References
- Dewhirst FE, Chen T, Izard J, et al. The human oral microbiome. J Bacteriol. 2010;192(19):5002–12.
- Rappe MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol. 2003;57(1):369–394.
- Turroni F, Ribbera A, Foroni E, et al. Human gut microbiota and bifidobacteria: from composition to functionality. Antonie Van Leeuwenhoek. 2008;94:35–50.
- Alverdy JC, Chang EB. 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. 2008;83(3):461–466.
- D’Onofrio A, Crawford JM, Stewart EJ, et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol. 2010;17(3):254–264.
- Vartoukian SR. Cultivation strategies for growth of uncultivated bacteria. J Oral Biosci. 2016;58(4):142–149.
- Vartoukian SR, Adamowska A, Lawlor M, et al. In vitro cultivation of ‘unculturable’ oral bacteria, facilitated by community culture and media supplementation with siderophores. PLoS One. 2016;11(1):e0146926.
- Vartoukian SR, Moazzez RV, Paster BJ, et al. First cultivation of health-associated tannerella sp. HOT-286 (BU063). J Dent Res. 2016;95(11):1308–1313.
- Kolenbrander PE, Andersen RN, Blehert DS, et al. Communication among oral bacteria. Microbiol Mol Biol Rev. 2002;66(3):486–505.
- Valm AM. 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.
- Mark Welch JL, Dewhirst FE, Borisy GG. Biogeography of the oral microbiome: the site-specialist hypothesis. Annu Rev Microbiol. 2019;73(1):335–358.
- Rodionov DA, Arzamasov AA, Khoroshkin MS, et al. Micronutrient requirements and sharing capabilities of the human gut microbiome. Front Microbiol. 2019;10:1316.
- Chen T, Yu WH, Izard J, et al. The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford). 2010;2010:baq013.
- Vartoukian SR, Palmer RM, Wade WG. Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett. 2010;309(1):1–7.
- Vartoukian SR, Palmer RM, Wade WG. Cultivation of a synergistetes strain representing a previously uncultivated lineage. Environ Microbiol. 2010;12(4):916–928.
- Guggenheim B, Giertsen E, Schupbach P, et al. Validation of an in vitro biofilm model of supragingival plaque. J Dent Res. 2001;80(1):363–370.
- Marchesi JR, Sato T, Weightman AJ, et al. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol. 1998;64(6):2333.
- Chun J, Lee JH, Jung Y, et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol. 2007;57(10):2259–2261.
- Kato J, Hashimoto M. Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol. 2007;3(1):132.
- Baba T, Ara T, Hasegawa M, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006;2(1). DOI:10.1038/msb4100050.
- Aziz RK, Bartels D, Best AA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9(1):75.
- Chen K, Chen L, Fan X, et al. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 2014;24(2):310–317.
- Fenn K, Strandwitz P, Stewart EJ, et al. Quinones are growth factors for the human gut microbiota. Microbiome. 2017;5(1):161.
- Hashimoto M, Ichimura T, Mizoguchi H, et al. Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol. 2005;55(1):137–149.
- Bentley R, Meganathan R. Biosynthesis of vitamin K (menaquinone) in bacteria. Microbiol Rev. 1982;46(3):241–280.
- Olsen I. Chemotaxonomy of bacteroides: a review. Acta Odontol Scand. 1994;52(6):354–367.
- Sakamoto M, Huang Y, Umeda M, et al. Detection of novel oral phylotypes associated with periodontitis. FEMS Microbiol Lett. 2002;217(1):65–69.
- Dashper SG, Ang CS, Veith PD, et al. Response of porphyromonas gingivalis to heme limitation in continuous culture. J Bacteriol. 2009;191(3):1044–1055.
- Kolenbrander PE, Palmer RJ Jr., Periasamy S, et al. Oral multispecies biofilm development and the key role of cell-cell distance. Nat Rev Microbiol. 2010;8:471–480.
- Periasamy S, Chalmers NI, Du-Thumm L, et al. 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):3250–3257.
- Kaeberlein T, Lewis K, Epstein SS. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science. 2002;296(5570):1127–1129.
- Nichols D, Lewis K, Orjala J, et al. Short peptide induces an “uncultivable” microorganism to grow in vitro. Appl Environ Microbiol. 2008;74(15):4889–4897.
- Lagier JC, Khelaifia S, Alou MT, et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol. 2016;1(12):16203.
- Meuric V, Rouillon A, Chandad F, et al. Putative respiratory chain of porphyromonas gingivalis. Future Microbiol. 2010;5(5):717–734.
- Olczak T, Simpson W, Liu X, et al. Iron and heme utilization in Porphyromonas gingivalis. FEMS Microbiol Rev. 2005;29(1):119–144.
- Morillo-Lopez V, Sjaarda A, Islam I, et al. Corncob structures in dental plaque reveal microhabitat taxon specificity. Microbiome. 2022;10(1):145.
- Yamashita Y, Takeshita T. The oral microbiome and human health. J Oral Sci. 2017;59(2):201–206.
- Diao J, Yuan C, Tong P, et al. Potential roles of the free salivary microbiome dysbiosis in periodontal diseases. Front Cell Infect Microbiol. 2021;11:711282.
- Relvas M, Regueira-Iglesias A, Balsa-Castro C, et al. 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.
- Rusthen S, Kristoffersen AK, Young A, et al. Dysbiotic salivary microbiota in dry mouth and primary sjogren’s syndrome patients. PLoS One. 2019;14(6):e0218319.
- Yang CY, Yeh YM, Yu HY, et al. Oral microbiota community dynamics associated with oral squamous cell carcinoma staging. Front Microbiol. 2018;9:862.
- Webb K, Zain NMM, Stewart I, et al. Porphyromonas pasteri and Prevotella nanceiensis in the sputum microbiota are associated with increased decline in lung function in individuals with cystic fibrosis. J Med Microbiol. 2022;711:001481.
- Webb K, Zain NMM, Stewart I, et al. Porphyromonas pasteri and Prevotella nanceiensis in the sputum microbiota are associated with increased decline in lung function in individuals with cystic fibrosis. J Med Microbiol. 2022:71(2):001481.