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Genome Announc. 2017 March; 5(10): e00021-17.
Published online 2017 March 9. doi:  10.1128/genomeA.00021-17
PMCID: PMC5347233

Genome Sequence of Porphyromonas gingivalis Strain A7A1-28


Porphyromonas gingivalis is an oral opportunistic pathogen. Sequenced P. gingivalis laboratory strains display limited diversity in antigens that modulate host responses. Here, we present the genome sequence of A7A1-28, a strain possessing atypical fimbrillin and capsule types, with a single contig of 2,249,024 bp and a G+C content of 48.58%.


Porphyromonas gingivalis is an anaerobic bacterium (1) associated with periodontal disease (2,4) and multiple systemic diseases (5,7). P. gingivalis may manipulate host responses to orchestrate dysbiosis and disease (8, 9), potentially through extensive variation in fimbrillin genotypes (10,12) and capsule serotypes (13, 14). Notably, common P. gingivalis laboratory strains display limited fimbrillin and capsule diversity (11, 15,18), limiting laboratory modeling of periodontal disease. This has extended to genome sequencing: fimbrillin type I, capsule absent (15, 17, 19) (ATCC 33277 [20] and 381 [21]), and fimbrillin type IV, capsule K1 (15, 17, 22, 23) (W83 [24] and A7436 [25]). Fimbrillin and capsule information is unavailable for other sequenced laboratory strains of P. gingivalis (26,28). A7A1-28 is a widely available strain that exhibits fimbrillin type II and capsule K3 (15, 17, 19). Isolated in 1985 by Neiders and Chen at SUNY-Buffalo (Buffalo, NY, USA) from a type 2 diabetes patient (29, 30), A7A1-28 stimulates in vitro responses that dramatically differ from those elicited by W83 or ATCC 33277 (13, 14); however, these differences have not been evaluated at the genome level. This study was undertaken to determine the complete genome sequence of A7A1-28 and facilitate investigations of the variety of host responses elicited by strains of P. gingivalis.

P. gingivalis strain A7A1-28 was obtained from Kesavalu Lakshmyya (University of Florida) and grown as previously described (31). Genomic DNA was obtained using the Wizard gDNA purification kit (Promega) and processed to generate shotgun and 8-kb paired-end libraries, which were sequenced using the 454 Life Sciences GS-20 instrument (32) (Roche). A total of 468,259 reads of 235,999,749 bp, with an average read length of 504 bp, were generated.

The GS-20 reads were assembled using Velvet version 0.7.63 ( (33) and Newbler version 2.3 (Roche) (32). Gaps between contigs were closed by editing in Consed ( (34,36) and by PCR-augmented Sanger sequencing. The genome was annotated using the RAST ( (37) and IMG-ER servers ( (38) and then amended using Gene Prediction Improvement Pipeline software (39).

The genome of P. gingivalis A7A1-28 has approximately 94-fold coverage and contains a single contig of 2,249,024 bp (G+C content of 48.58%). A total of 1,982 genes were annotated, which included 1,915 predicted coding sequences (CDSs), 53 tRNAs, 12 rRNAs, and one tmRNA. There are 229 subsystems in the genome. Further, 191 protein metabolism, 128 cofactors, vitamins, prosthetic groups, and pigments, 65 RNA metabolism, 94 DNA metabolism, 99 carbohydrate, and 17 membrane transport subsystem features were observed.

The annotated P. gingivalis A7A1-28 genome was compared to P. gingivalis strains W83, ATCC 33277, and TDC60 using RAST (37) and IMG-ER (38). All-to-all BLASTP comparisons of predicted protein sequences showed that A7A1-28 possesses 119 strain-specific CDSs, of which 98 are annotated as hypothetical proteins. Further, A7A1-28 contains a variety of mobile genetic elements, including seven Bacteroides conjugative transposons absent from W83, ATCC 33277, and TDC60. Genome synteny analysis revealed that the gene order in A7A1-28 resembles that of A7436 and AJW4, suggesting that local mutations may generate unique phenotypes observed in A7A1-28.

The availability of the A7A1-28 genome aids investigators in efforts to decipher interactions between P. gingivalis and host tissue, which are critical to homeostasis in the subgingival microbiome.

Accession number(s).

This genome sequencing project was deposited in GenBank under the accession number CP013131. The version described is the first version.


This study was supported by a University of Florida College of Dentistry Multi-Investigator Pilot Program project grant (to A.P.F.), as well as National Institute for Dental and Craniofacial Research grant DE013545-07S1 (to A.P.F.), and contract Y1-DE-6006-02 (to Los Alamos National Laboratory). We thank the staff of the University of Florida Interdisciplinary Center for Biotechnology Research, especially Regina Shaw, for excellent technical assistance.


Citation Xie G, Chastain-Gross RP, Bélanger M, Kumar D, Whitlock JA, Liu L, Farmerie WG, Zeng CL, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. 2017. Genome sequence of Porphyromonas gingivalis strain A7A1-28. Genome Announc 5:e00021-17.


1. Mayrand D, Holt SC 1988. Biology of asaccharolytic black-pigmented Bacteroides species. Microbiol Rev 52:134–152. [PMC free article] [PubMed]
2. Socransky SS, Haffajee AD, Cugini MA, Smith C, Kent RL Jr. 1998. Microbial complexes in subgingival plaque. J Clin Periodontol 25:134–144. doi:.10.1111/j.1600-051X.1998.tb02419.x [PubMed] [Cross Ref]
3. da Silva-Boghossian CM, do Souto RM, Luiz RR, Colombo AP 2011. Association of red complex, A. actinomycetemcomitans and non-oral bacteria with periodontal diseases. Arch Oral Biol 56:899–906. doi:.10.1016/j.archoralbio.2011.02.009 [PubMed] [Cross Ref]
4. Colombo AP, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, Socransky SS, Hasturk H, Van Dyke TE, Dewhirst F, Paster BJ 2009. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol 80:1421–1432. doi:.10.1902/jop.2009.090185 [PMC free article] [PubMed] [Cross Ref]
5. Vanterpool SF, Been JV, Houben ML, Nikkels PG, De Krijger RR, Zimmermann LJ, Kramer BW, Progulske-Fox A, Reyes L 2016. Porphyromonas gingivalis within placental villous mesenchyme and umbilical cord stroma is associated with adverse pregnancy outcome. PLoS One 11:e0146157. doi:.10.1371/journal.pone.0146157 [PMC free article] [PubMed] [Cross Ref]
6. Totaro MC, Cattani P, Ria F, Tolusso B, Gremese E, Fedele AL, D’Onghia S, Marchetti S, Di Sante G, Canestri S, Ferraccioli G 2013. Porphyromonas gingivalis and the pathogenesis of rheumatoid arthritis: analysis of various compartments including the synovial tissue. Arthritis Res Ther 15:R66. doi:.10.1186/ar4243 [PMC free article] [PubMed] [Cross Ref]
7. Serra e Silva Filho W, Casarin RC, Nicolela EL Jr, Passos HM, Sallum AW, Gonçalves RB 2014. Microbial diversity similarities in periodontal pockets and atheromatous plaques of cardiovascular disease patients. PLoS One 9:e109761. doi:.10.1371/journal.pone.0109761 [PMC free article] [PubMed] [Cross Ref]
8. Hajishengallis G, Lamont RJ 2014. Breaking bad: manipulation of the host response by Porphyromonas gingivalis. Eur J Immunol 44:328–338. doi:.10.1002/eji.201344202 [PMC free article] [PubMed] [Cross Ref]
9. Hajishengallis G. 2015. Periodontitis: from microbial immune subversion to systemic inflammation. Nat Rev Immunol 15:30–44. doi:.10.1038/nri3785 [PMC free article] [PubMed] [Cross Ref]
10. Nakagawa I, Inaba H, Yamamura T, Kato T, Kawai S, Ooshima T, Amano A 2006. Invasion of epithelial cells and proteolysis of cellular focal adhesion components by distinct types of Porphyromonas gingivalis fimbriae. Infect Immun 74:3773–3782. doi:.10.1128/IAI.01902-05 [PMC free article] [PubMed] [Cross Ref]
11. Enersen M, Nakano K, Amano A 2013. Porphyromonas gingivalis fimbriae. J Oral Microbiol 5:20265. doi:.10.3402/jom.v5i0.20265 [PMC free article] [PubMed] [Cross Ref]
12. Kato T, Kawai S, Nakano K, Inaba H, Kuboniwa M, Nakagawa I, Tsuda K, Omori H, Ooshima T, Yoshimori T, Amano A 2007. Virulence of Porphyromonas gingivalis is altered by substitution of fimbria gene with different genotype. Cell Microbiol 9:753–765. doi:.10.1111/j.1462-5822.2006.00825.x [PubMed] [Cross Ref]
13. Vernal R, León R, Silva A, van Winkelhoff AJ, Garcia-Sanz JA, Sanz M 2009. Differential cytokine expression by human dendritic cells in response to different Porphyromonas gingivalis capsular serotypes. J Clin Periodontol 36:823–829. doi:.10.1111/j.1600-051X.2009.01462.x [PubMed] [Cross Ref]
14. Vernal R, Diaz-Guerra E, Silva A, Sanz M, Garcia-Sanz JA 2014. Distinct human T-lymphocyte responses triggered by Porphyromonas gingivalis capsular serotypes. J Clin Periodontol 41:19–30. doi:.10.1111/jcpe.12176 [PubMed] [Cross Ref]
15. Aduse-Opoku J, Slaney JM, Hashim A, Gallagher A, Gallagher RP, Rangarajan M, Boutaga K, Laine ML, Van Winkelhoff AJ, Curtis MA 2006. Identification and characterization of the capsular polysaccharide (K-antigen) locus of Porphyromonas gingivalis. Infect Immun 74:449–460. doi:.10.1128/IAI.74.1.449-460.2006 [PMC free article] [PubMed] [Cross Ref]
16. Laine ML, Appelmelk BJ, van Winkelhoff AJ 1997. Prevalence and distribution of six capsular serotypes of Porphyromonas gingivalis in periodontitis patients. J Dent Res 76:1840–1844. doi:.10.1177/00220345970760120601 [PubMed] [Cross Ref]
17. Laine ML, van Winkelhoff AJ 1998. Virulence of six capsular serotypes of Porphyromonas gingivalis in a mouse model. Oral Microbiol Immunol 13:322–325. doi:.10.1111/j.1399-302X.1998.tb00714.x [PubMed] [Cross Ref]
18. Enersen M. 2011. Porphyromonas gingivalis: a clonal pathogen? Diversities in housekeeping genes and the major fimbriae gene. J Oral Microbiol 3:8487. doi:.10.3402/jom.v3i0.8487 [PMC free article] [PubMed] [Cross Ref]
19. Nakano K, Kuboniwa M, Nakagawa I, Yamamura T, Nomura R, Okahashi N, Ooshima T, Amano A 2004. Comparison of inflammatory changes caused by Porphyromonas gingivalis with distinct fimA genotypes in a mouse abscess model. Oral Microbiol Immunol 19:205–209. doi:.10.1111/j.0902-0055.2004.00133.x [PubMed] [Cross Ref]
20. Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H, Nakayama K, Toh H, Yoshimura F, Kuhara S, Hattori M, Hayashi T, Nakayama K 2008. Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res 15:215–225. doi:.10.1093/dnares/dsn013 [PMC free article] [PubMed] [Cross Ref]
21. Chastain-Gross RP, Xie G, Bélanger M, Kumar D, Whitlock JA, Liu L, Raines SM, Farmerie WG, Daligault HE, Han CS, Brettin TS, Progulske-Fox A 2017. Genome sequence of Porphyromonas gingivalis strain 381. Genome Announc 5(2):e01467-16. doi:.10.1128/genomeA.01467-16 [PMC free article] [PubMed] [Cross Ref]
22. Nagano K, Hasegawa Y, Abiko Y, Yoshida Y, Murakami Y, Yoshimura F 2012. Porphyromonas gingivalis FimA fimbriae: fimbrial assembly by fimA alone in the fim gene cluster and differential antigenicity among fimA genotypes. PLoS One 7:e43722. doi:.10.1371/journal.pone.0043722 [PMC free article] [PubMed] [Cross Ref]
23. Rodrigues PH, Reyes L, Chadda AS, Bélanger M, Wallet SM, Akin D, Dunn W Jr, Progulske-Fox A 2012. Porphyromonas gingivalis strain specific interactions with human coronary artery endothelial cells: a comparative study. PLoS One 7:e52606. doi:.10.1371/journal.pone.0052606 [PMC free article] [PubMed] [Cross Ref]
24. Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM 2003. Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83. J Bacteriol 185:5591–5601. doi:.10.1128/JB.185.18.5591-5601.2003 [PMC free article] [PubMed] [Cross Ref]
25. Chastain-Gross RP, Xie G, Bélanger M, Kumar D, Whitlock JA, Liu L, Farmerie WG, Daligault HE, Han CS, Brettin TS, Progulske-Fox A 2015. Genome sequence of Porphyromonas gingivalis Strain A7436. Genome Announc 3(5):e00927-15. doi:.10.1128/genomeA.00927-15 [PMC free article] [PubMed] [Cross Ref]
26. Xie G, Chastain-Gross RP, Bélanger M, Kumar D, Whitlock JA, Liu L, Farmerie WG, Daligault HE, Han CS, Brettin TS, Progulske-Fox A 2015. Genome sequence of Porphyromonas gingivalis Strain AJW4. Genome Announc 3(6):e01304-15. doi:.10.1128/genomeA.01304-15 [PMC free article] [PubMed] [Cross Ref]
27. Watanabe T, Maruyama F, Nozawa T, Aoki A, Okano S, Shibata Y, Oshima K, Kurokawa K, Hattori M, Nakagawa I, Abiko Y 2011. Complete genome sequence of the bacterium Porphyromonas gingivalis TDC60, which causes periodontal disease. J Bacteriol 193:4259–4260. doi:.10.1128/JB.05269-11 [PMC free article] [PubMed] [Cross Ref]
28. Siddiqui H, Yoder-Himes DR, Mizgalska D, Nguyen KA, Potempa J, Olsen I 2014. Genome sequence of Porphyromonas gingivalis strain HG66 (DSM 28984). Genome Announc 2(5):e00947-14. doi:.10.1128/genomeA.00947-14 [PMC free article] [PubMed] [Cross Ref]
29. Nisengard R. 1987. Bacterial invasion in periodontal disease. J Periodontol 58:331–339. doi:.10.1902/jop.1987.58.5.331 [Cross Ref]
30. Chen PB, Neiders ME, Millar SJ, Reynolds HS, Zambon JJ 1987. Effect of immunization on experimental Bacteroides gingivalis infection in a murine model. Infect Immun 55:2534–2537. [PMC free article] [PubMed]
31. Belanger M, Rodrigues P, Progulske-Fox A 2007. Genetic manipulation of Porphyromonas gingivalis. Curr Protoc Microbiol 13:Unit13C.2. doi:.10.1002/9780471729259.mc13c02s05 [PubMed] [Cross Ref]
32. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. doi:.10.1038/nature03959 [PMC free article] [PubMed] [Cross Ref]
33. Zerbino DR, Birney E 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi:.10.1101/gr.074492.107 [PubMed] [Cross Ref]
34. Ewing B, Green P 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194. doi:.10.1101/gr.8.3.186 [PubMed] [Cross Ref]
35. Ewing B, Hillier L, Wendl MC, Green P 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185. doi:.10.1101/gr.8.3.175 [PubMed] [Cross Ref]
36. Gordon D, Abajian C, Green P 1998. Consed: a graphical tool for sequence finishing. Genome Res 8:195–202. doi:.10.1101/gr.8.3.195 [PubMed] [Cross Ref]
37. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi:.10.1186/1471-2105-9-386 [PMC free article] [PubMed] [Cross Ref]
38. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC 2012. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122. doi:.10.1093/nar/gkr1044 [PMC free article] [PubMed] [Cross Ref]
39. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC 2010. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7:455–457. doi:.10.1038/nmeth.1457 [PubMed] [Cross Ref]

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