User:S4355889

From MicrobeWiki, the student-edited microbiology resource

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

Classification

Genome map of the Veillonella parvula genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes, GC content, GC skew.[2]

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 the french biologist Adrien Veillon, who first discovered the species in 1898[3][4], Veillonella parvula is a gram negative bacteria found in the human oral cavity[5][6] and the gastrointestinal tract[7]. The Veillonella genus is part of the Negativicutes class of bacteria which are known for their peculiar gram negative cell wall, which they have despite being a part of a largely gram positive phylum. V. parvula is an obligately anaerobic, auxotrophic, lactate fermenting and cocci shaped [2][8][9][5] bacteria. The species is small at 0.3-0.5µm[2].

Veillonella make close physical associations with many species, particularly those of the Streptococcus genus[10]. This is because it cannot metabolise common sugars[11] and will ferment other sources of energy. V. parvula ferments lactate, a common by-product of anaerobic respiration in bacteria. It will bind to the surface of other fermenting bacteria and metabolise the lactate as it is produced[12][10]. This benefits V. parvula as it does not have to compete for resources. Coaggregation of Veillonella species with certain Streptococcus species (each species has preferences) is also shown to promote biofilm formation[10] and the two species are known early colonisers in oral plaque communities[12].

It is important to understand this species of bacteria because of its role in human health. Though it is neither pathogenic or directly beneficial to humans, this species and its relatives in the genus are hugely important to microbial community composition and inter-species interactivity, particularly in oral plaques. Also V. parvula can be opportunistically pathogenic. Though this is uncommon, the severity of the infections is enough to warrant more research into this aspect.

Genome structure

Veillonella parvula, specifically the type strain DSM 2008, was sequenced and analysed in 2009 by Gronow et. al[2]. The genome is circular and is 2.13Mbp long, with the density of protein coding genes being about one gene per 1.1kbp. The genome contains 1920 genes, 97% being protein coding genes and the remaining coding for RNAs. 0.78% of the protein coding genes were predicted to be pseudogenes. The GC content was found to be 39% and there were no detected extrachromosomal elements.

Comparing to average bacterial properties[13], the genome size of V. parvula is normal but its protein coding density is quite low. This is not uncommon for members of the Firmicutes phylum[14][15].

Cell structure and metabolism

Diagram of simplified Veillonella lactate and succinate metabolism pathway. Many steps, enzymes and metabolites have been omitted. Lactate and succinate are shown in bold. ATP molecules are shown in red. End products of energy metabolism are shown in blue. The methylmalonyl decarboxylase is shown catalyzing the decarboxylisation of (S)Methymalonyl-CoA to propionyl-CoA. The energy produced in this reaction is used to produce a sodium gradient across the cytopasmic membrane. Based on papers by Delwiche[9] and Dimroth[16].

Members of the Negativicutes class, V. parvula being one, do not stain gram positive like other species of the Firmicutes phylum. They stain gram negative[4][2][17][9] and have the cell wall composition common to gram negative species: a lipopolysaccharide coated outer membrane, a thin peptidoglycan layer and an inner cytoplasmic membrane[18][19]. The thin peptidoglycan layer of members of the Vellonella genus characteristically contains diamine. To maintain this type of peptidoglycan two diamine compounds are required: cardaverine and putrescine. These two molecules are required for maintenance, and without them the integrity of the cell envelope[20] is compromised resulting in cell death. Another characteristic trait of the Veillonella genus’ cell wall is the presence of plamalogens in their cytoplasmic membrane, which are molecules used to regulate fluidity. Plasmenylethanolamine and plasmenylserine are plasmalogens present in and specific to V. parvula [17].

Hexokinase is required for the first step in glycolysis. Veillonella species have no detectable hexokinase activity [11], which partially explains why the genus is unable to metabolise glucose. Research by Rogosa "et. al."[11] shows that the rest of the glycolytic system in Veillonella is functional. The researchers suggest that the pathway could instead be a viable route for gluconeogenesis, ending in production of glucose-6-phosphate, because most of the pathway is expressed and functional.

As V. parvula does not acquire energy from sugars as other fermentative bacteria do, it uses lactate, malate and formate as a source of energy, which it metabolises anaerobically to produce acetate, carbon dioxide, hydrogen gas and propionate. Lactate and malate are common by-products of fermentation and so are plentiful in the oral and gastrointestinal microbiomes where there are many fermentative bacteria. In addition to this, V. parvula is able to take up succinate as a co-factor (and only as a cofactor) to improve growth rate[21]. About 50% of lactate that is metabolised is oxidised to pyruvate then degraded to acetate, yielding one ATP molecule. The other half is converted to succinate (malate and formate are intermediates) and then degraded to propionate by methlmalonyldecarboxylase (MMD). This reaction does not yield a net increase in ATP, but the energy produced when the membrane bound MMD catalyzes the reaction is used to generate an electrochemical sodium gradient across the cytoplasmic membrane[16]. In this way the bacteria are able to conserve the energy normally used to produce this gradient, explaining why growth rates increase when succinate is taken up in conjunction with lactate/malate/formate[21].

Ecology

Population growth of cultures containing three species after 4 and 8 hours. Cultures are grown on flow cells and provided with saliva with high lactate content. (Top row) Growth of Veillonella species with Streptococcus oralis and Porphyromonas gingervalis. (Bottom row) Growth of Veillonella species with Actinomyces oris and Porphyromonas gingervalis.[12]

There does not seem to be much interaction between human hosts and V. parvula, as it has a commensal relationship with them. Instead the bacteria interacts heavily with other bacterial species that in turn may interact with the hosts [12].

The Veillonella can utilise the lactate in the saliva of the oral cavity, but they have a higher growth rate when they are partnered to a lactate producing bacteria. They can form partnerships with species such as Actinomyces oris, Porphyromonas gingervalis[22] and any of the Streptococcus species[12], in which both partners have a higher growth rate than they would alone. The species that the different Veillonella species bind with affects whether there is an increase in growth rate and biofilm production[10], and the extent of that increase, for the two species. Perisamy[12] examined the relationships that Veillonella had with other species and found that the effect on growth caused by two-way species interactions did not predict the effect in three-way interactions. For example: though the researchers found that A. oris, P. gingervalis and Veillonella species could all interact for greater growth in two-way interactions, there was no increase in a community composed of all three species. This shows that the Veillonella have high specificity in regards to which species they will interact with for efficient utilisation of resources. It is because of this specificity and its position as an early plaque coloniser, that members of the Veillonella genus play a very important role in the plaque community. They dictate 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[10]. It has been associated with both healthy[23][24] and unhealthy plaque communities[25].

Pathology

Though V. parvula is a well-known oral species, it does not seem to be associated with endodontitis or dental caries. Whether the species is associated with gingivitis is contentious[26][27]. The V. parvula species can, in rare cases, be opportunistically pathogenic. It has been found to cause osteomyelitis[28], sepsis, bacteraemia[29][30][31], spondylodiscitis[32][33], urinary tract infection[34] and endocarditis[35]. Instances of V. parvula associated disease, as listed, are rare in healthy patients[36] and the host in almost every case has had a compromised immune system, commonly through diabetes, HIV, old age, pregnancy or some recessive disorder. Though it is rare to find instances of disease where Veillonella was the sole cause or major contributor, many polymicrobial infections are likely to have Veillonella present, given its importance in biofilm generation 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: it is often found in high abundance in the oral cavity and it is the best understood of the Veillonella. The reason it is not used because it is not a great model for gram negative bacteria and there are already better models (Pseudomonas aeruginosa) available for biofilm formation.

There have been some attempts to develop technologies that would help researchers better understand the biology of the Veillonella genus. A study by Liu et. al.[37] looks at developing transformation techniques in V. parvula with the aim of better understanding Veillonellaceae biology. A paper from 1975 showed that Veillonella can be made to fluoresce under long wave ultraviolet light[38], which is useful for segregating species of the genus from a community.

Current research

The current research involving V. parvula is made up mostly of metagenomic studies of the oral cavity[39][40][41][42][43], that aim to understand the microbiome as a whole. Publications that are not describing metagenomic studies have been either: discoveries of it’s role in diseases in conjunction with other microbes[44][45][46] or on the biology[47][48] of the organism relatively unstudied genus, though publications of these types are far less common than the metagenomics studies.

A very recent metagenomic study by Cuthbertson et. al.[45], 2016, is remarkable because it illuminates the properties and composition of a notoriously hard to study and complex microbiome, as well as providing a way to clinically identify periods of acute worsening of cystic fibrosis before they occur. In the paper these periods, known as cystic fibrosis pulmonary exacerbations (CFPEs), were found to be preceded by decreases in the proportional abundance of V. parvula/rogosae and decreases in the proportional abundances of P. melaninogenica/veroralis/histicola. The researchers proposed that this useful discovery could mean that the proportional abundance of these bacterial species could be used as a biomarker for CFPE onset. The power of this study came from its unprecedented coverage of the stages of the CFPEs, through a very high frequency of sampling from the lungs of patients. This allowed the researchers to also identify the core ‘metacommunity’ of the cystic fibrosis lung microbiota and shed light on the dynamics of this community, particularly in regards to CFPE treatment (usually a broad spectrum antibiotic).

References

  1. ↑ MICR3004
  2. ↑ 2.0 2.1 2.2 2.3 2.4 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
  3. ↑ List of prokaryotic names with standing in nomenclature
  4. ↑ 4.0 4.1 Veillon A, Zuber MM. Recherches sur quelques microbes strictement anaérobies et leur rôle en pathologie. Arch Med Exp 1898; 10:517-545.
  5. ↑ 5.0 5.1 Edlund, A., Yang, Y., Yooseph, S., Hall, A. P., Nguyen, D. D., Dorrestein, P. C., . . . McLean, J. S. (2015). Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism. ISME J, 9(12), 2605-2619. doi:10.1038/ismej.2015.72
  6. ↑ Mashima, I., Kamaguchi, A., & Nakazawa, F. (2011). The distribution and frequency of oral veillonella spp. in the tongue biofilm of healthy young adults. Curr Microbiol, 63(5), 403-407. doi:10.1007/s00284-011-9993-2
  7. ↑ 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
  8. ↑ http://www.genome.jp/dbget-bin/www_bget?vpr:Vpar_1247+vpr:Vpar_1248+vpr:Vpar_1762+vpr:Vpar_1763
  9. ↑ 9.0 9.1 9.2 Delwiche, E. A., Pestka, J. J., & Tortorello, M. L. (1985). The Veillonellae: Gram-Negative Cocci with a Unique Physiology. Annual Reviews, 39, 18.
  10. ↑ 10.0 10.1 10.2 10.3 10.4 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
  11. ↑ 11.0 11.1 11.2 Rogosa, M., Krichevsky, M. I., & Bishop, F. S. (1965). Truncated Glycolytic System in Veillonella. Journal of Bacteriology, 90(1), 7.
  12. ↑ 12.0 12.1 12.2 12.3 12.4 12.5 Periasamy, S., & Kolenbrander, P. E. (2010). Central Role of the Early Colonizer Veillonella sp. in Establishing Multispecies Biofilm Communities with Initial, Middle, and Late Colonizers of Enamel. Journal of Bacteriology, 192(12), 2965-2972. doi:10.1128/jb.01631-09
  13. ↑ Koonin, E. V., & Wolf, Y. I. (2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Research, 36(21), 6688-6719. doi:10.1093/nar/gkn668
  14. ↑ Schofeild, B. J., Skarshewski, A., Lachner, N., Ouwerkerk, D., Klieve, A. V., Dart, P., & Hugenholtz, P. (2016). Near complete genome sequence of the feed probiotic, Bacillus amyloliquefaciens H57. Standards in Genomic Sciences, 1(89), 7.
  15. ↑ Riedel, T., Bunk, B., Wittmann, J., Thürmer, A., Spröer, C., Gronow, S., . . . Overmann, J. (2015). Complete Genome Sequence of theClostridium difficileType Strain DSM 1296T. Genome Announcements, 3(5), e01186-01115. doi:10.1128/genomeA.01186-15
  16. ↑ 16.0 16.1 Dimroth, P. (1987). Sodium Ion Transport Decarboxylases and Other Aspects of Sodium Ion Cycling in Bacteria. Microbiological Reviews, 51(3), 20.
  17. ↑ 17.0 17.1 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.
  18. ↑ Delwiche, E. A., Pestka, J. J., & Tortorello, M. L. (1985). The Veillonellae: Gram-Negative Cocci with a Unique Physiology. Annual Reviews, 39, 18.
  19. ↑ 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
  20. ↑ Kamio, Y., & Nakamura, K. (1987). Putrescine and Cadaverine Are Constituents of Peptidoglycan in Veillonella alcalescens and Veillonella parvula. Journal of Bacteriology, 169(6), 3.
  21. ↑ 21.0 21.1 Denger, K., & Schink, B. (1992). Energy conservation by succinate decarboxylation in Veillonella parvula. Journal of General Microbiology, 138(5), 4.
  22. ↑ Periasamy, S., & Kolenbrander, P. E. (2009). Mutualistic Biofilm Communities Develop with Porphyromonas gingivalis and Initial, Early and Late Colonizers of Enamel. Journal of Bacteriology, 191(22), 8. doi:6804-6811
  23. ↑ 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.
  24. ↑ Desvarieux, M., Demmer, R. T., Rundek, T., Boden-Aibala, B., Jacobs, D. R., Sacco, R. L., & Papapanou, P. N. (2005). Peridontal Microbiota and Carotid Intima-Media Thickness. Circulation, 5(576), 14. doi:10.1161/01.CIR.0000154582.37101
  25. ↑ 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
  26. ↑ Kistler, J. O., Booth, V., Bradshaw, D. J., & Wade, W. G. (2013). Bacterial Community Development in Experimental Gingivitis. PLoS One, 8(8), e71227. doi:10.1371/journal.pone.0071227
  27. ↑ Moore, W. E., Holdeman, L. V., Smibert, R. M., Good, I. J., Burmeister, J. A., Palcanis, K. G., & Ranney, R. R. (1982). Bacteriology of experimental gingivitis in young adult humans. Infect Immun, 38(2). doi:651-667
  28. ↑ 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
  29. ↑ 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
  30. ↑ 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
  31. ↑ 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.
  32. ↑ 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
  33. ↑ 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
  34. ↑ 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
  35. ↑ 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
  36. ↑ Brook, I. (1996). Veillonella Infections in Children. Journal of Clinical Microbiology, 34(5), 2.
  37. ↑ 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
  38. ↑ Chow, A. W., Patten, V., & Guze, L. B. (1975). Rapid Screening of Veillonella by Ultraviolet Fluorescence. Journal of Clinical Microbiology, 2(6), 3.
  39. ↑ Wang, K., Lu, W., Tu, Q., Ge, Y., He, J., Zhou, Y., . . . Zhou, X. (2016). Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus. Sci Rep, 6, 22943. doi:10.1038/srep22943
  40. ↑ Pasolli, E., Truong, D. T., Malik, F., Waldron, L., & Segata, N. (2016). Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights. PLoS Comput Biol, 12(7), e1004977. doi:10.1371/journal.pcbi.1004977
  41. ↑ Arrieta, M., Steimsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist-Doutsch, S., . . . Finlay, B. B. (2015). Early infancy microbial and metabolic alterations affect risk of childhood asthma. Science Translational Medicine, 7(307), 14.
  42. ↑ Hirai, J., Yamagishi, Y., Kinjo, T., Hagihara, M., Sakanashi, D., Suematsu, H., . . . Mikamo, H. (2016). Osteomyelitis caused by Veillonella species: Case report and review of the literature. J Infect Chemother, 22(6), 417-420. doi:10.1016/j.jiac.2015.12.015
  43. ↑ Edlund, A., Yang, Y., Yooseph, S., Hall, A. P., Nguyen, D. D., Dorrestein, P. C., . . . McLean, J. S. (2015). Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism. ISME J, 9(12), 2605-2619. doi:10.1038/ismej.2015.72
  44. ↑ Pustelny, C., Komor, U., Pawar, V., Lorenz, A., Bielecka, A., Moter, A., . . . Haussler, S. (2015). Contribution of Veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system. Infect Immun, 83(1), 417-429. doi:10.1128/IAI.02234-14
  45. ↑ 45.0 45.1 Cuthbertson, L., Rogers, G. B., Walker, A. W., Oliver, A., Green, L. E., Daniels, T. W., . . . van der Gast, C. J. (2016). Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention. ISME J, 10(5), 1081-1091. doi:10.1038/ismej.2015.198
  46. ↑ 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
  47. ↑ Zhou, P., Liu, J., Li, X., Takahashi, Y., & Qi, F. (2015). The Sialic Acid Binding Protein, Hsa, in Streptococcus gordonii DL1 also Mediates Intergeneric Coaggregation with Veillonella Species. PLoS One, 10(11), e0143898. doi:10.1371/journal.pone.0143898
  48. ↑ Edlund, A., Liu, Q., Watling, M., To, T. T., Bumgarner, R. E., He, X., . . . McLean, J. S. (2016). High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model. Genome Announc, 4(1). doi:10.1128/genomeA.01684-15


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

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