Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species. 1. Introduction Nowadays DNA barcoding has become a justifiable tool for the assessment of global biodiversity patterns and it can allow diagnosis of known species to nontaxonomists [1]. DNA barcoding is a fast, accurate, and standardized method for species level identification, by using short DNA sequences. In 2003, Hebert from the University of Guelph, Ontario, Canada, proposed a new technique called DNA barcoding. Hebert and his associates published a paper entitled “Biological identifications through DNA barcodes”. They proposed a new system of species identification, that is, the discovery of species by using a short segment of DNA from a standardized region of the genome. That DNA sequence can be used to identify different species. DNA barcoding is the standardized research that facilitates biodiversity studies like species identification and discovery. This technique helps researchers to understand genetic and evolutionary relationships by assembling molecular, morphological, and distributional data [2]. Species-level identification by DNA barcoding is usually adapted by the recovery of a short DNA sequence from a standard part of the genome [3]. The sequence of barcode from each unknown specimen was then compared with a library of reference barcode sequences obtained from individuals of recognized identity [4]. DNA barcoding is an obligatory tool for species detection and specimen identification [5]. Using standardized identification method is very advantageous for mapping of all the species on Earth, especially when DNA sequencing technology is inexpensively obtainable. The term “DNA barcode” suggests that the standardized DNA sequences can identify taxa in the same way as the 11-digit Universal Product Code identifies retail products in market [6]. Lambert et al. (2005) scrutinized the opportunity of using DNA barcoding to measure the past diversity of the Earth’s biota [7]. The barcode of life data
References
[1]
M. E. Siddall, F. M. Fontanella, S. C. Watson, S. Kvist, and C. Erséus, “Barcoding bamboozled by bacteria: convergence to metazoan mitochondrial primer targets by marine microbes,” Systematic Biology, vol. 58, no. 4, pp. 445–451, 2009.
[2]
V. Savolainen, R. S. Cowan, A. P. Vogler, G. K. Roderick, and R. Lane, “Towards writing the encyclopaedia of life: an introduction to DNA barcoding,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 360, no. 1462, pp. 1805–1811, 2005.
[3]
P. D. N. Hebert, A. Cywinska, S. L. Ball, and J. R. DeWaard, “Biological identifications through DNA barcodes,” Proceedings of the Royal Society B Biological Sciences, vol. 270, no. 1512, pp. 313–321, 2003.
[4]
M. Hajibabaei, G. A. C. Singer, P. D. N. Hebert, and D. A. Hickey, “DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics,” Trends in Genetics, vol. 23, no. 4, pp. 167–172, 2007.
[5]
J. Bergsten, D. T. Bilton, T. Fujisawa et al., “The effect of geographical scale of sampling on DNA barcoding,” Systematic Biology, vol. 61, no. 5, pp. 851–869, 2012.
[6]
J. Neigel, A. Domingo, and J. Stake, “DNA barcoding as a tool for coral reef conservation,” Coral Reefs, vol. 26, no. 3, pp. 487–499, 2007.
[7]
D. M. Lambert, A. Baker, L. Huynen, O. Haddrath, P. D. N. Hebert, and C. D. Millar, “Is a large-scale DNA-based inventory of ancient life possible?” Journal of Heredity, vol. 96, no. 3, pp. 279–284, 2005.
[8]
S. Ratnasingham and P. D. N. Hebert, “BOLD: the barcode of life data system: (http://www.barcodinglife.org),” Molecular Ecology Notes, vol. 7, no. 3, pp. 355–364, 2007.
[9]
S. L. Ball and K. F. Armstrong, “DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae),” Canadian Journal of Forest Research, vol. 36, no. 2, pp. 337–350, 2006.
[10]
C. P. Amanda and M. Luciane, “DNA barcoding and traditional taxonomy unified through integrative taxonomy: a view that challenges the debate questioning both methodologies,” Biota Neotropica, vol. 10, no. 2, pp. 339–346, 2010.
[11]
P. Bonants, E. Groenewald, J. Y. Rasplus et al., “QBOL: a new EU project focusing on DNA barcoding of quarantine organisms,” EPPO Bulletin, vol. 40, no. 1, pp. 30–33, 2010.
[12]
E. A. Hugo, S. L. Chown, and M. A. McGeoch, “The microarthropods of sub-Antarctic Prince Edward Island: a quantitative assessment,” Polar Biology, vol. 30, no. 1, pp. 109–119, 2006.
[13]
A. Juen and M. Traugott, “Amplification facilitators and multiplex PCR: tools to overcome PCR-inhibition in DNA-gut-content analysis of soil-living invertebrates,” Soil Biology & Biochemistry, vol. 38, no. 7, pp. 1872–1879, 2006.
[14]
A. Juen and M. Traugott, “Revealing species-specific trophic links in soil food webs: Molecular identification of scarab predators,” Molecular Ecology, vol. 16, no. 7, pp. 1545–1557, 2007.
[15]
S. E. Miller, “Proposed standards for BARCODE records in INSDC (BRIs),” in Request document for continuation of support by the Alfred P. Sloan Foundation submitted by the Smithsonian Institution on behalf of Consortium for the barcode of Life: 22 January 2006 Robert H, pp. 36–38, 2005.
[16]
D. Rubinoff, “Utility of mitochondrial DNA barcodes in species conservation,” Conservation Biology, vol. 20, no. 4, pp. 1026–1033, 2006.
[17]
D. Rubinoff, S. Cameron, and K. Will, “A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification,” Journal of Heredity, vol. 97, no. 6, pp. 581–594, 2006.
[18]
K. W. Will, B. D. Mishler, and Q. D. Wheeler, “The perils of DNA barcoding and the need for integrative taxonomy,” Systematic Biology, vol. 54, no. 5, pp. 844–851, 2005.
[19]
K. W. Will and D. Rubinoff, “Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification,” Cladistics, vol. 20, no. 1, pp. 47–55, 2004.
[20]
M. J. Hickerson, C. P. Meyer, and C. Moritz, “DNA barcoding will often fail to discover new animal species over broad parameter space,” Systematic Biology, vol. 55, no. 5, pp. 729–739, 2006.
[21]
L. B. Beheregaray, “Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere,” Molecular Ecology, vol. 17, no. 17, pp. 3754–3774, 2008.
[22]
J. M. Guerra-Garcia, F. Espinosa, and J. C. Garcia-Gomez, “Trends in Taxonomy today: an overview about the main topics,” Zoological Baetica, vol. 19, pp. 15–49, 2008.
[23]
D. Begerow, H. Nilsson, M. Unterseher, and W. Maier, “Current state and perspectives of fungal DNA barcoding and rapid identification procedures,” Applied Microbiology and Biotechnology, vol. 87, no. 1, pp. 99–108, 2010.
[24]
S. L. Chiang and J. J. Mekalanos, “Use of signature-tagged transposon mutagenesis to identify Vibrio cholerae genes critical for colonization,” Molecular Microbiology, vol. 27, no. 4, pp. 797–805, 1998.
[25]
A. J. Darwin and V. L. Miller, “Identification of Yersinia enterocolitica genes affecting survival in an animal host using signature-tagged transposon mutagenesis,” Molecular Microbiology, vol. 32, no. 1, pp. 51–62, 1999.
[26]
P. H. Edelstein, M. A. C. Edelstein, F. Higa, and S. Falkow, “Discovery of virulence genes of Legionella pneumophila by using signature tagged mutagenesis in a guinea pig pneumonia model,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 14, pp. 8190–8195, 1999.
[27]
M. Hensel, J. E. Shea, C. Gleeson, M. D. Jones, E. Dalton, and D. W. Holden, “Simultaneous identification of bacterial virulence genes by negative selection,” Science, vol. 269, no. 5222, pp. 400–403, 1995.
[28]
J. Mecsas, I. Bilis, and S. Falkow, “Identification of attenuated Yersinia pseudotuberculosis strains and characterization of an orogastric infection in BALB/c mice on day 5 postinfection by signature-tagged mutagenesis,” Infection and Immunity, vol. 69, no. 5, pp. 2779–2787, 2001.
[29]
O. Makarova, N. Contaldo, S. Paltrinieri, G. Kawube, A. Bertaccini, and M. Nicolaisen, “DNA barcoding for identification of “Candidatus phytoplasmas” using a fragment of the elongation factor Tu gene,” PLoS ONE, vol. 7, no. 12, Article ID e52092, 2012.
[30]
K. L. Schneider, G. Marrero, A. M. Alvarez, and G. G. Presting, “Classification of plant associated bacteria using RIF, a computationally derived DNA marker,” PLoS ONE, vol. 6, no. 4, Article ID e18496, 2011.
[31]
J. W. W. Natalie, “Determining the microbial diversity in chaparral soils before and after wildfires through DNA barcoding,” Project Number-S1119, California State Science Fair, Project Summary, 2013.
[32]
L. Thao, T. James, B. Alexandra et al., “Bar-coded Enterobacteria: an undergraduate microbial ecology laboratory module,” The American Journal of Educational Research, vol. 1, no. 1, pp. 26–30, 2013.
[33]
J. K. Stahlhut, J. Gibbs, C. S. Sheffield, M. A. Smith, and L. Packer, “Wolbachia (Rickettsiales) infections and bee (Apoidea) barcoding: a response to Gerth et al,” Systematics and Biodiversity, vol. 10, no. 4, pp. 395–401, 2012.
[34]
P. D. N. Hebert and T. R. Gregory, “The promise of DNA barcoding for taxonomy,” Systematic Biology, vol. 54, no. 5, pp. 852–859, 2005.
[35]
M. Holloway, “Democratizing taxonomy,” Conservation in Practice, vol. 7, pp. 14–21, 2006.
[36]
D. H. Janzen, W. Hallwachs, P. Blandin et al., “Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity,” Molecular Ecology Resources, vol. 9, no. 1, pp. 1–26, 2009.
[37]
A. Hausmann, G. Haszprunar, A. H. Segerer, W. Speidel, G. Behounek, and P. D. N. Hebert, “Now DNA-barcoded: the butterflies and larger moths of Germany,” Spixiana, vol. 34, no. 1, pp. 47–58, 2011.
[38]
K. N. Magnacca and M. J. F. Brown, “DNA barcoding a regional fauna: Irish solitary bees,” Molecular Ecology Resources, vol. 12, no. 6, pp. 990–998, 2012.
[39]
C. S. Sheffield, P. D. N. Hebert, P. G. Kevan, and L. Packer, “DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies,” Molecular Ecology Resources, vol. 9, no. 1, pp. 196–207, 2009.
[40]
H. R. Taylor and W. E. Harris, “An emergent science on the brink of irrelevance: a review of the past 8years of DNA barcoding,” Molecular Ecology Resources, vol. 12, no. 3, pp. 377–388, 2012.
[41]
A. Zaldívar-Riverón, J. J. Martínez, F. S. Ceccarelli et al., “DNA barcoding a highly diverse group of parasitoid wasps (Braconidae: Doryctinae) from a Mexican nature reserve,” Mitochondrial DNA, vol. 21, no. 1, pp. 18–23, 2010.
[42]
G. Michael and B. Christoph, “A multilocus sequence typing (MLST) approach to diminish the problems that are associated with DNA barcoding: a reply to Stahlhut etal. 2012,” Systematics and Biodiversity, vol. 11, no. 1, pp. 15–17, 2013.
[43]
L. Baldo, J. C. D. Hotopp, K. A. Jolley et al., “Multilocus sequence typing system for the endosymbiont Wolbachia pipientis,” Applied and Environmental Microbiology, vol. 72, no. 11, pp. 7098–7110, 2006.
[44]
J. R. Dupuis, A. D. Roe, and F. A. H. Sperling, “Multi-locus species delimitation in closely related animals and fungi: one marker is not enough,” Molecular Ecology, vol. 21, no. 18, pp. 4422–4436, 2012.
[45]
M. L. Sogin, H. G. Morrison, J. A. Huber et al., “Microbial diversity in the deep sea and the underexplored ‘rare biosphere’,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 32, pp. 12115–12120, 2006.
[46]
A. Galimberti, F. de Mattia, A. Losa et al., “DNA barcoding as a new tool for food traceability,” Food Research International, vol. 50, no. 1, pp. 55–63, 2013.
[47]
E. F. DeLong, C. M. Preston, T. Mincer et al., “Community genomics among stratified microbial assemblages in the ocean's interior,” Science, vol. 311, no. 5760, pp. 496–503, 2006.
[48]
E. F. DeLong, “Microbial population genomics and ecology: the road ahead,” Environmental Microbiology, vol. 6, no. 9, pp. 875–878, 2004.
[49]
M. Leclerc, C. Juste, P. Marteau, R. Nalin, H. Blottiere, and J. Dore, “Intestinal metagenomics and nutrition,” Annuals of Nutrition and Metabolism, vol. 51, supplement 1, no. 13, 2007.
[50]
S. G. Tringe, C. Von Mering, A. Kobayashi et al., “Comparative metagenomics of microbial communities,” Science, vol. 308, no. 5721, pp. 554–557, 2005.
[51]
G. W. Tyson, J. Chapman, P. Hugenholtz et al., “Community structure and metabolism through reconstruction of microbial genomes from the environment,” Nature, vol. 428, no. 6978, pp. 37–43, 2004.
[52]
J. C. Venter, K. Remington, J. F. Heidelberg et al., “Environmental genome shotgun sequencing of the sargasso sea,” Science, vol. 304, no. 5667, pp. 66–74, 2004.
[53]
M. G. Links, T. J. Dumonceaux, S. M. Hemmingsen, and J. E. Hill, “The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data,” PLoS ONE, vol. 7, no. 11, Article ID e49755, 2012.
[54]
B. Chaban and J. E. Hill, “A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities,” International Society for Microbial Ecology, vol. 6, no. 2, pp. 430–439, 2012.
[55]
A. S. Tanabe and H. Toju, “Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants,” PLOS ONE, vol. 8, no. 10, Article ID e76910, 2013.
[56]
L. B. Mark, “Molecular systematics: counting angels with DNA,” Nature, vol. 421, no. 6919, pp. 122–124, 2003.
[57]
M. Blaxter and R. Floyd, “Molecular taxonomics for biodiversity surveys: already a reality,” Trends in Ecology and Evolution, vol. 18, no. 6, pp. 268–269, 2003.
[58]
M. L. Blaxter, “The promise of a DNA taxonomy,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 359, no. 1444, pp. 669–679, 2004.
[59]
A. Barberán and E. O. Casamayor, “Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities,” Aquatic Microbial Ecology, vol. 59, no. 1, pp. 1–10, 2010.
[60]
J. Wang, J. Soininen, J. He, and J. Shen, “Phylogenetic clustering increases with elevation for microbes,” Environmental Microbiology Reports, vol. 4, no. 2, pp. 217–226, 2012.
[61]
N. Mouquet, V. Devictor, C. N. Meynard et al., “Ecophylogenetics: advances and perspectives,” Biological Reviews, vol. 87, no. 4, pp. 769–785, 2012.
[62]
C. O. Webb, D. D. Ackerly, M. A. McPeek, and M. J. Donoghue, “Phylogenies and community ecology,” Annual Review of Ecology and Systematics, vol. 33, pp. 475–505, 2002.
[63]
N. R. Pace, “A molecular view of microbial diversity and the biosphere,” Science, vol. 276, no. 5313, pp. 734–740, 1997.
[64]
P. Hugenholtz, B. M. Goebel, and N. R. Pace, “Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity,” Journal of Bacteriology, vol. 180, no. 18, pp. 4765–4774, 1998.
[65]
T. P. Curtis, W. T. Sloan, and J. W. Scannell, “Estimating prokaryotic diversity and its limits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 16, pp. 10494–10499, 2002.
[66]
D. Wu, P. Hugenholtz, K. Mavromatis et al., “A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea,” Nature, vol. 462, no. 7276, pp. 1056–1060, 2009.
[67]
J. B. H. Martiny, B. J. M. Bohannan, J. H. Brown et al., “Microbial biogeography: putting microorganisms on the map,” Nature Reviews Microbiology, vol. 4, no. 2, pp. 102–112, 2006.
[68]
D. R. Nemergut, E. K. Costello, M. Hamady et al., “Global patterns in the biogeography of bacterial taxa,” Environmental Microbiology, vol. 13, no. 1, pp. 135–144, 2011.
[69]
L. Liu, X. Huang, R. Zhang, L. Jiang, and G. Qiao, “Phylogenetic congruence between Mollitrichosiphum (Aphididae: Greenideinae) and Buchnera indicates insect-bacteria parallel evolution,” Systematic Entomology, vol. 38, no. 1, pp. 81–92, 2013.
[70]
P. Buchner, Endosymbiosis of Animals with Plant Microorganisms, Interscience, New York, NY, USA, 1965.
[71]
P. Tallury, A. Malhotra, L. M. Byrne, and S. Santra, “Nanobioimaging and sensing of infectious diseases,” Advanced Drug Delivery Reviews, vol. 62, no. 4-5, pp. 424–437, 2010.
[72]
D. Zhang, D. J. Carr, and E. C. Alocilja, “Fluorescent bio-barcode DNA assay for the detection of Salmonella enterica serovar Enteritidis,” Biosensors and Bioelectronics, vol. 24, no. 5, pp. 1377–1381, 2009.
[73]
J. B.-H. Tok, F. Y. S. Chuang, M. C. Kao et al., “Metallic striped nanowires as multiplexed immunoassay platforms for pathogen detection,” Angewandte Chemie, vol. 45, no. 41, pp. 6900–6904, 2006.
[74]
M. Han, X. Gao, J. Z. Su, and S. Nie, “Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules,” Nature Biotechnology, vol. 19, no. 7, pp. 631–635, 2001.
[75]
H. Lee, J. Kim, H. Kim, J. Kim, and S. Kwon, “Colour-barcoded magnetic microparticles for multiplexed bioassays,” Nature Materials, vol. 9, no. 9, pp. 745–749, 2010.
[76]
X. Duan, L. Liu, F. Feng, and S. Wang, “Cationic conjugated polymers for optical detection of DNA methylation, lesions, and single nucleotide polymorphisms,” Accounts of Chemical Research, vol. 43, no. 2, pp. 260–270, 2010.
[77]
H. Ho, A. Najari, and M. Leclerc, “Optical detection of DNA and proteins with cationic polythiophenes,” Accounts of Chemical Research, vol. 41, no. 2, pp. 168–178, 2008.
[78]
S. W. Thomas III, G. D. Joly, and T. M. Swager, “Chemical sensors based on amplifying fluorescent conjugated polymers,” Chemical Reviews, vol. 107, no. 4, pp. 1339–1386, 2007.
[79]
H. N. Kim, Z. Guo, W. Zhu, J. Yoon, and H. Tian, “Recent progress on polymer-based fluorescent and colorimetric chemosensors,” Chemical Society Reviews, vol. 40, no. 1, pp. 79–93, 2011.
[80]
Y. Li, Y. T. H. Cu, and D. Luo, “Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes,” Nature Biotechnology, vol. 23, no. 7, pp. 885–889, 2005.
[81]
H. ？zhalici-ünal and B. A. Armitage, “Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron,” ACS Nano, vol. 3, no. 2, pp. 425–433, 2009.
[82]
D. Akin, J. Sturgis, K. Ragheb et al., “Bacteria-mediated delivery of nanoparticles and cargo into cells,” Nature Nanotechnology, vol. 2, no. 7, pp. 441–449, 2007.
[83]
X. Feng, G. Yang, L. Liu et al., “A convenient preparation of multi-spectral microparticles by bacteria-mediated assemblies of conjugated polymer nanoparticles for cell imaging and barcoding,” Advanced Materials, vol. 24, no. 5, pp. 637–641, 2012.
[84]
B. Liu, X. Zhang, H. Huang, Y. Zhang, F. Zhou, and G. Wang, “A novel molecular typing method of Mycobacteria based on DNA barcoding visualization,” Journal of Clinical Bioinformatics, vol. 4, article 4, 2014.
[85]
M. Liong, A. N. Hoang, J. Chung et al., “Magnetic barcode assay for genetic detection of pathogens,” Nature Communications, vol. 4, article 1752, 2013.
[86]
S. Dufort, M. Richard, S. Lantuejoul, and F. De Fraipont, “Pyrosequencing, a method approved to detect the two major EGFR mutations for anti EGFR therapy in NSCLC,” Journal of Experimental and Clinical Cancer Research, vol. 30, no. 1, article 57, 2011.
[87]
H. D. Hill and C. A. Mirkin, “The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange,” Nature Protocols, vol. 1, no. 1, pp. 324–336, 2006.
[88]
G. Schneider, U. Dobrindt, B. Middendorf et al., “Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic Escherichia coli in vitro support the role of conjugation for horizontal transfer of genomic islands,” BMC Microbiology, vol. 11, article 210, 2011.
[89]
G. Wang, J. Xu, G. Xu, Y. Zhang, F. Li, and J. Suo, “Predicting a novel pathogenicity island in Helicobacter pylori by genomic barcoding,” World Journal of Gastroenterology, vol. 19, no. 30, pp. 5006–5010, 2013.
[90]
M. Callanan, P. Kaleta, J. O'Callaghan et al., “Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion,” Journal of Bacteriology, vol. 190, no. 2, pp. 727–735, 2008.
[91]
E. Altermann, W. M. Russell, M. A. Azcarate-Peril et al., “Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 11, pp. 3906–3912, 2005.
[92]
O. O'Sullivan, J. O'Callaghan, A. Sangrador-Vegas et al., “Comparative genomics of lactic acid bacteria reveals a niche-specific gene set,” BMC Microbiology, vol. 9, article 50, 2009.
[93]
I. D. Peikon, D. I. Gizatullina, and A. M. Zador, “In vivo generation of DNA sequence diversity for cellular barcoding,” Nucleic Acids Research, 2014.
[94]
J. Lim, S. Kim, H. Eo et al., “BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources,” BMC Genomics, vol. 10, supplement 3, article S8, 2009.
[95]
E. Check, “Cowrie study strikes a blow for traditional taxonomy,” Nature, vol. 438, no. 7069, pp. 722–723, 2005.
