Micah I. Krichevsky

Numerical Taxonomy of Mycobactin-Dependent Mycobacteria, Emended Description of Mycobacterium avium, and Description of Mycobacterium avium subsp. avium subsp. nov., Mycobacterium avium subsp. paratuberculosis subsp. nov., and Mycobacterium avium subsp. silvaticum subsp. nov.

We performed a numerical taxonomy analysis of 38 Mycobacterium paratuberculosis and related mycobacterial strains, including wood pigeon mycobacteria; this analysis was based on 22 tests, which were selected for their potential discriminative value from a total of 51 tests studied and produced four well-defined clusters. Cluster 1 contained the M. paratuberculosis strains, including two strains isolated from Crohns disease patients; cluster 2 contained Mycobacterium avium and Mycobacterium intracellulare reference strains; cluster 3 consisted of the wood pigeon mycobacteria; and the only strain in cluster 4 was M. paratuberculosis 316F, which is used for antigen and vaccine production. Strains in cluster 1 were mycobactin dependent even when they were subcultured, whereas strains in cluster 3 were unable to grow on egg medium and their growth was stimulated by pH 5.5. Growth stimulation by pyruvate, resistance to D-cycloserine (50 micrograms/ml), and alkaline phosphatase activity also were characteristics that were useful for discriminating between clusters 1 and 3. The results of previous DNA-DNA hybridization studies have demonstrated that M. avium Chester 1901, M. paratuberculosis Bergey et al. 1923, and the wood pigeon mycobacteria belong to a single genomic species, and we propose that the name of this species should be M. avium. On the basis of the results of previous genomic analyses based on restriction fragment length, the results of polymorphism studies, and DNA patterns determined by field inversion gel electrophoresis as well as the results of our phenotypic study, we propose that the species should be divided into subspecies which correspond to pathogenicity and host range characteristics.(ABSTRACT TRUNCATED AT 250 WORDS)

Taxonomic Probability Matrix for Use With Slowly Growing Mycobacteria

A probability matrix for identification was developed from data derived from a series of cooperative studies of slowly growing mycobacteria. The matrix includes feature frequencies exhibited by 14 numerical taxonomy clusters in 34 tests. The clusters correspond to 13 defined species. The matrix is designed primarily to screen strains either for membership in 1 of the 14 taxa or for exclusion from these taxa and, thus, to determine whether the strains are in need of further characterization. The matrix was used in the analysis of 298 strains. Two related parameters were used as decision thresholds. First, the probability of the most likely taxon must be 99 times greater than that of the second most likely taxon. Second, the absolute likelihood of the strain being in the most likely taxon must be at least 0.01 times that of a “perfect” strain of the taxon. By using these thresholds and additional judgments, 83 strains were found to be appropriate for further study, with a likelihood that 53% of these strains belong to unrepresented taxa.

Automatic digital data acquisition and computer calculation in amino acid analysis

Abstract Amino acid analysis data acquisition and computation have been automated by (1) measuring the ninhydrin color with a spectrophotometer which is linear with respect to optical density, (2) digitizing the data directly from the photometer circuit by means of a digital voltmeter, and (3) formating and punching the digital data in paper tape so that each data word is identified as to channel of information (i.e., cuvet position and wavelength), and processing the punched data on a computer using a FORTRAN program. The program edits the data with regard to noise, compensates for baseline changes of various types, splits unresolved peaks, and calculates peak areas over a range of optical densities from 0 to 3.000. This system, in daily use in our laboratory, provides increased accuracy and saves approximately 2 man hours per analysis.

Extracellular invertase in Streptococcus mutans and Streptococcus salivarius

Summary Cultures of representative oral streptococci were fractionated and assayed for glycosyltransferases and invertase. Considerable extracellular invertase activity was found in five Streptococcus mutans strains and one Streptococcus salivarius strain. For example, in cultures of S. mutans LM-7, grown with glucose as the energy source, the invertase activity in the medium was ten times greater than the activity found associated with the cells. The invertase was characterized as a β-fructofuranosidase (EC 3.2.1.26). In the cases studied, the extra- and intracellular invertases are always present, but their levels vary independently and depend on the carbohydrate in the medium.

Computer Methods for Describing Groups from Binary Phenetic Data: Modification of Numerical Taxonomy Programs to Increase Flexibility

The logic of modifications to numerical taxonomy programs is described. The programs modified are to calculate and store interstrain similarities, to arrange the data by cluster analysis, and to calculate inter- and intragroup statistics. The modifications included increasing the efficiency of the similarity calculations, storing intermediate matrices on disks for later use, and permitting the calculation of group statistics on any arbitrary groups of strains as well as taxonomic groups without recalculating interstrain similarities. Changing communication paths of information allowed using the programs flexibly for ecological as well as taxonomic analyses, reduced program execution costs, increased program versatility, and reduced errors.

Synthesis of glucose 1-phosphate-U-14C and specifically labeled sucroses using sucrose phosphorylase

A simplified and improved method for the synthesis of G-1-P-14C and specifically labeled sucroses has been developed. Using a preparation of enzyme easily purified from Leuconostoc mesenteroides, high yeilds (61%–72%) of sucroses were obtained. The radiochemical purity was quite high. The specific conditions for bacterial growth, enzyme purification and sucrose synthesis (utilizing paper chromatographic techniques) are completely described.

Computer Methods for Describing Groups from Binary Phenetic Data: Preliminary Summary and Editing of Data

Summarizing and editing binary phenetic data before further analysis are an accepted practice. The microbiologist tabulates basic information about a strain by feature matrix and uses this information as an aid in editing that matrix. Interactive computer technology can be used to aid in this process. Advantages of such computer-aided matrix editing include (i) preliminary analysis of the data, (ii) automation of routine operations, (iii) reduced costs of subsequent analyses, and (iv) improved results of subsequent analyses. The reduced costs and improved results are demonstrated by running a cluster analysis program on data before and after editing.

Acid Production from Glucose and Sucrose by Growing Cultures of Caries-Conducive Streptococci

Acid production was determined for several strains of caries-conducive streptococci growing on glucose and sucrose. The yield of acid per mol of sucrose was the same as that from two hexose units. It was determined by macroscopic and microscopic observations of the culture that extracellular polymer was formed from sucrose during growth, but the amount of sucrose diverted to polymer formation was less than that anticipated from visual observations.

Abbreviations of Names of Genera Suggested for Coding Microbiological Data

A list of abbreviations of generic names appearing in the eighth edition of Bergeys Manual is presented. The list includes names of accepted genera and other genera cited as synonymous or of uncertain status. Since names of the latter still appear in the literature or are used in subspecialties of microbiology, abbreviations for these genera are also given. The abbreviations have been found useful when coding data for computer storage and analysis. Because of the saving in space, a larger number of strain characteristics can be stored in a computerized data bank. In addition, the abbreviations are often mnemonic, a helpful characteristic.

Levan Formation by Odontomyces viscosus

The authors present some physiological parameters involved in levan formation by Odontomyces viscosus, a filamentous organism in gingival plaque of the hamster.