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Chapter 3 : Taxonomic Characterization of Prokaryotic Microorganisms

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Abstract:

Prokaryote microorganisms constitute a major part of the genetic diversity of our planet and they play a pivotal role in the biochemical processes of the biosphere. This chapter presents microbiologists in biotechnology and molecular biology with the basic conceptual framework and the currently accepted procedures for characterization and consistent naming of newly isolated prokaryotic strains. Prokaryote taxonomy is a highly dynamic science. There is no official classification of prokaryotes, and classification schemes change in accordance with the development of new techniques and approaches. Genotype-based methods used in the characterization of prokaryotes include the sequencing of single genes (16S rRNA, 23S rRNA, the intergenic transcribed spacer [ITS] between these two genes, different housekeeping genes) and molecular fingerprinting techniques, as well as methods that provide information on the entire genome: the determination of the mol% guanine + cytosine, DNA-DNA hybridization to compare genomes, and in some cases even complete genome sequencing. Multilocus sequence typing (MLST) or multilocus sequence analysis (MLSA) are powerful tools to obtain taxonomic information on the species level and the interspecies variability. The method was first developed to characterize bacterial pathogens. Comparisons of protein sequence-based phylogenies have by and large confirmed the general structure of the 16S rRNA gene phylogenetic tree. A full genome sequence provides a view of the genetic information in a microbe at the highest possible resolution. It can therefore be considered the “ultimate source” of molecular information for taxonomic and phylogenetic studies.

Citation: Felis G, Torriani S, Van Hylckama Vlieg J, Oren A. 2010. Taxonomic Characterization of Prokaryotic Microorganisms, p 28-42. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch3

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Bacteria and Archaea
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RNA Polymerase beta Subunit
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Bacterial Proteins
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Flow sheet showing the different stages in the taxonomic characterization of new isolates of prokaryotes.

Citation: Felis G, Torriani S, Van Hylckama Vlieg J, Oren A. 2010. Taxonomic Characterization of Prokaryotic Microorganisms, p 28-42. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch3
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Tables

Generic image for table
TABLE 1

Sequences of universal primers available for amplification of ribosomal genes from Bacteria and Archaea

Citation: Felis G, Torriani S, Van Hylckama Vlieg J, Oren A. 2010. Taxonomic Characterization of Prokaryotic Microorganisms, p 28-42. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch3

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