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Applied Microbiology and Biotechnology

, Volume 98, Issue 8, pp 3425–3436 | Cite as

DNA barcoding to map the microbial communities: current advances and future directions

  • Chiranjib Chakraborty
  • C. George Priya Doss
  • Bidhan C. Patra
  • Sanghamitra Bandyopadhyay
Mini-Review

Abstract

During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.

Keywords

Microbial community DNA barcode Next generation sequencing Barcode marker gene Biodiversity 

Notes

Acknowledgments

The authors take this opportunity to thank the management of Galgotias University and VIT University for providing the facilities and encouragement to carry out this work. The authors have declared that no conflict of interest exists.

References

  1. Ali AB, De Baere R, Van der Auwera G, De Wachter R, Van de Peer Y (2001) Phylogenetic relationships among algae based on complete large-subunit rRNA sequences. Int J Syst Evol Microbiol 51:737–749PubMedGoogle Scholar
  2. Armougom F, Raoult D (2008) Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans. BMC Genomics 9:576PubMedCentralPubMedGoogle Scholar
  3. Arnot DE, Roper C, Bayoumi RA (1993) Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circumsporozoite gene can genetically barcode isolates. Mol Biochem Parasitol 61:15–24PubMedGoogle Scholar
  4. Baayen RP, O'Donnell K, Breeuwsma S, Geiser DM, Waalwijk C (2001) Molecular relationships of fungi within the Fusarium redolensF. hostae clade. Phytopathology 91:1037–1044PubMedGoogle Scholar
  5. Begerow D, Nilsson H, Unterseher M, Maier W (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 87:99–108PubMedGoogle Scholar
  6. Besansky NJ, Severson DW, Ferdig MT (2003) DNA barcoding of parasites and invertebrate diseases vectors: what you don’t know can hurt you. Trends Parasitol 19:545–546PubMedGoogle Scholar
  7. Bialek R, González GM, Begerow D, Zelck UE (2005) Coccidioidomycosis and blastomycosis: advances in molecular diagnosis. FEMS Immunol Med Microbiol 45:355–360PubMedGoogle Scholar
  8. Blaxter M (2003) Molecular systematics: counting angels with DNA. Nature 421:122–124PubMedGoogle Scholar
  9. Brent R (2000) Genomic biology. Cell 100:169–183PubMedGoogle Scholar
  10. Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M (2011) Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One 6:e16931PubMedCentralPubMedGoogle Scholar
  11. Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA (2001) Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104:901–912PubMedGoogle Scholar
  12. Cao C, Dhumpa R, Bang DD, Ghavifekr Z, Høgberg J, Wolff A (2009) Detection of avian influenza virus by fluorescent DNA barcode-based immunoassay with sensitivity comparable to PCR. Analyst 135:337–342PubMedGoogle Scholar
  13. Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF, Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288PubMedCentralPubMedGoogle Scholar
  14. Casiraghi M, Labra M, Ferri E, Galimberti A, De Mattia F (2010) DNA barcoding: a six-question tour to improve users' awareness about the method. Brief Bioinform 11:440–453PubMedGoogle Scholar
  15. Chaban B, Hill JE (2012) A ‘universal’ type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities. ISME J 6:430–439PubMedCentralPubMedGoogle Scholar
  16. Chakraborty C, Agrawal A (2013) Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties. Cell Biochem Biophys 67:645–656PubMedGoogle Scholar
  17. Chakraborty C, Doss GPC (2013) Sirtuins family—recent development as a drug target for aging, metabolism, and age related diseases. Curr Drug Targets 14:666–675PubMedGoogle Scholar
  18. Chakraborty C, Agoramoorthy G, Hsu MJ (2011) Exploring the evolutionary relationship of insulin receptor substrate family using computational biology. PLoS One 6:e16580PubMedCentralPubMedGoogle Scholar
  19. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madrinan S, Petersen G, Seberg O, Jørgsensen T, Cameron KM, Carine M, Pedersen P, Hedderson TAJ, Conrad F, Salazar GA, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L, Wilkinson M (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56:295–299Google Scholar
  20. Cho Y, Qiu YL, Kuhlmann P, Palmer JD (1998) Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci U S A 95:14244–14249PubMedCentralPubMedGoogle Scholar
  21. Church GM, Gao Y, Kosuri S (2012) Next-generation digital information storage in DNA. Science 337:1628PubMedGoogle Scholar
  22. Clarridge JE (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17:840–862PubMedCentralPubMedGoogle Scholar
  23. Conklin KY, Kurihara A, Sherwood AR (2009) A molecular method for identification of the morphologically plastic invasive algal genera Eucheuma and Kappaphycus (Rhodophyta, Gigartinales) in Hawaii. J Appl Phycol 21:691–699Google Scholar
  24. Consortium for the Barcode of Life (2009) http://www.barcoding.si.edu Accessed 21 December 2009
  25. Curtin C (2009) Humans as host. Genome Tech 38–43Google Scholar
  26. DasGupta B, Konwar KM, Mandoiu II, Shvartsman (2005) DNA-BAR: ditinguisher selection for DNA barcoding. Bioinformatics 21:3424–3426PubMedGoogle Scholar
  27. Doss GPC, Chakraborty C, Rajith B, Nagasundaram N (2013) Modeling and molecular dynamics approach to characterize the functional nsSNPs in hTERT by means of local DNA sequence context and regularity. J Mol Model 19:3517–3527PubMedGoogle Scholar
  28. Druzhinina IS, Kopchinskiy AG, Komoñ M, Bissett J, Szakacs G, Kubicek CP (2005) An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet Biol 42:813–828PubMedGoogle Scholar
  29. Eberhardt U (2010) A constructive step towards selecting a DNA barcode for fungi. New Phytol 187:265–268PubMedGoogle Scholar
  30. Editorial (2011) Microbiology by numbers. Nat Rev Microbiol 9(9):628Google Scholar
  31. Ertz D, Miadlikowska J, Lutzoni F, Dessein S, Raspé O, Vigneron N, Hofstetter V, Diederich P (2009) Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focusing on the genus Opegrapha. Mycol Res 113:141–152PubMedGoogle Scholar
  32. Famà P, Wysor B, Kooistra WH, Zuccarello GC (2002) Molecular phylogeny of the genus Caulerpa (Caulerpales, Chlorophyta) inferred from chloroplast tufA gene1. J Phycol 38:1040–1050Google Scholar
  33. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SCH (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS One 3:e2802PubMedCentralPubMedGoogle Scholar
  34. Fell JW, Boekhout T, Fonseca A, Scorzetti G, Statzell-Tallman A (2000) Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int J Syst Evol Microbiol 50:1351–1371PubMedGoogle Scholar
  35. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323:741–742PubMedGoogle Scholar
  36. Fredericq S, Freshwater DW, Hommersand MH (1999) Observations on the phylogenetic systematics and biogeography of the Solieriaceae (Gigartinales, Rhodophyta) inferred from rbcL sequences and morphological evidence. Hydrobiol 398(399):25–38Google Scholar
  37. Friedrich MJ (2008) Microbiome project seeks to understand human body’s microscopic residents. JAMA 300:777–778PubMedGoogle Scholar
  38. Geiser DM, Klich MA, Frisvad JC, Peterson SW, Varga J, Samson RA (2007) The current status of species recognition and identification in Aspergillus. Stud Mycol 59:1–10PubMedCentralPubMedGoogle Scholar
  39. George PDC, Nagasundaram N, Chakraborty C, Chen L, Zhu H (2013) Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach. Hum Genomics 7:10. doi: 10.1186/1479-7364-7-10 Google Scholar
  40. Godfray HJC (2002) Challenges for taxonomy: the discipline will have to reinvent itself if it is to survive and flourish. Nature 417:17–19PubMedGoogle Scholar
  41. Gou H, Guan G, Liu A, Ma M, Xu Z, Liu Z, Ren Q, Li Y, Yang J, Chen Z, Yin H, Luo J (2012) A DNA barcode for Piroplasmea. Acta Trop 124:92–97PubMedGoogle Scholar
  42. Großkopf R, Janssen PH, Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64:960–969PubMedCentralPubMedGoogle Scholar
  43. Hajibabaei M, Singer GA, Hebert PD, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23:167–172PubMedGoogle Scholar
  44. Hawksworth DL (2006) Pandora's mycological box: molecular sequences vs. morphology in understanding fungal relationships and biodiversity. Rev Iberoam Micol 23:127–133PubMedGoogle Scholar
  45. Hawksworth DL, Kalin-Arroyo MT (1995) Magnitude and distribution of biodiversity. In: Heywood VH (ed) Global biodiversity assessment. Cambridge University Press. Cambridge, p. 107–191Google Scholar
  46. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321Google Scholar
  47. Hebert PDN, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B 270:S96–S99Google Scholar
  48. Hiorns WD, Methe BA, Nierzwicki-Bauer SA, Zehr JP (1997) Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl Environ Microbiol 63:2957–2960PubMedCentralPubMedGoogle Scholar
  49. Hoef-Emden K (2012) Pitfalls of establishing DNA barcoding systems in Protists: the Cryptophyceae as a test case. PLoS One 7:e43652PubMedCentralPubMedGoogle Scholar
  50. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS One 6:e19254PubMedCentralPubMedGoogle Scholar
  51. Huang CH, Chang MT, Huang L (2012) Species identification of Wickerhamomyces anomalus and related taxa using β-tubulin (β-tub) DNA barcode marker. Yeast 29:531–535PubMedGoogle Scholar
  52. Hughes KW, Petersen RH, Lickey EB (2009) Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species' delimitation across Basidiomycete fungi. New Phytol 182:795–798PubMedGoogle Scholar
  53. Hughey JR, Silva PC, Hommersand MH (2001) Solving taxonomic and nomenclatural problems in Pacific Gigartinaceae (Rhodophyta) using DNA from type material. J Phycol 37:1091–1109Google Scholar
  54. Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P (2011) ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res 39(Database issue):D576–582PubMedCentralPubMedGoogle Scholar
  55. Janda JM, Abbott SL (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 45:2761–2764PubMedCentralPubMedGoogle Scholar
  56. Jarman SN, Elliott NG (2000) DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, ‘living fossils’ from the Triassic. J Evol Biol 13:624–633Google Scholar
  57. Jones YL, Peters SM, Weland C, Ivanova NV, Yancy HF (2013) Potential use of DNA barcodes in regulatory science: identification of the U.S. Food and Drug Administration's "Dirty 22," contributors to the spread of foodborne pathogens. J Food Prot 76:144–149PubMedGoogle Scholar
  58. Karnati SK, Yu Z, Sylvester JT, Dehority BA, Morrison M, Firkins JL (2003) Technical note: specific PCR amplification of protozoal 18S rDNA sequences from DNA extracted from ruminal samples of cows. J Anim Sci 81:812–815PubMedGoogle Scholar
  59. Kemler M, Göker M, Oberwinkler F, Begerow D (2006) Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes). BMC Evol Biol 6:35PubMedCentralPubMedGoogle Scholar
  60. Kemler M, Lutz M, Göker M, Oberwinkler F, Begerow D (2009) Hidden diversity in the non-caryophyllaceous plant-parasitic members of Microbotryum (Pucciniomycotina: Microbotryales). Syst Biodivers 7:297–306Google Scholar
  61. Kher CP, Doerder FP, Cooper J, Ikonomi P, Achilles-Day U, Küpper FC, Lynn DH (2011) Barcoding Tetrahymena: discriminating species and identifying unknowns using the cytochrome c oxidase subunit I (cox-1) barcode. Protist 162:2–13PubMedGoogle Scholar
  62. Kipling WW, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20:47–55Google Scholar
  63. Knowlton N (1993) Sibling species in the sea. Annu Rev Ecol Syst 24:189–216Google Scholar
  64. Kosakyan A, Heger TJ, Leander BS, Todorov M, Mitchell EA, Lara E (2012) COI barcoding of Nebelid testate Amoebae (Amoebozoa: Arcellinida): extensive cryptic diversity and redefinition of the Hyalospheniidae Schultze. Protist 163:415–434PubMedGoogle Scholar
  65. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA apacer region. PLoS One 2:e508PubMedCentralPubMedGoogle Scholar
  66. Krüger M, Krüger C, Walker C, Stockinger H, Schüssler A (2012) Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level. New Phytol 193:970–984PubMedGoogle Scholar
  67. Kurtzman CP, Robnett CJ (1998) Identification and phylogeny of Ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van Leeuwenhoek 73:331–371PubMedGoogle Scholar
  68. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A 105:2923–2928PubMedCentralPubMedGoogle Scholar
  69. LaJeunesse TC (2001) Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the ITS region: in search of a “species” level marker. J Phycol 37:866–880Google Scholar
  70. Lawton JH, Bignell DE, Bolton B, Bloemers GF, Eggleton P, Hammond PM, Hodda M, Holt RD, Larsen TB, Mawdsley NA, Stork NE, Srivastava DS, Watt AD (1988) Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest. Nature 391:72–76Google Scholar
  71. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444:1022–1023PubMedGoogle Scholar
  72. Li Y, Jiao L, Yao YJ (2013) Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis. Mol Phylogenet Evol 68:373–379PubMedGoogle Scholar
  73. Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE (2012) The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One 7:e49755PubMedCentralPubMedGoogle Scholar
  74. Locke SA, Daniel McLaughlin J, Marcogliese DJ (2010) DNA barcodes show cryptic diversity and a potential physiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea) parasitizing freshwater fishes in the St. Lawrence River, Canada. Mol Ecol 19:2813–2827PubMedGoogle Scholar
  75. Lorenz JG, Jackson WE, Beck JC, Hanner R (2005) The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philos Trans R Soc Lond B Biol Sci 360:1869–1877PubMedCentralPubMedGoogle Scholar
  76. Losos JB, Arnold SJ, Bejerano G, Brodie ED 3rd, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL (2013) Evolutionary biology for the 21st century. PLoS Biol 11:e1001466PubMedCentralPubMedGoogle Scholar
  77. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 104:11436–11440PubMedCentralPubMedGoogle Scholar
  78. Maan S, Maan NS, Nomikou K, Veronesi E, Bachanek-Bankowska K, Belaganahalli MN, Attoui H, Mertens PP (2011) Complete genome characterisation of a novel 26th bluetongue virus serotype from Kuwait. PLoS One 6:e26147PubMedCentralPubMedGoogle Scholar
  79. May RM (1988) How many species are there on earth? Science 241(4872):1441–1449PubMedGoogle Scholar
  80. Merker JD, O'Grady N, Gojenola L, Dao M, Lenta R, Yeakley JM, Schrijver I (2013) Feasibility of using microbeads with holographic barcodes to track DNA specimens in the clinical molecular laboratory. Peer J 1:e91PubMedCentralPubMedGoogle Scholar
  81. Metting FB (1996) Biodiversity and application of microalgae. J Ind Microbiol 17:477–489Google Scholar
  82. Meyer MT, Genkov T, Skepper JN, Jouhet J, Mitchell MC, Spreitzer RJ, Griffiths H (2012) Rubisco small-subunit α-helices control pyrenoid formation in Chlamydomonas. Proc Natl Acad Sci U S A 109:19474–19479PubMedCentralPubMedGoogle Scholar
  83. Michel H, Behr J, Harrenga A, Kannt A (1998) Cytochrome c oxidase: structure and spectroscopy. Annu Rev Biophys Biomol Struct 27:329–356PubMedGoogle Scholar
  84. Nassonova E, Smirnov A, Fahrni J, Pawlowski J (2010) Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae. Protist 161:102–115PubMedGoogle Scholar
  85. O'Donnell K, Sutton DA, Fothergill A, McCarthy D, Rinaldi MG, Brandt ME, Zhang N, Geiser DM (2008) Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex. J Clin Microbiol K46:2477–2490Google Scholar
  86. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740PubMedGoogle Scholar
  87. Packer L, Gibbs J, Sheffield C, Hanner R (2009) DNA barcoding and the mediocrity of morphology. Mol Ecol Resour 9:42–50PubMedGoogle Scholar
  88. Patel JB (2001) 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol Diagn 6:313–32PubMedGoogle Scholar
  89. Paulus B, Nilsson RH, Hallenberg N (2007) Phylogenetic studies in Hypochnicium (Basidiomycota), with special emphasis on species from New Zealand. N Z J Bot 45:139–150Google Scholar
  90. Pedersen ML (2010) DNA barcode profiling: a new platform for the investigation of genome integrity. Genome Biol 11:P3Google Scholar
  91. Pino-Bodas R, Martín MP, Burgaz AR, Lumbsch HT (2013) Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy. Mol Ecol Resour 13:1058–1068PubMedGoogle Scholar
  92. Poll C, Brune T, Begerow D, Kandeler E (2009) Small-scale diversity and succession of fungi in the detritusphere of rye residues. Microb Ecol 59:130–140PubMedGoogle Scholar
  93. Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609PubMedGoogle Scholar
  94. Quaedvlieg W, Groenewald JZ, de Jesús Yáñez-Morales M, Crous PW (2012) DNA barcoding of Mycosphaerella species of quarantine importance to Europe. Persoonia 29:101–115PubMedCentralPubMedGoogle Scholar
  95. Ranasinghe PD, Satoh H, Oshiki M, Oshima K, Suda W, Hattori M, Mino T (2012) Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA gene. Water Sci Technol 66:2155–2161PubMedGoogle Scholar
  96. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394PubMedGoogle Scholar
  97. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131PubMedCentralPubMedGoogle Scholar
  98. Rickerts V, Just-Nubling G, Konrad F, Kern J, Lambrecht E, Bohme A, Jacobi V, Bialek R (2006) Diagnosis of invasive aspergillosis and mucormycosis in immunocompromised patients by seminested PCR assay of tissue samples. Eur J Clin Microbiol Infect Dis 25:8–13PubMedGoogle Scholar
  99. Robba L, Russell SJ, Barker GL, Brodie J (2006) Assessing the use of the mitochondrial COX1 marker for use in DNA barcoding of red algae (Rhodophyta). Am J Bot 93:1101–1108PubMedGoogle Scholar
  100. Ross PJ, Donaldson SL, Saunders GW (2003) A molecular investigation of Mazzaella (Gigartinales Rhodophyta) morphologically intermediate between Mazzaella linearis and M. splendens. Bot Mar 46:202–213Google Scholar
  101. Rubinoff D (2006) Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 20:1026–1033PubMedGoogle Scholar
  102. Rubinoff D, Cameron S, Will K (2006) A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. J Hered 97:581–594PubMedGoogle Scholar
  103. Santamaria M, Vicario S, Pappadà G, Scioscia G, Scazzocchio C, Saccone C (2009) Towards barcode markers in fungi: an intron map of Ascomycota mitochondria. BMC Bioinforma 10(Suppl 6):S15Google Scholar
  104. Saunders GW (2005) Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc Lond B Biol Sci 360:1879–1888PubMedCentralPubMedGoogle Scholar
  105. Saunders GW, McDevit DC (2012) Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms. Methods Mol Biol 858:207–222PubMedGoogle Scholar
  106. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691PubMedCentralPubMedGoogle Scholar
  107. Schmidt TM, Relman DA (1994) Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods Enzymol 235:205–222PubMedGoogle Scholar
  108. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 109:6241–6246PubMedCentralPubMedGoogle Scholar
  109. Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A (2002) Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res 2:495–517PubMedGoogle Scholar
  110. Seberg O, Petersen G (2009) How many loci does it take to DNA barcode a crocus? PLoS One 4:e4598PubMedCentralPubMedGoogle Scholar
  111. Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (2013) Computational metaomics for microbial community studies. Mol Syst Biol 14:666Google Scholar
  112. Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9:83–89PubMedGoogle Scholar
  113. Seifert KA, Samson RA, Dewaard JR, Houbraken J, Levesque CA, Moncalvo JM, Louis-Seize G, Hebert PDN (2007) Prospects for fungus identification using COI DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci U S A 104:3901–3906PubMedCentralPubMedGoogle Scholar
  114. Sherwood AR, Sauvage T, Kurihara A, Conklin KY, Presting GG (2010) A comparative analysis of COI, LSU and UPA marker data for the Hawaiian florideophyte Rhodophyta: implications for DNA barcoding of red algae. Cryptogam Algol 31:451–465Google Scholar
  115. Smirnov AV (2002) Re-description of Vannella mira (Gymnamoebia, Vannellidae)—an often mentioned but poorly known amoeba species. Protistology 2:178–185Google Scholar
  116. Smirnov AV, Goodkov AV (1999) An illustrated list of the basic morphotypes of Gymnamoebia (Rhizopoda, Lobosea). Protistology 1:20–29Google Scholar
  117. Smith MA, Bertrand C, Crosby K, Eveleigh ES, Fernandez-Triana J, Fisher BL, Gibbs J, Hajibabaei M, Hallwachs W, Hind K, Hrcek J, Huang DW, Janda M, Janzen DH, Li Y, Miller SE, Packer L, Quicke D, Ratnasingham S, Rodriguez J, Rougerie R, Shaw MR, Sheffield C, Stahlhut JK, Steinke D, Whitfield J, Wood M, Zhou X (2012) Wolbachia and DNA barcoding insects: patterns, potential, and problems. PLoS One 7:e36514PubMedCentralPubMedGoogle Scholar
  118. Snedden R (2007) The diversity of life: from single cells to multicellular organisms. Heinemann Library. comGoogle Scholar
  119. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155Google Scholar
  120. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X, Rosselló-Mora R, Swings J, Trüper 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 52:1043–1047PubMedGoogle Scholar
  121. Stein LD (2008) Bioinformatics: alive and kicking. Genome Biol 9:114PubMedCentralPubMedGoogle Scholar
  122. Stephen JR, McCaig AE, Smith Z, Prosser JI, Embley TM (1996) Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl Environ Microbiol 62:4147–4154PubMedCentralPubMedGoogle Scholar
  123. Stockinger H, Krüger M, Schüßler A (2010) DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 187:461–474PubMedGoogle Scholar
  124. Stone M (2009) NIH builds substantial human microbiome project. Microbe 4:451–456Google Scholar
  125. Suttle CA (2007) Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5:801–812PubMedGoogle Scholar
  126. Tai V, Lindstrom SC, Saunders GW (2001) Phylogeny of the Dumontiaceae (Gigartinales Rhodophyta) and associated families based on SSU rDNA and internal transcribed spacer sequence data. J Phycol 37:184–196Google Scholar
  127. Tan J, Lim PE, Phang SM, Hong DD, Sunarpi H, Hurtado AQ (2012) Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta). PLoS One 7:e52905PubMedCentralPubMedGoogle Scholar
  128. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003) A plea for DNA taxonomy. Trends Ecol Evol 18:70–74Google Scholar
  129. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804–810PubMedCentralPubMedGoogle Scholar
  130. Valentini A, Pompanon F, Taberlet P (2008) DNA barcoding for ecologists. Trends Ecol Evol 24:110–117PubMedGoogle Scholar
  131. Wei C, Wang G, Chen X, Huang H, Liu B, Xu Y, Li F (2011) Identification and typing of human enterovirus: a genomic barcode approach. PLoS One 6:e26296PubMedCentralPubMedGoogle Scholar
  132. Wilson EO (1999) The diversity of life. WW Norton and Company.Google Scholar
  133. Witt JD, Threloff DK, Hebert PD (2006) DNA barcoding reveals extraordinary cryptic diversity in an Amphipod genus: implications for desert spring conservation. Mol Ecol 15:3073–3082PubMedGoogle Scholar
  134. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271PubMedCentralPubMedGoogle Scholar
  135. Woese CR (1996) Whither microbiology? Phylogenetic trees. Curr Biol 6:1060–1063PubMedGoogle Scholar
  136. Wong EHK, Hanner RH (2008) DNA barcoding detects market substitution in North American seafood. Food Res Int 41:828–837Google Scholar
  137. Woo PC, Lau SK, Teng JL, Tse H, Yuen KY (2008) Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 14:908–934PubMedGoogle Scholar
  138. Xiang L, Song J, Xin T, Zhu Y, Shi L, Xu X, Pang X, Yao H, Li W, Chen S (2013) DNA barcoding the commercial Chinese caterpillar fungus. FEMS Microbiol Lett. doi: 10.1111/1574-6968.12233 Google Scholar
  139. Yin HQ, Jia MX, Shi LJ, Yang S, Zhang LY, Zhang QM, Wang SQ, Li G, Zhang JG (2011) Nanoparticle-based bio-barcode assay for the detection of bluetongue virus. J Virol Methods 178:225–228PubMedGoogle Scholar
  140. Yule GU (1924) A mathematical theory of evolution based on the conclusions of Dr. J. C. Willis, FRS. Phil Trans R Soc B 213:21–87Google Scholar
  141. Zhao S, He P (2011) Molecular identification based on ITS sequences for Kappaphycus and Eucheuma cultivated in China. Chinese J Oceanol Limnol 29:1287–1296Google Scholar
  142. Zuccarello GC, Critchley AT, Smith J, Sieber V, Lhonneur GB, West JA (2006) Systematics and genetic variation in commercial Kappaphycus and Eucheuma (Solieriaceae, Rhodophyta). J Appl Phycol 18:643–651Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Chiranjib Chakraborty
    • 1
  • C. George Priya Doss
    • 2
  • Bidhan C. Patra
    • 3
  • Sanghamitra Bandyopadhyay
    • 4
  1. 1.Department of Bioinformatics, School of Computer and Information SciencesGalgotias UniversityGreater NoidaIndia
  2. 2.Medical Biotechnology Division, School of Biosciences and TechnologyVIT UniversityVelloreIndia
  3. 3.Department of ZoologyVidyasagar UniversityMidnaporeIndia
  4. 4.Machine Intelligence UnitIndian Statistical InstituteKolkataIndia

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