Lactobacillus acidophilus is a commercially significant bacterial probiotic, originally isolated from the human gastrointestinal tract and designated Bacillus acidophilus in 1900. Throughout the development of methods to identify and characterise bacteria, L. acidophilus has undergone multiple taxonomic revisions and is now the type species of a phylogenetic subgroup in the highly diverse and h...

Recent advancements in chemotaxonomic and molecular biology-based identification methods have clarified the taxonomy of the genus Actinomyces and have led to the recognition of several new Actinomyces and related species. Actinomyces-like gram-positive rods have increasingly been isolated from various clinical specimens. Thus, an easily accessible scheme for reliable differentiation at the spec...

Pfister, Robert M. (Lamont Geological Observatory, Palisades, N.Y.), and Paul R. Burkholder. Numerical taxonomy of some bacteria isolated from Antarctic and tropical seawaters. J. Bacteriol. 90:863-872. 1965.-Microorganisms from Antarctic seas and from tropical waters near Puerto Rico were examined with a series of morphological, physiological, and biochemical tests. The results of these analys...

A comparative study of the bacterial flora of the water of Chesapeake Bay and Tokyo Bay was undertaken to assess similarities and differences between the autochthonous flora of the two geographical sites and to test the hypothesis that, given similarities in environmental parameters, similar bacterial populations will be found, despite extreme geographic distance between locations. A total of 1...

Cryptic genes are phenotypically silent DNA sequences, not normally expressed during the life cycle of an individual. They may, however, be activated in a few individuals of a large population by mutation, recombination, insertion elements, or other genetic mechanisms. A consideration of the microbial literature concerning biochemical evolution, physiology, and taxonomy provides the basis for a...

The polymerase chain reaction (PCR) based random amplified polymorphic DNA (RAPD) assay, morphological, physiological, biochemical and antimicrobial susceptibility test methods have been evaluated for use in the taxonomy of isolated thermotolerant Bacillus from Jordanian hot springs, with specific reference to strains Geobacillus stearothermophilus (ATCC 12980), Bacillus circulans (ATCC 4513) a...

Multidimensional scaling (MDS) was applied to the numerical taxonomy of Candida species based on isoenzyme profiles. Multidimensional scaling uses proximity measures to generate a spatial configuration of points in multidimensional space where distances between points reflect similarity among types. The biochemical profiles of 35 types of Candida species based on 26 tests consisting of isoenzym...

Background Reconstruction and applications of genome scale metabolic models have truly influenced the field of systems biology [1,2]. These models have a promising ability to describe cellular phenotypes accurately and to relate the annotated genome sequence to the physiological functions of a cell [3,4]. Gluconacetobacter has been extensively characterized and is a model system for cellulose b...

Although the hybrid discipline of biochemical systematics has been a distinct field of study for only about ten years, it has had a telling impact on taxonomic practice. Nevertheless, the chemical approach, with its emphasis on the exact, tends to exlude much of the wealth of natural phenomena that are the backbone of taxonomy. It is necessary for the chemist and biochemist to acquire a better ...

The NCBI Taxonomy is a valuable resource for coordinating information about biological taxa. Its 378,802 taxonomy nodes cover the superkingdoms of Archaea, Bacteria, Eukaryotes, Viruses and Viriods, down to subspecies and strains. However, the size and scope present practical problems when using the Taxonomy in applications, specifically when using the NCBI Taxonomy in a search interface for sp...