Skip to main content
SpringerLink
Log in

Molecular approaches: advantages and artifacts in assessing bacterial diversity

  • Review
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

Bacteria account for a major proportion of Earth’s biological diversity. They play essential roles in quite diverse environments and there has been an increasing interest in bacterial biodiversity. Research using novel and efficient tools to identify and characterize bacterial communities has been the key for elucidating biological activities with potential for industrial application. The current approach used for defining bacterial species is based on phenotypic and genomic properties. Traditional and novel DNA-based molecular methods are improving our knowledge of bacterial diversity in nature. Advances in molecular biology have been important for studies of diversity, considerably improving our knowledge of morphological, physiological, and ecological features of bacterial taxa. DNA–DNA hybridization, which has been used for many years, is still considered the golden standard for bacteria species identification. PCR-based methods investigating 16S rRNA gene sequences, and other approaches, such as the metagenome, have been used to study the physiology and diversity of bacteria and to identify novel genes with potential pharmaceutical and other biotechnological applications. We examined the advantages and limitations of molecular methods currently used to analyze bacterial diversity; these are mainly based on the 16S rRNA gene. These methods have allowed us to examine microorganisms that cannot be cultivated by routine methods and have also been useful for phylogenetic studies. We also considered the importance of improvements in microbe culture techniques and how we can combine different methods to allow a more appropriate assessment of bacterial diversity and to determine their real potential for industrial applications.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629–2635

    PubMed  CAS  Google Scholar 

  2. Amann R, Fuchs BM, Behrens S (2001) The identification of microorganisms by fluorescence in situ hybridization. Curr Opin Biotechnol 12:231–236

    PubMed  CAS  Google Scholar 

  3. Arber W (2000) Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24:1–7

    PubMed  CAS  Google Scholar 

  4. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541–555

    PubMed  CAS  Google Scholar 

  5. Bernardet JF, Vancanneyt M, Matte-Taillieza O, Grisez L, Tailliez P, Bizet C, Nowakowski M, Kerouault B, Swings J (2005) Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals. Syst Appl Microbiol 28:640–660

    PubMed  CAS  Google Scholar 

  6. Bodrossy L, Holmes EM, Holmes AJ, Kovács KL, Murrell JC (1997) Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov. Arch Microbiol 168:493–503

    PubMed  CAS  Google Scholar 

  7. Brady SF, Clardy J (2004) Palmitoylputrescine, an antibiotic isolated from the heterologous expression. J Nat Prod 67:1283–1286

    PubMed  CAS  Google Scholar 

  8. Brümmer IHM, Felske A, Wagner-Döbler I (2003) Diversity and seasonal variability of β-Proteobacteria in biofilms of polluted rivers: analysis by temperature gradient gel electrophoresis and cloning. Appl Environ Microbiol 69:4463–4473

    PubMed  Google Scholar 

  9. Bull AT, Ward AC, Goodfellow M (2000) Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev 64:573–606

    PubMed  CAS  Google Scholar 

  10. Chan M, Maiden MCJ, Spratt BG (2001) Database-driven multilocus sequence typing (MLST) of bacterial pathogens. Bioinformatics 17:1077–1083

    PubMed  CAS  Google Scholar 

  11. Cho J, Tiedje JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67:3677–3682

    PubMed  CAS  Google Scholar 

  12. Christensen JJ, Kilian M, Fussing V, Andresen J, Blom J, Korner B (2005) Aerococcus urinae: polyphasic characterization of the species. APMIS 113:517–525

    PubMed  CAS  Google Scholar 

  13. Chun J, Hug A, Colwell RR (1999) Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl Environ Microbiol 65:2202–2208

    PubMed  CAS  Google Scholar 

  14. Cohan FM (2001) Bacterial species and speciation. Syst Biol 50:513–524

    PubMed  CAS  Google Scholar 

  15. Colwell RR (1970) Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104:410–433

    PubMed  CAS  Google Scholar 

  16. Cottrell MT, Moore JA, Kirchman DL (1999) Chitinases from uncultured marine microorganisms. Appl Environ Microbiol 65:2553–2557

    PubMed  CAS  Google Scholar 

  17. Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P (2005) Metagenomic gene discovery: past, present and future. Trends Biotechnol 23:321–329

    PubMed  CAS  Google Scholar 

  18. Crosa JH, Brenner DJ, Falkow S (1973) Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol 115:904–911

    PubMed  CAS  Google Scholar 

  19. Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380

    PubMed  Google Scholar 

  20. Dahllöf I (2002) Molecular community analysis of microbial diversity. Curr Opin Biotechnol 13:213–217

    PubMed  Google Scholar 

  21. Dar SA, Kuenen JG, Muyzer G (2005) Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities. Appl Environ Microbiol 71:2325–2330

    PubMed  CAS  Google Scholar 

  22. de las Rivas B, Marcobal A, Muñoz R (2006) Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiol 152:85–93

    Google Scholar 

  23. Demain AL (2006) From natural products discovery to commercialization: a success story. J Ind Microbiol Biotechnol 33:486–495

    PubMed  CAS  Google Scholar 

  24. Deutschbauer AM, Chivian D, Arkin AP (2006) Genomics for environmental microbiology. Curr Opin Biotechnol 17:1–7

    Google Scholar 

  25. Dolzani L, Tonin E, Lagatolla C, Monti-Bragadin C (1994) Typing of Staphylococcus aureus by amplification of the 16S-23S intergenic spacer sequences. FEMS Microbiol Lett 119:167–174

    PubMed  CAS  Google Scholar 

  26. Donachie SP, Hou S, Lee KS, Riley CW, Pikina A, Belishe C, Kempe S, Gregory TS, Bossuyt A, Boerema J, Liu J, Freitas TA, Malahoff A, Alam M (2004) The Hawaiian archipelago: a microbial diversity hotspot. Microbiol Ecol 48:509–520

    CAS  Google Scholar 

  27. Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669

    PubMed  CAS  Google Scholar 

  28. Eardly BD, Nour SM, van Berkum P, Selander RK (2005) Rhizobial 16S rRNA and dnaK genes: mosaicism and the uncertain phylogenetic placement of Rhizobium galegae. Appl Environ Microbiol 71:1328–1335

    PubMed  CAS  Google Scholar 

  29. Eilers H, Pernthaler J, Glöckner FO, Amann R (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66:3044–3051

    PubMed  CAS  Google Scholar 

  30. Enright MC, Spratt BG, Kalia A, Cross JH, Bessen D (2001) Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Infect Immun 69:2416–2427

    PubMed  CAS  Google Scholar 

  31. Entcheva P, Liebl W, Johann A, Hartsch T, Streit W (2001) Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol 67:89–99

    PubMed  CAS  Google Scholar 

  32. Euzéby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 47:590–592

    PubMed  Google Scholar 

  33. Feil EJ, Maiden MCJ, Achtman M, Spratt BG (1999) The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitides. Mol Biol Evol 16:1496–1502

    PubMed  CAS  Google Scholar 

  34. Fogel GB, Collins CR, Li J, Brunk CF (1999) Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microbiol Ecol 38:93–113

    CAS  Google Scholar 

  35. Forney LJ, Zhou X, Brown CJ (2004) Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7:210–220

    PubMed  CAS  Google Scholar 

  36. Fry J (2000) Bacterial diversity and ‘unculturables’. Microbiol Today 27:186–188

    Google Scholar 

  37. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739

    PubMed  CAS  Google Scholar 

  38. Gich FB, Amer E, Figueras JB, Abella CA, Balaguer MD, Poch M (2000) Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA). Int Microbiol 3:103–106

    PubMed  CAS  Google Scholar 

  39. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68:4301–4306

    PubMed  CAS  Google Scholar 

  40. Gillman LM, Gunton J, Turenne CY, Wolfe J, Kabani AM (2001) Identification of Mycobacterium species by multiple-fluorescence PCR–single-strand conformation polymorphism analysis of the 16S rRNA gene. J Clin Microbiol 39:3085–3091

    PubMed  CAS  Google Scholar 

  41. Giraffa G, Paris A, Valcavi L, Gatti M, Neviani E (2001) Genotypic and phenotypic heterogeneity of Streptococcus thermophilus strains isolated from dairy products. J Appl Microbiol 91:937–943

    PubMed  CAS  Google Scholar 

  42. Guerra B, Junker E, Schroeter A, Malorny B, Lehmann S, Helmuth R (2003) Phenotypic and genotypic characterization of antimicrobial resistance in German Escherichia coli isolates from cattle, swine and poultry. J Antimicrob Chemother 52:489–492

    PubMed  CAS  Google Scholar 

  43. Gupta RS (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367–402

    PubMed  CAS  Google Scholar 

  44. Hacene H, Rafa F, Chebhouni N, Boutaiba S, Bhatnagar T, Baratti JC, Ollivier B (2004) Biodiversity of prokaryoticmic microflora in El Golea Salt lake, Algerian Sahara. J Arid Environ 58:273–284

    Google Scholar 

  45. Hanage WP, Fraser F, Spratt BG (2005) Fuzzy species among recombinogenic bacteria. BMC Biol 3:1–7

    Google Scholar 

  46. Hanh MW (2004) Broad diversity of viable bacteria in “sterile” (0.2 mm) filtered water. Res Microbiol 155:688–691

    Google Scholar 

  47. Hassen A, Saidi N, Cherif M, Boudabous A (1998) Resistance of environmental bacteria to heavy metals. Bioresour Technol 64:7–15

    CAS  Google Scholar 

  48. Healy FG, Ray RM, Aldrich HC, Wilkie AC, Ingram LO, Shanmugam KT (1995) Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Appl Environ Microbiol 43:667–674

    CAS  Google Scholar 

  49. Hoffmann H, Roggenkamp A (2003) Population genetics of the nomenspecies enterobacter cloacae. Appl Environ Microbiol 69:5306–5318

    PubMed  CAS  Google Scholar 

  50. Hoffmann H, Stindl S, Stumpf A, Mehlen A, Monget D, Heesemann J, Schleifer KH, Roggenkamp A (2005) Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance. Syst Appl Microbiol 28:206–212

    PubMed  CAS  Google Scholar 

  51. Hongoh Y, Yuzawa H, Ohkuma M, Kudo T (2003) Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiol Lett 221:299–304

    PubMed  CAS  Google Scholar 

  52. Horner-Devine MC, Carney KM, Bohannan BJM (2004) An ecological perspective on bacterial biodiversity. Proc R Soc Lond 271:113–122

    Google Scholar 

  53. Horz H, Yimga MT, Liesack W (2001) Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl Environ Microbiol 67:4177–4185

    PubMed  CAS  Google Scholar 

  54. Hugenholtz P, Goebel B, Pace NR (1998a) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  CAS  Google Scholar 

  55. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998b) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376

    PubMed  CAS  Google Scholar 

  56. Iversen C, Waddington M, On SLW, Forsythe S (2004) Identification and phylogeny of Enterobacter sakazakii relative to Enterobacter and Citrobacter species. J Clin Microbiol 42:5368–5370

    PubMed  CAS  Google Scholar 

  57. Iwamoto T, Nasu M (2001) Current bioremediation practice and perspective. J Biosci Bioeng 92:1–8

    PubMed  CAS  Google Scholar 

  58. Janda JM, Abbott SL (2002) Bacterial identification for publication: when is enough enough? J Clin Microbiol 40:1887–1891

    PubMed  Google Scholar 

  59. Jaspers E, Nauhaus, Cypionka H, Overmann J (2001) Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. FEMS Microbiol Ecol 36:153–164

    CAS  Google Scholar 

  60. Jaspers E, Overmann J (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70:4831–4839

    PubMed  CAS  Google Scholar 

  61. Jensen MA, Webster JA, Straus N (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 59:945–952

    PubMed  CAS  Google Scholar 

  62. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129

    PubMed  ADS  CAS  Google Scholar 

  63. Keller M, Zengler K (2004) Tapping into microbial diversity. Nat Rev Microbiol 2:141–150

    PubMed  CAS  Google Scholar 

  64. Kemp PF, Aller JY (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47:161–177

    CAS  Google Scholar 

  65. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29:181–184

    PubMed  CAS  Google Scholar 

  66. Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl Environ Microbiol 69:1408–1416

    PubMed  CAS  Google Scholar 

  67. Lebuhn M, Bathe S, Achouak W, Hartmann A, Heulin T, Schloter M (2006) Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species. Syst Appl Microbiol 29:265–275

    PubMed  CAS  Google Scholar 

  68. Lagacé L, Pitre M, Jacques M, Roy D (2004) Identification of the bacterial community of maple sap by using amplified ribosomal DNA (rDNA) restriction analysis and rDNA sequencing. Appl Environ Microbiol 70:2052–2060

    PubMed  Google Scholar 

  69. Levin BR, Bergstrom CT (2000) Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. PNAS 97:6981–6985

    PubMed  ADS  CAS  Google Scholar 

  70. López-López A, Bartual SG, Stal L, Onyshchenko O, Rodríguez-Valera F (2005) Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodiiin the Mediterranean Sea. Environ Microbiol 7:649–659

    PubMed  Google Scholar 

  71. Lorenz P, Schleper C (2002) Metagenome—a challenging source of enzyme discovery. Mol Catal B Enzym 19–20:13–19

    Google Scholar 

  72. Lyautey E, Lacoste B, Ten-Hage L, Rols J, Garabetian F (2005) Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: methodological settings and fingerprints interpretation. Water Res 39:380–388

    PubMed  CAS  Google Scholar 

  73. Marshall S, Melito PL, Woodward DL, Johnson WM, Rodgers FG, Mulvey M (1999) Rapid identification of Campylobacter, Arcobacter, and Helicobacter isolates by PCR-Restriction Fragment Length Polymorphism analysis of the 16S rRNA gene. J Clin Microbiol 37:4158–4160

    PubMed  CAS  Google Scholar 

  74. Masson L, Maynard C, Brousseau R, Goh S, Hemmingsen SM, Hill JE, Paccagnella A, Oda R, Kimura N (2006) Identification of pathogenic Helicobacter species by chaperonin-60 differentiation on plastic DNA arrays. Genomics 87:104–112

    PubMed  CAS  Google Scholar 

  75. Matsuda M, Tazumi A, Kagawa S, Sekizuka T, Murayama O, Moore JE, Millar BC (2006) Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis. BMC Vet Res 2:1–4

    PubMed  CAS  Google Scholar 

  76. McCaig AE, Grayston SJ, Prosser JI, Glover A (2001) Impact of cultivation on characterisation of species composition of soil bacterial communities. FEMS Microbiol Ecol 35:37–48

    CAS  Google Scholar 

  77. McInerney JO, Wernecke M, Mullarkey M, Powell R (2002) Bacteria and Archaea: molecular techniques reveal astonishing novel diversity. Biodiversity 3:3–10

    Google Scholar 

  78. McMullan G, Christie JM, Rahman TJ, Banat IM, Ternan NG, Marchant R (2004) Habitat, applications and genomics of the aerobic, thermophilic genus Geobacillus. Biochem Soc Trans 32:214–217

    PubMed  CAS  Google Scholar 

  79. Mechichi T, Stackebrandt E, Gadon N, Fuchs G (2002) Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylaceticasp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckeliisp. nov. Arch Microbiol 178:26–35

    PubMed  CAS  Google Scholar 

  80. Mehlen A, Goeldner M, Ried S, Stindl S, Ludwig W, Schleifer K (2004) Development of a fast DNA-DNA hybridization method based on melting profiles in microplates. Syst Appl Microbiol 27:689–695

    PubMed  CAS  Google Scholar 

  81. Miteva VI, Scheridant PP, Brenchley JE (2004) Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Appl Environ Microbiol 70:202–213

    PubMed  CAS  Google Scholar 

  82. Morris CE, Bardin M, Berge O, Frey-Klett P, Fromin N, Girardin H, Guinebretière MH, Lebaron P, Thiéry JM, Troussellier M (2002) Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999. Microbiol Mol Biol Rev 66:592–616

    PubMed  Google Scholar 

  83. Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt D, Vancanneyt M, Swingers J (2005) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiol 151:2141–2150

    CAS  Google Scholar 

  84. Nee S (2003) Unveiling prokaryotic diversity. Trends Ecol Evol 18:62–63

    Google Scholar 

  85. O’Sullivan LA, Fuller KE, Thomas EM, Turley CM, Fry JC, Weightman AJ (2004) Distribution and culturability of the uncultivated ‘AGG58 cluster’ of the Bacteroidetes phylum in aquatic environments. FEMS Microbiol Ecol 47:359–370

    CAS  Google Scholar 

  86. Oremland RS, Capone DG, Stolz JF, Fuhrman J (2005) Whither or wither geomicrobiology in the era of ‘community metagenomics’. Nat Rev Microbiol 3:572–578

    PubMed  CAS  Google Scholar 

  87. Oren A (2004) Prokaryote diversity and taxonomy: current status and future challenges. Philol Trans R Soc Lond 359:623–638

    CAS  Google Scholar 

  88. Palumbo AV, Schryver JC, Fields MW, Bagwell CE, Zhou JZ, Yan T, Liu X, Brandt CC (2004) Coupling of functional gene diversity and geochemical data from environmental samples. Appl Environ Microbiol 70:6525–6534

    PubMed  CAS  Google Scholar 

  89. Palys T, Berger E, Mitrica I, Nakamura LK, Cohan FM (2000) Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species. Int J Syst Evol Microbiol 50:1021–1028

    PubMed  CAS  Google Scholar 

  90. Palys T, Nakamura LK, Cohan FM (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 47:1145–1156

    PubMed  CAS  Google Scholar 

  91. Papamanoli E, Kotzekidou P, Tzanetakis N, Litopoulou-Tzanetaki E (2002) Characterization of Micrococcaceae isolated from dry fermented sausage. Food Microbiol 19:441–449

    CAS  Google Scholar 

  92. Pearce DA, van der Gast CJ, Lawley B, Ellis-Evans JC (2003) Bacterioplankton community diversity in a maritime Antarctic lake, determined by culture-dependent and culture-independent techniques. FEMS Microbiol Ecol 45:59–70

    CAS  Google Scholar 

  93. Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J (2005) Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J Clin Microbiol 43:2291–2302

    PubMed  CAS  Google Scholar 

  94. Pretzer G, Snel J, Molenaar D, Wiersma A, Bron PA, Lambert J, de Vos VM, van der Meer R, Smits MA, Kleerebezem M (2005) Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum. J Bacteriol 187:6128–6136

    PubMed  CAS  Google Scholar 

  95. QI Y, Patra G, Liang X, Williams LE, Rose S, Redkar RJ, Delvecchio VG (2001) Utilization of the rpoB gene as a specific chromosomal marker for real-time PCR detection of Bacillus anthracis. Appl Environ Microbiol 67:3720–3727

    Google Scholar 

  96. Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552

    PubMed  CAS  Google Scholar 

  97. Rodríguez-Valera F (2002) Approaches to prokaryotic biodiversity: a population genetics perspective. Environ Microbiol 4:628–633

    PubMed  Google Scholar 

  98. Rodríguez-Valera F (2004) Environmental genomics, the big picture? FEMS Microbiol Lett 231:153–158

    PubMed  Google Scholar 

  99. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  PubMed  Google Scholar 

  100. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

    PubMed  CAS  Google Scholar 

  101. Santosa DA (2001) Rapid extraction and purification of environmental DNA for molecular cloning applications and molecular diversitym studies. Mol Biotechnol 17:59–64

    PubMed  CAS  Google Scholar 

  102. Schirmer A, Gadkari R, Reeves CD, Ibrahim F, DeLong EF, Hutchinson CR (2005) Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissolute. Appl Environ Microbiol 71:4840–4849

    PubMed  CAS  Google Scholar 

  103. Schleifer K (2004) Microbial diversity: facts, problems and prospects. System Appl Microbiol 27:3–9

    Google Scholar 

  104. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691

    PubMed  Google Scholar 

  105. Schmalenberger A, Schwieger F, Tebbe CC (2001) Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67:3557–3563

    PubMed  CAS  Google Scholar 

  106. Sievert SM, Kuever J, Muyzer G (2000) Identification of 16S ribosomal DNA-defined bacterial populations at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl Environ Microbiol 66:3102–3109

    PubMed  CAS  Google Scholar 

  107. Stabili L, Cavallo RA (2004) Biodiversity of culturable heterotrophic bacteria in the southern adriatic sea Italian coastal waters. Sci Mar 68:31–41

    Article  CAS  Google Scholar 

  108. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüpper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047

    PubMed  CAS  Google Scholar 

  109. Staley JT, Krieg NR (1989) Classification of prokaryotic organisms: an overwiew. In: Williams ST, Sharpe ME, Holtz JG (eds) Bergey’s manual of systematic bacteriology, vol4.. Williams and Wilkins, Baltimore, MD, pp 2299–2306

  110. Steele HL, Streit WR (2005) Metagenomics: advances in ecology and biotechnology. FEMS Microbiol Lett 247:105–111

    PubMed  CAS  Google Scholar 

  111. Streit WR, Schmitz RA (2004) Metagenomics—the key to the uncultured microbes. Curr Opin Microbiol 7:492–498

    PubMed  CAS  Google Scholar 

  112. Teusink B, Smid EJ (2006) Modelling strategies for the industrial exploitation of lactic acid bacteria. Nature 4:46–56

    CAS  Google Scholar 

  113. Thompson FL, Iida T, Swings J (2004) Biodiversity of Vibrios. Microbiol Mol Biol Res 68:403–431

    CAS  Google Scholar 

  114. Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:1064–1066

    PubMed  ADS  CAS  Google Scholar 

  115. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554–557

    PubMed  ADS  CAS  Google Scholar 

  116. van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindström K, Eardly BD (2003) Discordant phylogenies within the rrn loci of Rhizobia. J Bacteriol 185:2988–2998

    PubMed  Google Scholar 

  117. Vandamme P, Pot B, Gillis M, De vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

    PubMed  CAS  Google Scholar 

  118. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69:6235–6242

    PubMed  CAS  Google Scholar 

  119. Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900

    PubMed  CAS  Google Scholar 

  120. Zézé A, Mutch LA, Young JPW (2001) Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil. Environ Microbiol 3:363–70

    PubMed  Google Scholar 

  121. Ward DM (1998) A natural species concept for prokaryotes. Curr Opin Microbiol 1:271–277

    PubMed  CAS  Google Scholar 

  122. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Morre WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  123. Wertz JE, Goldstone C, Gordon DM, Riley MA (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16:1236–1248

    PubMed  CAS  Google Scholar 

  124. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95:6578–6583

    PubMed  ADS  CAS  Google Scholar 

  125. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    PubMed  CAS  Google Scholar 

  126. Wu X, Walker MJ, Hornitzky M, Chin J (2005) Development of a group-specific PCR combined with ARDRA for the identification of Bacillus species of environmental significance. J Microbiol Methods 64:107–119

    PubMed  Google Scholar 

Download references

Acknowledgments

We appreciate the financial support given by PELD and CNPq in the form of a scholarship to Daniela Santos Pontes.

Author information

Authors and Affiliations

  1. Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, CEP 31.270-901, MG, Brazil

    Daniela Santos Pontes, Cláudia Iracema Lima-Bittencourt, Edmar Chartone-Souza & Andréa Maria Amaral Nascimento

Authors
  1. Daniela Santos Pontes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cláudia Iracema Lima-Bittencourt
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Edmar Chartone-Souza
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andréa Maria Amaral Nascimento
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andréa Maria Amaral Nascimento.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pontes, D.S., Lima-Bittencourt, C.I., Chartone-Souza, E. et al. Molecular approaches: advantages and artifacts in assessing bacterial diversity. J Ind Microbiol Biotechnol 34, 463–473 (2007). https://doi.org/10.1007/s10295-007-0219-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10295-007-0219-3

Keywords

Search

Navigation