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Volume 18, Number 3—March 2012
Research

A Systematic Approach for Discovering Novel, Clinically Relevant Bacteria

Robert Schlaberg1Comments to Author , Keith E. Simmon1, and Mark A. Fisher
Author affiliations: University of Utah School of Medicine, Salt Lake City, Utah, USA (R. Schlaberg, M.A. Fisher); ARUP Laboratories, Salt Lake City (R. Schlaberg, K.E. Simmon, M.A. Fisher)

Main Article

Table 3

Anatomical sites and possible novel bacterial isolates*

Source Identity, % Best species-level match Cluster Gram stain morphology Comment†
Tissue 98.8 Acidovorax delafieldii N GNR
Tissue 97.2 Actinoallomurus fulvus N GPR
CSF 98.3 Actinomyces meyeri Y GPR
Pericardial fluid 94.4 Anaerococcus prevotii N GPC
Tissue 94.8 Capnocytophaga sputigena N GNR
CSF 93.8 Chryseobacterium taiwanense Y GNR Planobacterium taklimakanense, short reference sequence
CSF 98.3 Corynebacterium mucifaciens Y GPR
Tissue 98.6 Cupriavidus gilardii Y GNR
CSF 97.1 Erwinia chrysanthemi Y‡ GNR
Tissue 97.7 E. chrysanthemi Y‡ GNR
CSF 97.2 Globicatella sanguinis Y GPC
Tissue 96.2 Kocuria kristinae Y GPC
CSF 92.4 Desmospora activa Y GPR Kroppenstedtia eburnea
Synovial fluid 91.2 Laceyella sacchari N GVR
Tissue 96.0 Microbacterium thalassium Y‡ GPR
Tissue 95.9 M. thalassium Y‡ GVR
Tissue 96.9 Neisseria canis N GNC
Tissue 97.9 Neisseria zoodegmatis Y GNCB
Biopsy specimen 98.7 Nocardia beijingensis Y GPR
Brain 98.9 Nocardia nova Y GPR
Tissue 98.9 Nocardia transvalensis N GPR
CSF 96.1 Phenylobacterium immobile N GNR
Tissue 97.5 Prosthecomicrobium enhydrum N GVR
Tissue 95.2 Pseudomonas pohangensis Y‡ GNR
Tissue 95.2 Pseudomonas pohangensis Y‡ GNR
CSF 98.5 Rothia dentocariosa Y GPR Rothia aeria, short reference sequence
Tissue 98.0 Streptococcus mitis Y GPC
Valve 96.8 Streptococcus oralis Y GPC
CSF 98.0 Streptococcus sanguinis Y GPC
CSF 96.4 Streptomyces prasinopilosus N GPR
CSF 96.8 Terrabacter terrae N GPC
Tissue 97.8 Williamsia serinedens N GPR Williamsia deligens, short reference sequence

*GNR, gram-negative rods; GPR, gram-positive rods; CSF, cerebrospinal fluid; GPC, gram-positive cocci; GVR, gram-variable rods; GNC, gram-negative cocci; GNCB, gram-negative coccobacilli; Y, isolates belonging to tentative novel taxa represented multiple times in this study.
†Results of manual review of BLASTn analysis (23).
‡These pairs of isolates belong to the same 3 respective clusters.

Main Article

References
  1. Woo  PC, Lau  SK, Teng  JL, Tse  H, Yuen  KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect. 2008;14:908–34. DOIPubMedGoogle Scholar
  2. Relman  DA, Loutit  JS, Schmidt  TM, Falkow  S, Tompkins  LS. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med. 1990;323:1573–80. DOIPubMedGoogle Scholar
  3. Relman  DA, Schmidt  TM, MacDermott  RP, Falkow  S. Identification of the uncultured bacillus of Whipple’s disease. N Engl J Med. 1992;327:293–301. DOIPubMedGoogle Scholar
  4. Wilson  KH, Blitchington  R, Frothingham  R, Wilson  JA. Phylogeny of the Whipple’s-disease-associated bacterium. Lancet. 1991;338:474–5. DOIPubMedGoogle Scholar
  5. Tringe  SG, Hugenholtz  P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol. 2008;11:442–6. DOIPubMedGoogle Scholar
  6. National Institutes of Health. Human Microbiome Project. Program initiatives [cited 2011 Apr 9]. http://commonfund.nih.gov/hmp/initiatives.aspx#reference
  7. Pace  NR. A molecular view of microbial diversity and the biosphere. Science. 1997;276:734–40. DOIPubMedGoogle Scholar
  8. Pace  NR. Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev. 2009;73:565–76. DOIPubMedGoogle Scholar
  9. Yarza  P, Richter  M, Peplies  J, Euzeby  J, Amann  R, Schleifer  KH, The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol. 2008;31:241–50. DOIPubMedGoogle Scholar
  10. Clarridge  JE III. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17:840–62. DOIPubMedGoogle Scholar
  11. Petti  CA. Detection and identification of microorganisms by gene amplification and sequencing. Clin Infect Dis. 2007;44:1108–14. DOIPubMedGoogle Scholar
  12. Drancourt  M, Raoult  D. Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository. J Clin Microbiol. 2005;43:4311–5. DOIPubMedGoogle Scholar
  13. National Center for Biotechnology Information. BLAST nucleotide database [cited 2012 Jan 23]. ftp://ftp.ncbi.nlm.nih.gov/blast/db
  14. Petti  CA, Bosshard  PP, Brandt  ME, Clarridge  JE, Feldblyum  TV, Foxall  P, Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; approved guidelines. Wayne (PA): Clinical and Laboratory Standards Institute; 2008.
  15. Stackebrandt  E, Goebel  BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994;44:846–9. DOIGoogle Scholar
  16. Fraser  C, Alm  EJ, Polz  MF, Spratt  BG, Hanage  WP. The bacterial species challenge: making sense of genetic and ecological diversity. Science. 2009;323:741–6. DOIPubMedGoogle Scholar
  17. Keswani  J, Whitman  WB. Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol. 2001;51:667–78.PubMedGoogle Scholar
  18. Palys  T, Nakamura  LK, Cohan  FM. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol. 1997;47:1145–56. DOIPubMedGoogle Scholar
  19. Drancourt  M, Bollet  C, Carlioz  A, Martelin  R, Gayral  JP, Raoult  D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol. 2000;38:3623–30.PubMedGoogle Scholar
  20. Fox  GE, Wisotzkey  JD, Jurtshuk  P Jr. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol. 1992;42:166–70. DOIPubMedGoogle Scholar
  21. Bosshard  PP, Abels  S, Zbinden  R, Bottger  EC, Altwegg  M. Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation). J Clin Microbiol. 2003;41:4134–40. DOIPubMedGoogle Scholar
  22. Drancourt  M, Berger  P, Raoult  D. Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans. J Clin Microbiol. 2004;42:2197–202. DOIPubMedGoogle Scholar
  23. Stackebrandt  E, Ebers  J. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today. November 2006. p. 152–5.
  24. Simmon  KE, Croft  AC, Petti  CA. Application of SmartGene IDNS software to partial 16S rRNA gene sequences for a diverse group of bacteria in a clinical laboratory. J Clin Microbiol. 2006;44:4400–6. DOIPubMedGoogle Scholar
  25. Simmon  KE, Hall  L, Woods  CW, Marco  F, Miro  JM, Cabell  C, Phylogenetic analysis of viridans group streptococci causing endocarditis. J Clin Microbiol. 2008;46:3087–90. DOIPubMedGoogle Scholar
  26. Versalovic  J; American Society for Microbiology. Manual of clinical microbiology. 10th ed. Washington: ASM Press; 2011. p. 443–71.
  27. Cock  PJ, Antao  T, Chang  JT, Chapman  BA, Cox  CJ, Dalke  A, Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422–3. DOIPubMedGoogle Scholar
  28. DSMZ. Bacterial nomenclature up-to-date (approved lists, validation lists) [cited 2012 Jan 23]. http://www.dsmz.de/bacterial-diversity/bacterial-nomenclature-up-to-date.html
  29. Tamura  K, Dudley  J, Nei  M, Kumar  S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9. DOIPubMedGoogle Scholar
  30. Yarza  P, Ludwig  W, Euzeby  J, Amann  R, Schleifer  KH, Glockner  FO, Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol. 2010;33:291–9. DOIPubMedGoogle Scholar
  31. Euzeby  JP. List of prokaryotic names with standing in nomenclature. 2010 [cited 2012 Jan 23]. http://www.bacterio.cict.fr/
  32. von Jan  M, Riegger  N, Pötter  G, Schumann  P, Verbarg  S, Spröer  C, Kroppenstedtia eburnea gen. nov., sp. nov., a novel thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009. Int J Syst Evol Microbiol. 2011;61:2304–10. DOIPubMedGoogle Scholar
  33. Coenye  T, Vandamme  P. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol Lett. 2003;228:45–9. DOIPubMedGoogle Scholar
  34. Pei  AY, Oberdorf  WE, Nossa  CW, Agarwal  A, Chokshi  P, Gerz  EA, Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol. 2010;76:3886–97. DOIPubMedGoogle Scholar
  35. Keller  PM, Rampini  SK, Buchler  AC, Eich  G, Wanner  RM, Speck  RF, Recognition of potentially novel human disease-associated pathogens by implementation of systematic 16S rRNA gene sequencing in the diagnostic laboratory. J Clin Microbiol. 2010;48:3397–402. DOIPubMedGoogle Scholar
  36. Stackebrandt  E, Frederiksen  W, Garrity  GM, Grimont  PA, Kampfer  P, Maiden  MC, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol. 2002;52:1043–7. DOIPubMedGoogle Scholar
  37. Christensen  H, Bisgaard  M, Frederiksen  W, Mutters  R, Kuhnert  P, Olsen  JE. Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 revision). Int J Syst Evol Microbiol. 2001;51:2221–5. DOIPubMedGoogle Scholar

Main Article

1These authors contributed equally to this article.

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Page updated: February 16, 2012
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