New Strategies on Molecular Biology Applied to Microbial Systematics

Abstract

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50's and 60's. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint.

Advances in Chemical and Biological Methods to Identify Microorganisms—From Past to Present

“…While these methods continue to hold place in certain settings, molecular-based techniques have provided unprecedented insights into bacterial identification and typing. To name a few examples, genotypic methods have enabled the identification of a large diversity of previously unknown taxa, the characterization of uncultivable bacteria, and facilitated metagenomics studies on large and diverse bacterial communities [172]. Both clinical and research setting have provided in depth insights into bacterial virulence, pathogenesis, antibiotic resistance, and epidemiological typing, as well as identification of novel, emerging, and re-emerging species [173].…”

Diversity of Streptomyces spp. in Eastern Himalayan region – computational RNomics approach to phylogeny

“…A robust phylogeny is central for ongoing efforts in many groups to reconstruct system-wide metabolic models of Streptomyces and related species [4], which are used for systematic strain-engineering in biotechnology. Molecular systematics, which includes both classification and identification, has its origin in the early nucleic acid hybridization studies, but has achieved a new status following the introduction of nucleic acid sequencing techniques [5]. Significance of phylogenetic studies based on 16S rDNA sequences is increasing in the systematics of actinomycetes [6].…”

Molecular fingerprinting methods for the discrimination between C. albicans and C. dubliniensis

“…The PFGE bases on the concept that the limit of the size of DNA separable by conventional electrophoresis in agarose (over 50 kb) may be enlarged by introducing pulses or changes in the direction of the electric field subjecting the DNA to an electrophoretic field that alternates in its direction (Sullivan et al , 1996; Höfling et al , 1997). Larger DNA molecules require greater time to re‐orient than smaller molecules thus enabling resolution (Williams and Lewis, 2000).…”

“…Specific chromosomes can be identified using Southern blot hybridization with chromosome‐specific DNA probes (Soll, 2000). The development of pulsed‐field gel electrophoresis (PFGE), orthogonal‐field‐alternation gel electrophoresis (OFAGE), and variations upon these basic electrophoretic karyotyping systems such as contour‐clamped homogeneous electric field gel electrophoresis (CHEF) and transverse alternating‐field electrophoresis (TAFE) permitted the electrophoretic separation of chromosome‐sized of the yeasts DNA molecules and also the demonstration of frequent chromosome‐length polymorphisms (Merz, 1990; Sullivan et al , 1996; Höfling et al , 1997; Soll, 2000; Williams and Lewis, 2000).…”