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Bacterial taxonomy comprises systematics (theory of classification), nomenclature (formal process of naming), and identification. There are two basic approaches to classification. Similarities may be derived between microorganisms by numerical taxonomic methods based on a range of present-day observable characteristics (phenetics), drawing in particular on conventional morphological and physiological test characters as well as chemotaxonomic markers such as whole-cell protein profiles, mol% G+C content, and DNA-DNA homologies. By contrast, phylogenetics, the process of reconstructing possible evolutionary relationships, uses nucleotide sequences from conserved genes that act as molecular chronometers. A combination of both phenetics and phylogenetics is referred to as polyphasic taxonomy, and is the recommended strategy in description of new species and genera. Numerical analysis of small-subunit ribosomal RNA genes (rDNA) leading to the construction of branching trees representing the distance of divergence from a common ancestor has provided the mainstay of microbial phylogenetics. The approach has some limitations, particularly in the discrimination of closely related taxa, and there is a growing interest in the use of alternative loci as molecular chronometers, such as gyrA and RNAase P sequences. Comparison of the degree of congruence between phylogenetic trees derived from different genes provides a valuable test of the extent they represent gene trees or species trees. Rapid expansion in genome sequences will provide a rich source of data for future taxonomic analysis that should take into account population structure of taxa and novel methods for analysis of nonclonal bacterial populations. [ABSTRACT FROM AUTHOR]

Helicobacter pylori is a curved mlcroaerobic bacterium that was first lsolated from human antral gastric biopsy material in 1982 by Marshall and colleagues in Perth, Western Australia (1). Since then, enormous interest has developed in the micro-organism that now appears to be one of the most common human bacterial pathogens, estimated to be infecting at least one third of the world population (2). Although most Individuals appear to be asymptomatic H. pylon is implicated as a key risk factor in a number of gastrointestinal diseases, including duodenal and gastric ulceration and gas- tric cancer (3). Most clinical and basic research aspects have been exten- sively reviewed (4), but some key features of the general epidemlology of H pylon infections are as follows: [ABSTRACT FROM AUTHOR]

Campylobacters are the most frequently identified cause of acute bacterial diarrhea in humans in England and in many other developed countries. Although C jejuni and C coli are numerically the most important species in cases of campylobacter enteritis, there is a growing awareness that some of the other 13 species of Campylobactermay also be linked with human disease. However, precise identification of these organisms is rarely carried out in clincal laboratories, and the significance of most species or subtypes in causing human disease is unknown [ABSTRACT FROM AUTHOR]

Since Helicobacter pylori was first described in 1983 (1), the study of genomic DNA has been central to the development of its microbiology and molecular genetics. For instance, DNA base composition estimation (mol% G+C) was crucial in demonstrating affinities of the microorganism to the genus Campylobacter (2). Likewise, DNA-DNA hybridization assays revealed a high degree of base sequence homology between different isolates of H. pylori, yet a low relatedness to Campylobacter fetus and other species of Campylobacter (3). In 1987, rRNA-DNA hybridization and hybrid thermal stability analyses were used to show that H. pylori was phylogenetically distinct from Campylobacter sensu stricto and that the species merited classification in a new genus (4). The most significant application of DNA analysis has been in showing the diversity between genomes of different strains within H. pylori. The first indication of such genome diversity was from restriction endonuclease digest analysis of genomic DNA (6) and was subsequently confirmed by ribosomal RNA gene analysis and polymerase chain reaction (PCR)-based analysis of urease and other genes (7). [ABSTRACT FROM AUTHOR]

The isolation of genomic DNA from a microorganism generally comprises three stages: cultivation of the cells, disruption to release cell contents, and chemical purification of the DNA. Two widely used methods for the preparation of bacterial DNA are those described by Marmur (1) and Kirby (2), but procedures are frequently modified to suit the particular organisms under study. [ABSTRACT FROM AUTHOR]