Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W: Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res. 2008, 87 (11): 1016-1020. 10.1177/154405910808701104.
Article
CAS
PubMed
Google Scholar
Ahn J, Yang L, Paster BJ, Ganly I, Morris L, Pei Z, Hayes RB: Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. PLoS One. 2011, 6 (7): e22788-10.1371/journal.pone.0022788.
Article
CAS
PubMed Central
PubMed
Google Scholar
Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A: The oral metagenome in health and disease. ISME J. 2012, 6 (1): 46-56. 10.1038/ismej.2011.85.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA: Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 2010, 4 (8): 962-974. 10.1038/ismej.2010.30.
Article
PubMed Central
PubMed
Google Scholar
Marsh PD: Dental plaque as a biofilm and a microbial community - implications for health and disease. BMC Oral Health. 2006, 6 (Suppl 1): S14-10.1186/1472-6831-6-S1-S14.
Article
PubMed Central
PubMed
Google Scholar
Wilson M: The oral cavity and its indigenous microbiota. Microbial inhabitants of humans. Edited by: Wilson M. 2005, New York: Cambridge University Press, 318-374.
Google Scholar
Jenkinson HF, Lamont RJ: Oral microbial communities in sickness and in health. Trends Microbiol. 2005, 13 (12): 589-595. 10.1016/j.tim.2005.09.006.
Article
CAS
PubMed
Google Scholar
Palmer RJ, Gordon SM, Cisar JO, Kolenbrander PE: Coaggregation-mediated interactions of streptococci and actinomyces detected in initial human dental plaque. J Bacteriol. 2003, 185 (11): 3400-3409. 10.1128/JB.185.11.3400-3409.2003.
Article
CAS
PubMed
Google Scholar
Kolenbrander PE, Andersen RN, Blehert DS, Egland PG, Foster JS, Palmer RJ: Communication among oral bacteria. Microbiol Mol Biol Rev. 2002, 66 (3): 486-505. 10.1128/MMBR.66.3.486-505.2002.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hojo K, Nagaoka S, Ohshima T, Maeda N: Bacterial interactions in dental biofilm development. J Dent Res. 2009, 88 (11): 982-990. 10.1177/0022034509346811.
Article
CAS
PubMed
Google Scholar
Dige I, Raarup MK, Nyengaard JR, Kilian M, Nyvad B: Actinomyces naeslundii in initial dental biofilm formation. Microbiology. 2009, 155 (Pt 7): 2116-2126.
Article
CAS
PubMed
Google Scholar
Kolenbrander PE, Andersen RN, Moore LV: Coaggregation of Fusobacterium nucleatum, Selenomonas flueggei, Selenomonas infelix, Selenomonas noxia, and Selenomonas sputigena with strains from 11 genera of oral bacteria. Infect Immun. 1989, 57 (10): 3194-3203.
CAS
PubMed Central
PubMed
Google Scholar
Periasamy S, Kolenbrander PE: Aggregatibacter actinomycetemcomitans builds mutualistic biofilm communities with Fusobacterium nucleatum and Veillonella species in saliva. Infect Immun. 2009, 77 (9): 3542-3551. 10.1128/IAI.00345-09.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jakubovics NS, Gill SR, Iobst SE, Vickerman MM, Kolenbrander PE: Regulation of gene expression in a mixed-genus community: stabilized arginine biosynthesis in Streptococcus gordonii by coaggregation with Actinomyces naeslundii. J Bacteriol. 2008, 190 (10): 3646-3657. 10.1128/JB.00088-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Frias-Lopez J, Duran-Pinedo A: Effect of periodontal pathogens on the metatranscriptome of a healthy multispecies biofilm model. J Bacteriol. 2012, 194 (8): 2082-2095. 10.1128/JB.06328-11.
Article
CAS
PubMed Central
PubMed
Google Scholar
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J: Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010, 89: 19.10.1-19.10.21.
Google Scholar
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005, 15 (10): 1451-1455. 10.1101/gr.4086505.
Article
CAS
PubMed Central
PubMed
Google Scholar
Goecks J, Nekrutenko A, Taylor J: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11 (8): R86-10.1186/gb-2010-11-8-r86.
Article
PubMed Central
PubMed
Google Scholar
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C: Metagenomic biomarker discovery and explanation. Genome Biol. 2011, 12 (6): R60-10.1186/gb-2011-12-6-r60.
Article
PubMed Central
PubMed
Google Scholar
Liu Y, Hu T, Zhang J, Zhou X: Characterization of the Actinomyces naeslundii ureolysis and its role in bacterial aciduricity and capacity to modulate pH homeostasis. Microbiol Res. 2006, 161 (4): 304-310. 10.1016/j.micres.2005.11.002.
Article
CAS
PubMed
Google Scholar
Takahashi N, Nyvad B: The role of bacteria in the caries process: ecological perspectives. J Dent Res. 2011, 90 (3): 294-303. 10.1177/0022034510379602.
Article
CAS
PubMed
Google Scholar
Socransky SS, Haffajee AD, Cugini MA, Smith C, Kent RL: Microbial complexes in subgingival plaque. J Clin Periodontol. 1998, 25 (2): 134-144. 10.1111/j.1600-051X.1998.tb02419.x.
Article
CAS
PubMed
Google Scholar
Chalmers NI, Palmer RJ, Kolenbrander PE, Cisar JO: Characterization of a Streptococcus sp.-Veillonella sp. community micromanipulated from dental plaque. J Bacteriol. 2008, 190 (24): 8145-8154. 10.1128/JB.00983-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, Reading NC, Villablanca EJ, Wang S, Mora JR, Umesaki Y, Mathis D, Benoist C, Relman DA, Kasper DL: Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012, 149 (7): 1578-1593. 10.1016/j.cell.2012.04.037.
Article
CAS
PubMed Central
PubMed
Google Scholar
Dethlefsen L, McFall-Ngai M, Relman DA: An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007, 449 (7164): 811-818. 10.1038/nature06245.
Article
CAS
PubMed
Google Scholar
Filoche S, Wong L, Sissons CH: Oral biofilms: emerging concepts in microbial ecology. J Dent Res. 2010, 89 (1): 8-18. 10.1177/0022034509351812.
Article
CAS
PubMed
Google Scholar
Rajilic-Stojanovic M, Heilig HG, Tims S, Zoetendal EG, de Vos WM: Long-term monitoring of the human intestinal microbiota composition. Environ Microbiol. 2012, 15: 1146-1159.
Article
Google Scholar
Abiko Y, Sato T, Mayanagi G, Takahashi N: Profiling of subgingival plaque biofilm microflora from periodontally healthy subjects and from subjects with periodontitis using quantitative real-time PCR. J Periodontal Res. 2010, 45 (3): 389-395. 10.1111/j.1600-0765.2009.01250.x.
Article
CAS
PubMed
Google Scholar
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M: KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007, 35 (Web Server issue): W182-W185.
Article
PubMed Central
PubMed
Google Scholar
Björk GR, Hagervall TG: Transfer RNA modification. EcoSal—Escherichia coli and Salmonella: cellular and molecular biology. Edited by: Böck RCI JB, Neidhardt FC, Nyström T, Rudd KE, Squires CL. 2005, Washington, D.C: ASM Press
Google Scholar
Grosjean H: Fine tuning of RNA functions by modification and editing. Topics in Current Genetics. Edited by: Hohmann S. 2005, New York: Springer Verlag
Google Scholar
Shin JH, Lee HW, Kim SM, Kim J: Proteomic analysis of Acinetobacter baumannii in biofilm and planktonic growth mode. J Microbiol. 2009, 47 (6): 728-735. 10.1007/s12275-009-0158-y.
Article
CAS
PubMed
Google Scholar
Kreth J, Merritt J, Shi W, Qi F: Co-ordinated bacteriocin production and competence development: a possible mechanism for taking up DNA from neighbouring species. Mol Microbiol. 2005, 57 (2): 392-404. 10.1111/j.1365-2958.2005.04695.x.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bhattacharjee MK, Fine DH, Figurski DH: tfoX (sxy)-dependent transformation of Aggregatibacter (Actinobacillus) actinomycetemcomitans. Gene. 2007, 399 (1): 53-64. 10.1016/j.gene.2007.04.026.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pollack-Berti A, Wollenberg MS, Ruby EG: Natural transformation of Vibrio fischeri requires tfoX and tfoY. Environ Microbiol. 2010, 12 (8): 2302-2311.
PubMed Central
PubMed
Google Scholar
Human Microbiome Project Consortium: A framework for human microbiome research. Nature. 2012, 486 (7402): 215-221. 10.1038/nature11209.
Article
Google Scholar
McNab R, Ford SK, El-Sabaeny A, Barbieri B, Cook GS, Lamont RJ: LuxS-based signaling in Streptococcus gordonii: autoinducer 2 controls carbohydrate metabolism and biofilm formation with Porphyromonas gingivalis. J Bacteriol. 2003, 185 (1): 274-284. 10.1128/JB.185.1.274-284.2003.
Article
CAS
PubMed Central
PubMed
Google Scholar
Nobbs AH, Vajna RM, Johnson JR, Zhang Y, Erlandsen SL, Oli MW, Kreth J, Brady LJ, Herzberg MC: Consequences of a sortase A mutation in Streptococcus gordonii. Microbiology. 2007, 153 (Pt 12): 4088-4097.
Article
CAS
PubMed
Google Scholar
Ton-That H, Marraffini LA, Schneewind O: Protein sorting to the cell wall envelope of Gram-positive bacteria. Biochim Biophys Acta. 2004, 1694 (1–3): 269-278.
Article
CAS
PubMed
Google Scholar
Ton-That H, Mazmanian SK, Faull KF, Schneewind O: Anchoring of surface proteins to the cell wall of Staphylococcus aureus. Sortase catalyzed in vitro transpeptidation reaction using LPXTG peptide and NH(2)-Gly(3) substrates. J Biol Chem. 2000, 275 (13): 9876-9881. 10.1074/jbc.275.13.9876.
Article
CAS
PubMed
Google Scholar
Mishra A, Wu C, Yang J, Cisar JO, Das A, Ton-That H: The Actinomyces oris type 2 fimbrial shaft FimA mediates co-aggregation with oral streptococci, adherence to red blood cells and biofilm development. Mol Microbiol. 2010, 77: 841-854.
CAS
PubMed Central
PubMed
Google Scholar
Jakubovics NS, Kerrigan SW, Nobbs AH, Stromberg N, van Dolleweerd CJ, Cox DM, Kelly CG, Jenkinson HF: Functions of cell surface-anchored antigen I/II family and Hsa polypeptides in interactions of Streptococcus gordonii with host receptors. Infect Immun. 2005, 73 (10): 6629-6638. 10.1128/IAI.73.10.6629-6638.2005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jakubovics NS, Stromberg N, van Dolleweerd CJ, Kelly CG, Jenkinson HF: Differential binding specificities of oral streptococcal antigen I/II family adhesins for human or bacterial ligands. Mol Microbiol. 2005, 55 (5): 1591-1605. 10.1111/j.1365-2958.2005.04495.x.
Article
CAS
PubMed
Google Scholar
Kolenbrander PE, Palmer RJ, Periasamy S, Jakubovics NS: Oral multispecies biofilm development and the key role of cell-cell distance. Nat Rev Microbiol. 2010, 8 (7): 471-480. 10.1038/nrmicro2381.
Article
CAS
PubMed
Google Scholar
McNab R, Holmes AR, Clarke JM, Tannock GW, Jenkinson HF: Cell surface polypeptide CshA mediates binding of Streptococcus gordonii to other oral bacteria and to immobilized fibronectin. Infect Immun. 1996, 64 (10): 4204-4210.
CAS
PubMed Central
PubMed
Google Scholar
McNab R, Jenkinson HF, Loach DM, Tannock GW: Cell-surface-associated polypeptides CshA and CshB of high molecular mass are colonization determinants in the oral bacterium Streptococcus gordonii. Mol Microbiol. 1994, 14 (4): 743-754. 10.1111/j.1365-2958.1994.tb01311.x.
Article
CAS
PubMed
Google Scholar
Stratul S, Didilescu A, Hanganu C, Greabu M, Totan A, Spinu T, Onisei D, Rusu D, Jentsch H, Sculean A: On the molecular basis of biofilm formation. Oral biofilms and systemic infections. TMJ. 2008, 58: 118-123.
Google Scholar
Loozen G, Ozcelik O, Boon N, De Mol A, Schoen C, Quirynen M, Teughels W: Inter-bacterial correlations in subgingival biofilms: a large-scale survey. J Clin Periodontol. 2014, 41 (1): 1-10. 10.1111/jcpe.12167.
Article
PubMed
Google Scholar
Ammann TW, Belibasakis GN, Thurnheer T: Impact of early colonizers on in vitro subgingival biofilm formation. PLoS One. 2013, 8 (12): e83090-10.1371/journal.pone.0083090.
Article
PubMed Central
PubMed
Google Scholar
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37 (Database issue): D141-D145.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH: V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J Microbiol Methods. 2010, 83 (2): 250-253. 10.1016/j.mimet.2010.08.008.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410. 10.1016/S0022-2836(05)80360-2.
Article
CAS
PubMed
Google Scholar
Warnes G, Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B: gplots: Various R programming tools for plotting data. The Comprehensive R Archive Network. 2009
Google Scholar
Huang Y, Gilna P, Li W: Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics. 2009, 25 (10): 1338-1340. 10.1093/bioinformatics/btp161.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pruesse E, Peplies J, Glockner FO: SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012, 28 (14): 1823-1829. 10.1093/bioinformatics/bts252.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35 (21): 7188-7196. 10.1093/nar/gkm864.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE: The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford). 2010, 2010: baq013-
Article
Google Scholar
Pruitt KD, Tatusova T, Brown GR, Maglott DR: NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012, 40 (Database issue): D130-D135.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tripp HJ, Hewson I, Boyarsky S, Stuart JM, Zehr JP: Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies. Nucleic Acids Res. 2011, 39 (20): 8792-8802. 10.1093/nar/gkr576.
Article
CAS
PubMed Central
PubMed
Google Scholar
Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11 (10): R106-10.1186/gb-2010-11-10-r106.
Article
CAS
PubMed Central
PubMed
Google Scholar
Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA: Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007, 35 (Web Server issue): W71-W74.
Article
PubMed Central
PubMed
Google Scholar