% being protein coding genes and 3.18% being RNA coding genes. This means the density of protein coding genes is ~1 gene:1.1kbp. 0.78% of protein coding gene were predicted to be pseudogenes. The GC content is 38.63% and there were no detected extrachromosomal elements.

Comparing to average bacterial properties[REF], the genome size of V. parvula is normal but but its protein coding density is quite low, but this is not uncommon for Firmicutes [REFS].

Cell structure and metabolism

LACTATE+SUCCINATE METABOLISM DIAGRAM

Vellonellae do not gram stain positive like other species of the Firmicute phylum. They stain gram negative[3] [Prevot, Zuber anyone who sees them] and have the cell wall composition common of gram negatives: an lipopolysaccharide coated outer membrane, a thin peptidoglycan layer and an inner cytoplasmic membrane [12][13]. Vellonella characteristically have two diamine compounds that are required for cell growth: cardaverine and putrescine. These two molecules are required for maintenance of the diamine containing peptidoglycan in Vellonella cell walls and the integrity of the cell envelope[14]. Veillonella also contain plamalogens in their cytoplasmic membrane, which are molecules used to regulate fluidity. Plasmalogen type can be species specific. Plasmenylethanolamine and plasmenylserine are plasmalogens present in V. parvula [15].

Veillonella have no detectable hexokinase activity [16]. Hexokinase is required for the first step in glycolysis, which partially explains why the speci are unable to metabolise glucose. Research by Rogosa et. al. shows that the rest of the glycolytic system in Veillonella is functional, and they suggest that though the pathway cannot be used for glycolysis it could be a viable route for the production of glucose-6-phosphate through gluconeogenesis.

V. parvula uses lactate, malate and formate as a source of energy, with which it metabolises anaerobically to produce acetate, carbon dioxide, hydrogen gas and propionate. It metabolises these compounds by converting them to pyruvate before degrading them to acetate, producing about ATP per mole [17][18] [12]. In addition to this, V. parvula is able to take succinate as a co-factor to improve growth rate. In V. parvula about 50% of lactate that is metabolised is to pyruvate then degraded to actetate. The other half is converted to succinate (malate and formate are intermediates) which is degraded to propionate by methlmalonyldecarboxylase (MMD). This reaction does not yield a net increase in ATP, but the MMD is membrane bound and its reaction is coupled to the production of a sodium electrochemical gradient[18]. In this way the bacteria is able to conserve energy normally used to produce this gradient, meaning growth rates are increased when succinate is taken up in conjunction with lactate/malate/formate[17].

Ecology

SPECIES INTERACTION PICTURES

Veillonella sp. are mesophilic, heterotrophic and obligately anaerobic organisms [VEIL paper and gronow paper]. They are found in heterothermic veterbrates [Gronow paper 5]. V. parvula is found in humans and is most abundant within the intestinal tract [intestinal paper] and within the oral cavity [Any of them and all of them]. It has been found within the vaginal community [Vaginosis ref and a paper??], within the bone/bone marrow [osteo] and Veillonella species have been found on the epidermis [REF], though this is abnormal and occurs during infection.

There does not seem to be much interaction between the host and V. parvula, instead the bacteria interacts heavily with other bacterial species that in turn may interact with the host [REFS].

Veillonella utilise the lactate in saliva in the oral cavity. They can form partnerships with other species such as Streptococcus oralis, Actinomyces oris and Porphyromonas gingervalis [perisamy->21][perisamy] in which both partners have a higher growth rate than they would alone. The species that Veillonella binds with affects whether there is an increase in growth rate, and if there is by how much, for the two species. Perisamy [REF] examined the relationships and effects that Veillonella had with other species and found that not only was the effect on growth specific to the partnership, but the effect on growth caused by two-way species interaction did not predict the effect in a three-way interaction. For example: though the researchers found that A. oris, P. gingervalis and Veillonella sp. Could all interact for greater growth in partnerships, there was no increase in growth in a three species community. This suggests high specificity of which species can interact together for efficient utilisation of resources.

It is because of this specificity in species interaction and its positon as an early plaque coloniser that Veillonella plays a very important role in the plaque community, as it dictates which of the later colonising species will have a greater abundance in the plaque. V. parvula induces greater growth and biofilm production in the Streptococcus species mutans and sanguinus [biofilm ref], and has been associated with both healthier[stingu] and more disease associated plaque communities[pus_peridontitis].

Pathology

Veillonella have a commensal relationship with humans, but can, in rare cases, be opportunistically pathogenic. In these cases, the species found is commonly V. parvula. V. parvula has been found to be associated with osteomyelitis [REF], sepsis and bacteraemia[19][20][21], spondylodiscitis[22][23], urinary tract infection[24] and endocarditis[25]. Instances of V. parvula associated disease as listed are very rare in healthy patients[26] and the host in almost every case has had a compromised immune system through diabetes, HIV, old age, pregnancy, etc. It should be noted is that it is rare to find instances of disease where V. parvula is a major contributor but it is likely that it is involved with many polymicrobial infections, given its importance for biofilm production and multispecies interaction.

Application to biotechnology

As V. parvula is not usually pathogenic there is not much funded research being done to find drug targets for it. As a model organism, V. parvula is good as it is often found in high abundance in the the oral cavity and of the Veillonella it is the most understood, but it is not a great representative of a gram negative bacteria and there are already better biofilm producing models (P. aeruginosa) available. This means it is not being used to develop techniques for modelling.

A study by Liu et. al.[27] looks at developing transformation techniques in V. parvula with the aim of better understanding Veillonellaea biology. A paper from 1975 shows that Veillonella can be made to fluoresce under long wave ultraviolet light[28], which is useful for segregating species of the genus from a community.

Current research

Summarise some of the most recent discoveries regarding this species.

References

  1. ↑ MICR3004
  2. ↑ List of prokaryotic names with standing in nomenclature
  3. ↑ 3.0 3.1 Veillon A, Zuber MM. Recherches sur quelques microbes strictement anaérobies et leur rôle en pathologie. Arch Med Exp 1898; 10:517-545.
  4. ↑ van den Bogert, B., Erkus, O., Boekhorst, J., de Goffau, M., Smid, E. J., Zoetendal, E. G., & Kleerebezem, M. (2013). Diversity of human small intestinal Streptococcus and Veillonella populations. FEMS Microbiol Ecol, 85(2), 376-388. doi:10.1111/1574-6941.12127
  5. ↑ 5.0 5.1 Gronow, S., Welnitz, S., Lapidus, A., Nolan, M., Ivanova, N., Glavina Del Rio, T., . . . Lucas, S. (2010). Complete genome sequence of Veillonella parvula type strain (Te3). Stand Genomic Sci, 2(1), 57-65. doi:10.4056/sigs.521107
  6. ↑ http://www.genome.jp/dbget-bin/www_bget?vpr:Vpar_1247+vpr:Vpar_1248+vpr:Vpar_1762+vpr:Vpar_1763
  7. ↑ 7.0 7.1 7.2 Mashima, I., & Nakazawa, F. (2014). The influence of oral Veillonella species on biofilms formed by Streptococcus species. Anaerobe, 28, 54-61. doi:10.1016/j.anaerobe.2014.05.003
  8. ↑ Silva-Boghossian, C. M., Neves, A. B., Resende, F. A., & Colombo, A. P. (2013). Suppuration-associated bacteria in patients with chronic and aggressive periodontitis. J Periodontol, 84(9), e9-e16. doi:10.1902/jop.2013.120639
  9. ↑ Stingu, C. S., Jentsch, H., Eick, S., Schaumann, R., Knofler, G., & Rodloff, A. (2012). Microbial profile of patients with periodontitis compared with healthy subjects. Quintessence International, 43(2), 9.
  10. ↑ Africa, C. W., Nel, J., & Stemmet, M. (2014). Anaerobes and bacterial vaginosis in pregnancy: virulence factors contributing to vaginal colonisation. Int J Environ Res Public Health, 11(7), 6979-7000. doi:10.3390/ijerph110706979
  11. ↑ Al-Otaibi, F. E., & Al-Mohizea, M. M. (2014). Non-vertebral Veillonella species septicemia and osteomyelitis in a patient with diabetes: a case report and review of the literature. Journal of Medical Case Reports, 8(365), 5. doi:10.1186/1752-1947-8-365
  12. ↑ 12.0 12.1 Delwiche, E. A., Pestka, J. J., & Tortorello, M. L. (1985). The Veillonellae: Gram-Negative Cocci with a Unique Physiology. Annual Reviews, 39, 18.
  13. ↑ Jumas-Bilak, E., Carlier, J. P., Jean-Pierre, H., Teyssier, C., Gay, B., Campos, J., & Marchandin, H. (2004). Veillonella montpellierensis sp. nov., a novel, anaerobic, Gram-negative coccus isolated from human clinical samples. Int J Syst Evol Microbiol, 54(Pt 4), 1311-1316. doi:10.1099/ijs.0.02952-0
  14. ↑ Kamio, Y., & Nakamura, K. (1987). Putrescine and Cadaverine Are Constituents of Peptidoglycan in Veillonella alcalescens and Veillonella parvula. Journal of Bacteriology, 169(6), 3.
  15. ↑ Olsen, I. (1997). Salient structural features in the chemical composition of oral anaerobes, with particular emphasis on plasmalogens and sphingolipids. Reviews in Medical Microbiology, 8(1), 3.
  16. ↑ Rogosa, M., Krichevsky, M. I., & Bishop, F. S. (1965). Truncated Glycolytic System in Veillonella. Journal of Bacteriology, 90(1), 7.
  17. ↑ 17.0 17.1 Denger, K., & Schink, B. (1992). Energy conservation by succinate decarboxylation in Veillonella parvula. Journal of General Microbiology, 138(5), 4.
  18. ↑ 18.0 18.1 Dimroth, P. (1987). Sodium Ion Transport Decarboxylases and Other Aspects of Sodium Ion Cycling in Bacteria. Microbiological Reviews, 51(3), 20.
  19. ↑ Yagihashi, Y., & Arakaki, Y. (2012). Acute pyelonephritis and secondary bacteraemia caused by Veillonella during pregnancy. BMJ Case Rep, 2012. doi:10.1136/bcr-2012-007364
  20. ↑ Strach, M., Siedlar, M., Kowalczyk, D., Zembala, M., & Grodzicki, T. (2006). Sepsis caused by Veillonella parvula infection in a 17-year-old patient with X-linked agammaglobulinemia (Bruton's disease). J Clin Microbiol, 44(7), 2655-2656. doi:10.1128/JCM.00467-06
  21. ↑ Arrosagary, P. M., Salas, C., Morales, M., Correas, M., Barros, J. M., & Cordon, M. L. (1987). Bilateral Abscessed Orchiepididymitis Associated with Sepsis Caused by Veillonella parvula and Clostridium perfringens: Case Report and Review of the Literature. Journal of Clinical Microbiology, 25(8), 2.
  22. ↑ Kishen, T. J., Lindstrom, S. T., Etherington, G., & Diwan, A. D. (2012). Veillonella spondylodiscitis in a healthy 76-year-old lady. Eur Spine J, 21 Suppl 4, 413-417. doi:10.1007/s00586-011-1871-x
  23. ↑ Marriott, D., Stark, D., & Harkness, J. (2007). Veillonella parvula discitis and secondary bacteremia: a rare infection complicating endoscopy and colonoscopy? J Clin Microbiol, 45(2), 672-674. doi:10.1128/JCM.01633-06
  24. ↑ Berenger, B. M., Chui, L., Borkent, A., & Lee, M. C. (2015). Anaerobic urinary tract infection caused by Veillonella parvula identified using cystine-lactose-electrolyte deficient media and matrix-assisted laser desorption ionization-time of flight mass spectrometry. IDCases, 2(2), 44-46. doi:10.1016/j.idcr.2015.02.002
  25. ↑ Oh, S., Havlen, P. R., & Hussain, N. (2005). A Case of Polymicrobial Endocarditis due to Anaerobic Organisms in an Injection Drug User. Journal of General Internal Medicine, 20(10), 958-958. doi:10.1111/j.1525-1497.2005.0176.x
  26. ↑ Brook, I. (1996). Veillonella Infections in Children. Journal of Clinical Microbiology, 34(5), 2.
  27. ↑ Liu, J., Merritt, J., & Qi, F. (2011). Genetic transformation of Veillonella parvula. FEMS Microbiol Lett, 322(2), 138-144. doi:10.1111/j.1574-6968.2011.02344.x
  28. ↑ Chow, A. W., Patten, V., & Guze, L. B. (1975). Rapid Screening of Veillonella by Ultraviolet Fluorescence. Journal of Clinical Microbiology, 2(6), 3.

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Notes

TEMPORARY: TO BE DELETED AFTER FINISH

HILPERT, W. & DIMROTH, P. (1982). Conversion of the chemical energy of methylmalonyl-CoA decarboxylation into a Na+ gradient. Nature, London 2%, 584-585. HILPERT, W. & DIMROTH, P. (1991). On the mechanism of sodium ion translocation by methylmalonyl-CoA decarboxylasef from Veillonella alcalescens. European Journal of Biochemistry 195, 79-86.

This page was written by Callum Le Lay for the MICR3004 course, Semester 2, 2016

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