Identification of a Growth Factor Required for Culturing Specific Fastidious Oral Bacteria

Overview

Journal J Oral Microbiol

Specialty Dentistry

Date 2022 Dec 1

PMID 36452178

Authors

Pallavi Murugkar

Eric Dimise

Eric Stewart

Stephane N Viala

Jon Clardy

Floyd E Dewhirst

Kim Lewis

Affiliations

Soon will be listed here.

Abstract

Aims: The aim of this research was to isolate oral bacteria that are dependent for growth on adjacent bacteria producing a required growth factor and to identify the chemical structure of the growth factor.

Methods: strain KLE1280, could be cultivated with and as helper strains. A deletion mutant library of E. coli was screened to determine genes involved in production of the growth factor. Compounds produced by the growth factor's pathway were screened to see if they would stimulate growth of strain KLE1280. The genomes of species related to KLE1280 were screened for presence of the factor's synthetic pathway.

Results: Analysis of the deletion mutant library and growth studies identified 1,2-dihydroxy-2-naphthoic acid (DHNA) and menaquinone-4 (MK4) as the growth factors. Strain KLE1280 was shown to lack five genes in the menaquinone synthesis pathway but to possess the two genes necessary to convert DHNA to menaquinone. Genome analysis found that 8 species in genera and lack five genes in the menaquinone synthesis pathway.

Conclusions: Addition of DHNA to culture media allows isolation of strains of several oral species that are not recovered using standard media.

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References

Lagier J, Khelaifia S, Alou M, Ndongo S, Dione N, Hugon P . Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol. 2016; 1:16203. DOI: 10.1038/nmicrobiol.2016.203. View

Vartoukian S, Adamowska A, Lawlor M, Moazzez R, Dewhirst F, Wade W . In Vitro Cultivation of 'Unculturable' Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores. PLoS One. 2016; 11(1):e0146926. PMC: 4713201. DOI: 10.1371/journal.pone.0146926. View

Fenn K, Strandwitz P, Stewart E, Dimise E, Rubin S, Gurubacharya S . Quinones are growth factors for the human gut microbiota. Microbiome. 2017; 5(1):161. PMC: 5738691. DOI: 10.1186/s40168-017-0380-5. View

Alverdy J, Chang E . The re-emerging role of the intestinal microflora in critical illness and inflammation: why the gut hypothesis of sepsis syndrome will not go away. J Leukoc Biol. 2007; 83(3):461-6. DOI: 10.1189/jlb.0607372. View

Kolenbrander P, Palmer Jr R, Periasamy S, Jakubovics N . Oral multispecies biofilm development and the key role of cell-cell distance. Nat Rev Microbiol. 2010; 8(7):471-80. DOI: 10.1038/nrmicro2381. View

Kolenbrander P, Andersen R, Blehert D, Egland P, Foster J, Palmer Jr R . Communication among oral bacteria. Microbiol Mol Biol Rev. 2002; 66(3):486-505, table of contents. PMC: 120797. DOI: 10.1128/MMBR.66.3.486-505.2002. View

Nichols D, Lewis K, Orjala J, Mo S, Ortenberg R, OConnor P . Short peptide induces an "uncultivable" microorganism to grow in vitro. Appl Environ Microbiol. 2008; 74(15):4889-97. PMC: 2519364. DOI: 10.1128/AEM.00393-08. View

Valm A . The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease. J Mol Biol. 2019; 431(16):2957-2969. PMC: 6646062. DOI: 10.1016/j.jmb.2019.05.016. View

Relvas M, Regueira-Iglesias A, Balsa-Castro C, Salazar F, Pacheco J, Cabral C . Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models. Sci Rep. 2021; 11(1):929. PMC: 7806737. DOI: 10.1038/s41598-020-79875-x. View

10.

Dashper S, Ang C, Veith P, Mitchell H, Lo A, Seers C . Response of Porphyromonas gingivalis to heme limitation in continuous culture. J Bacteriol. 2008; 191(3):1044-55. PMC: 2632107. DOI: 10.1128/JB.01270-08. View

11.

Welch J, Dewhirst F, Borisy G . Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis. Annu Rev Microbiol. 2019; 73:335-358. PMC: 7153577. DOI: 10.1146/annurev-micro-090817-062503. View

12.

Vartoukian S, Moazzez R, Paster B, Dewhirst F, Wade W . First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063). J Dent Res. 2016; 95(11):1308-13. PMC: 5076754. DOI: 10.1177/0022034516651078. View

13.

Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M . Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006; 2:2006.0008. PMC: 1681482. DOI: 10.1038/msb4100050. View

14.

Donofrio A, Crawford J, Stewart E, Witt K, Gavrish E, Epstein S . Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol. 2010; 17(3):254-64. PMC: 2895992. DOI: 10.1016/j.chembiol.2010.02.010. View

15.

Marchesi J, Sato T, Weightman A, Martin T, Fry J, Hiom S . Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol. 1998; 64(2):795-9. PMC: 106123. DOI: 10.1128/AEM.64.2.795-799.1998. View

16.

Kaeberlein T, Lewis K, Epstein S . Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science. 2002; 296(5570):1127-9. DOI: 10.1126/science.1070633. View

17.

Diao J, Yuan C, Tong P, Ma Z, Sun X, Zheng S . Potential Roles of the Free Salivary Microbiome Dysbiosis in Periodontal Diseases. Front Cell Infect Microbiol. 2021; 11:711282. PMC: 8493099. DOI: 10.3389/fcimb.2021.711282. View

18.

Periasamy S, Chalmers N, Du-Thumm L, Kolenbrander P . Fusobacterium nucleatum ATCC 10953 requires Actinomyces naeslundii ATCC 43146 for growth on saliva in a three-species community that includes Streptococcus oralis 34. Appl Environ Microbiol. 2009; 75(10):3250-7. PMC: 2681650. DOI: 10.1128/AEM.02901-08. View

19.

Vartoukian S, Palmer R, Wade W . Strategies for culture of 'unculturable' bacteria. FEMS Microbiol Lett. 2010; 309(1):1-7. DOI: 10.1111/j.1574-6968.2010.02000.x. View

20.

Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, Keyamura K . Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol. 2004; 55(1):137-49. DOI: 10.1111/j.1365-2958.2004.04386.x. View