Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.
References
[1]
Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, et al. (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13: R42.
[2]
Shields RC, Mokhtar N, Ford M, Hall MJ, Burgess JG, et al. (2013) Efficacy of a marine bacterial nuclease against biofilm forming microorganisms isolated from chronic rhinosinusitis. PLoS One 8: e55339.
[3]
Pettigrew MM, Laufer AS, Gent JF, Kong Y, Fennie KP, et al. (2012) Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children. Appl Environ Microbiol 78: 6262–6270.
[4]
Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, Brinkman FS (2009) The association of virulence factors with genomic islands. PLoS One 4: e8094.
[5]
Boyd EF, Brussow H (2002) Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol 10: 521–529.
Sing A, Hogardt M, Bierschenk S, Heesemann J (2003) Detection of differences in the nucleotide and amino acid sequences of diphtheria toxin from Corynebacterium diphtheriae and Corynebacterium ulcerans causing extrapharyngeal infections. J Clin Microbiol 41: 4848–4851.
[8]
Sing A, Bierschenk S, Heesemann J (2005) Classical diphtheria caused by Corynebacterium ulcerans in Germany: amino acid sequence differences between diphtheria toxins from Corynebacterium diphtheriae and C. ulcerans. Clin Infect Dis 40: 325–326.
[9]
Rasko DA, Sperandio V (2010) Anti-virulence strategies to combat bacteria-mediated disease. Nat Rev Drug Discov 9: 117–128.
[10]
Zhang R, Zhang CT (2006) The impact of comparative genomics on infectious disease research. Microbes Infect 8: 1613–1622.
[11]
Heydari H, Wee WY, Lokanathan N, Hari R, Mohamed Yusoff A, et al. (2013) MabsBase: A Mycobacterium abscessus Genome and Annotation Database. PLoS One 8: e62443.
[12]
Uchiyama I, Mihara M, Nishide H, Chiba H (2013) MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. Nucleic Acids Res 41: D631–635.
[13]
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, et al. (2012) IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 40: D115–122.
[14]
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, et al. (2013) GenBank. Nucleic Acids Res 41: D36–42.
[15]
Bernard K (2012) The genus Corynebacterium and other medically relevant coryneform-like bacteria. J Clin Microbiol 50: 3152–3158.
[16]
Burkovski A (2013) Cell envelope of corynebacteria: structure and influence on pathogenicity. ISRN Microbiol 2013: 935736.
[17]
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
[18]
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26: 1608–1615.
[19]
Meyer F, Overbeek R, Rodriguez A (2009) FIGfams: yet another set of protein families. Nucleic Acids Res 37: 6643–6654.
[20]
Chen L, Yang J, Yu J, Yao Z, Sun L, et al. (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33: D325–328.
[21]
Yang J, Chen L, Sun L, Yu J, Jin Q (2008) VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res 36: D539–542.
[22]
Chen L, Xiong Z, Sun L, Yang J, Jin Q (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40: D641–645.
[23]
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
[24]
Birney E, Clamp M (2004) Biological database design and implementation. Brief Bioinform 5: 31–38.
[25]
Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH (2009) JBrowse: a next-generation genome browser. Genome Res 19: 1630–1638.
[26]
Stein LD, Mungall C, Shu S, Caudy M, Mangone M, et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12: 1599–1610.
[27]
Westesson O, Skinner M, Holmes I (2013) Visualizing next-generation sequencing data with JBrowse. Brief Bioinform 14: 172–177.
[28]
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639–1645.
[29]
Darzentas N (2010) Circoletto: visualizing sequence similarity with Circos. Bioinformatics 26: 2620–2621.
[30]
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
[31]
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39: W347–352.
[32]
Sekizuka T, Yamamoto A, Komiya T, Kenri T, Takeuchi F, et al. (2012) Corynebacterium ulcerans 0102 carries the gene encoding diphtheria toxin on a prophage different from the C. diphtheriae NCTC 13129 prophage. BMC Microbiol 12: 72.
Wilkinson L, Friendly M (2009) The History of the Cluster Heat Map. American Statistician 63: 179–184.
[36]
Wu XY, Chapman T, Trott DJ, Bettelheim K, Do TN, et al. (2007) Comparative analysis of virulence genes, genetic diversity, and phylogeny of commensal and enterotoxigenic Escherichia coli isolates from weaned pigs. Appl Environ Microbiol 73: 83–91.
[37]
Clinton LK, Bankowski MJ, Shimasaki T, Sae-Ow W, Whelen AC, et al.. (2013) Culture-Negative Prosthetic Valve Endocarditis with Concomitant Septicemia Due to a Nontoxigenic Corynebacterium diphtheriae biotype gravis in a Patient with Multiple Risk Factors. J Clin Microbiol.
[38]
Funke G, Altwegg M, Frommelt L, von Graevenitz A (1999) Emergence of related nontoxigenic Corynebacterium diphtheriae biotype mitis strains in Western Europe. Emerg Infect Dis 5: 477–480.
[39]
Gubler J, Huber-Schneider C, Gruner E, Altwegg M (1998) An outbreak of nontoxigenic Corynebacterium diphtheriae infection: single bacterial clone causing invasive infection among Swiss drug users. Clin Infect Dis 27: 1295–1298.
[40]
Reacher M, Ramsay M, White J, De Zoysa A, Efstratiou A, et al. (2000) Nontoxigenic Corynebacterium diphtheriae: an emerging pathogen in England and Wales? Emerg Infect Dis 6: 640–645.
[41]
Romney MG, Roscoe DL, Bernard K, Lai S, Efstratiou A, et al. (2006) Emergence of an invasive clone of nontoxigenic Corynebacterium diphtheriae in the urban poor population of Vancouver, Canada. J Clin Microbiol 44: 1625–1629.
[42]
Shashikala P, Reddy PV, Prashanth K, Kanungo R, Devi S, et al. (2011) Persistence of nontoxigenic Corynebacterium diphtheriae biotype gravis strains in Pondicherry, Southern India. J Clin Microbiol 49: 763–764.
[43]
Wojewoda CM, Koval CE, Wilson DA, Chakos MH, Harrington SM (2012) Bloodstream infection caused by nontoxigenic Corynebacterium diphtheriae in an immunocompromised host in the United States. J Clin Microbiol 50: 2170–2172.
[44]
Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehoever P, et al. (2011) Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. BMC Genomics 12: 383.
[45]
De Zoysa A, Efstratiou A, Hawkey PM (2005) Molecular characterization of diphtheria toxin repressor (dtxR) genes present in nontoxigenic Corynebacterium diphtheriae strains isolated in the United Kingdom. J Clin Microbiol 43: 223–228.
[46]
Rogers EA, Das A, Ton-That H (2011) Adhesion by pathogenic corynebacteria. Adv Exp Med Biol 715: 91–103.
