S T Williams

University of Liverpool, Liverpool, England, United Kingdom

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Publications (13)30.88 Total impact

  • FEMS Microbiology Letters 03/2006; 26(2):175 - 180. · 2.05 Impact Factor
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    ABSTRACT: Computer assisted identification systems require that databases on the test results of the species are of high quality. One reason for poor quality is the inadvertent inclusion of strains that do not belong to a taxon; this can readily occur in groups where ancillary criteria (e.g. serology) are not available. A possible strategy is to exclude strains that are very atypical in their properties, i.e. that are very outlying, provided an objective criterion can be used. A computer program, OUTLIER, for the detection of outlying strains in bacterial clusters was evaluated. A brief description of the theory and operation of the program is given. The program uses as an objective criterion the degree to which the strain data fits a chi-square. This allows easy identification of aberrant strains that should be excluded in constructing a database. The program utilizes 1.0 data and calculations are based upon a choice of one of four identification coefficients. The relative merits of these four coefficients were examined for eight sets of bacterial data. Two of the coefficients, -log10 Willcox likelihood and Taxonomic distance squared appear to show little significant differences and we recommend these for routine work, with the first being the more useful. The Pattern distance squared was useful in indicating where atypical strains may be metabolically less active or slow-growing members of a cluster rather than true outliers. The Variance-weighted Taxonomic distance squared behaved anomalously and we do not recommend it.
    The Journal of applied bacteriology 05/1989; 66(4):339-52.
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    ABSTRACT: The character state data obtained for clusters defined in a previous phenetic classification were used to construct two probabilistic matrices for Streptomyces species. These superseded an original published identification matrix by exclusion of other genera and the inclusion of more Streptomyces species. Separate matrices were constructed for major and minor clusters. The minimum number of diagnostic characters for each matrix was selected by computer programs for determination of character separation indices (CHARSEP) and a selection of group diagnostic properties (DIACHAR). The resulting matrices consisted of 26 phena x 50 characters (major clusters) and 28 phena x 39 characters (minor clusters). Cluster overlap (OVERMAT program) was small in both matrices. Identification scores were used to evaluate both matrices. The theoretically best scores for the most typical example of each cluster (MOSTTYP program) were all satisfactory. Input of test data for randomly selected cluster representatives resulted in correct identification with high scores. The major cluster matrix was shown to be practically sound by its application to 35 unknown soil isolates, 77% of which were clearly identified. The minor cluster matrix provides tentative probabilistic identifications as the small number of strains in each cluster reduces its ability to withstand test variation. A diagnostic table for single-membered clusters, constructed using the CHARSEP and DIACHAR programs, was also produced.
    Journal of general microbiology 02/1989; 135(1):121-33.
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    Microbiology-sgm. 01/1985; 131(7):1681-1689.
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    ABSTRACT: The character state data obtained for clusters defined at the 77.5% SSM similarity level in the phenetic numerical classification described by Williams et al. (1983) were used to construct a probabilistic identification matrix. The 23 phena included were the major clusters (19 Streptomyces, 2 Streptoverticillium and 'Nocardia' mediterranea) and one minor cluster (Streptomyces fradiae). The characters most diagnostic for these clusters were selected using Sneath's CHARSEP and DIACHAR programs. The resulting matrix consisted of 41 characters x 23 phena. Identification scores, determined by Sneath's MATIDEN program were used to evaluate the matrix. Theoretical assessment was achieved by determination of the cluster overlap (OVERMAT), the identification scores for the Hypothetical Medium Organism of each cluster (MOSTTYP), and the scores for randomly selected cluster representatives using the classification data of Williams et al. (1983). The matrix was evaluated practically by the independent re-determination of the characters for the same cluster representatives, which also provided a measure of test error. Finally it was used to identify unknown isolates from a range of habitats. The results showed that the matrix was theoretically sound. Test error was within acceptable limits and did not distort identifications. Of the unknown isolates, 80% were clearly identified with a cluster. It is suggested that the matrix could form the basis for a more objective identification and grouping of the large number of Streptomyces species which have been described.
    Journal of general microbiology 07/1983; 129(6):1815-30.
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    ABSTRACT: Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for 139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.
    Journal of general microbiology 07/1983; 129(6):1743-813.
  • M Goodfellow, S T Williams
    Annual Review of Microbiology 02/1983; 37:189-216. · 12.90 Impact Factor
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    E. M. H. WELLINGTON, S. T. WILLIAMS
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    ABSTRACT: A study was made of the morphology, cell wall chemotype, and phage suscep- tibility of Actinoplanes armeniacus ATCC 15676, the type strain of the species (Kalakoutskii and Kusnetsov, Mikrobiologiya 33:553-560,1964). The spore chains produced by A. armeniacus on its aerial mycelium are similar to those typical of streptomycetes. No spore vesicles ("sporangia") were observed. Whole-cell hy- drolysates contained LL-diaminopimelic acid. Phage activity spectra showed extensive cross-reactions between streptomycetes and A. armeniacus ATCC 15676, whereas a phage propagated on this strain lysed a range of Streptomyces species. On the basis of these characteristics, the transfer of A. armeniacus Kalakoutskii and Kusnetsov to the genus Streptomyces is proposed as Strepto- myces armeniacus (Kalakoutskii and Kusnetsov) comb. nov. The type strain of this taxon is ATCC 15676. An amended description of this species is given. Kalakoutskii and Kusnetsov (6) described a new species of Actinoplanes, Actinoplanes ar- meniacus, which was characterized by the pro- duction of a well-developed aerial mycelium bearing spiral spore chains and "sporangia" con- taining motile zoospores. The formation of flag- ellated spores in spore vesicles is a feature of Actinoplanes spp. (3, 4). Production of single spore chains on the aerial mycelium has not been reported for any of the other eight species included in the genus Actinoplanes (10-13), al- though Willoughby (21) reported a conidial ac- tinoplanete which produced tufts of conidios- pores similar to the contents of the vesicles but lacking an inflated vesicular sheath. Actino- planes species have a wall of chemotype 11, containing meso-diaminopimelic acid (meso- DAP) with the sugars xylose and arabinose (8). Actinoplanes armeniacus was included in the Approved Lists of Bacterial Names (18) and in a review of the genus Actinoplanes (12). During our studies on actinophage host ranges, A. armeniacus was found to be suscep- tible to a wide range of phages active on Strep- tomyces species. Among several hundred phage- host cross-reactions (Wellington and Williams, in K. P. Schaal and G. Pulverer, ed., Actinomy- cetes, in press), this was the only example of phage apparently cross-infecting members of dif- ferent cell wall chemotypes sensu Lechevalier and Lechevalier (9). This prompted a taxonomic study of A. armeniacus, in which it was revealed that this species is a member of the genus Strep- tomyces. The results also demonstrate how se- lected phages may be used as an aid in the recognition of genera of the order Actinomyce- tales.
    International journal of systematic bacteriology 01/1981; 31(1). · 2.27 Impact Factor
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    Microbiology-sgm. 01/1980; 119(1):173-178.
  • A. L. Carter, S. T. Williams, T. McNeilly
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    ABSTRACT: Observations of pollen tube behaviour on the stigma surface have shown that germination and growth of compatible pollen tubes is unaffected by stigma age. However, incompatible pollen tubes fail to become attached to the papillae of mature stigmas whilst on young stigmas many of the incompatible pollen tubes spread over and adhere to the papillae. Scars and holes were found in connection with successful pollen tube penetration of papillae.
    Euphytica 01/1975; 24(1):133-141. · 1.64 Impact Factor
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    S T Williams, M Goodfellow
    Journal of Bacteriology 03/1966; 91(2):907. · 3.19 Impact Factor
  • S.T. Williams, T. McNeilly, E.M.H. Wellington
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    ABSTRACT: Aspects of the decomposition of metal tolerant vegetation growing on mine waste containing high concentrations of lead and zinc were studied and compared with those on an adjacent uncontaminated site. High concentrations of Pb and, to a lesser extent, Zn, accumulated in metal-tolerant grass. Retarded decomposition of this vegetation as compared with that on the uncontaminated site was indicated by a greater accumulation of litter, less humus formation, reduced soil urease activity and smaller microbial and microfaunal populations. Some evidence for increased metal tolerance in microbes from the mine waste was obtained. Concentrations of lead tolerated under laboratory conditions were much lower than those extracted from the mine waste and its vegetation, probably due to the lack of an accurate method for assessing the availability of lead in soil and vegetation.
    Soil Biology and Biochemistry 9(4):271–275. · 4.41 Impact Factor
  • V.A. Orchard, M. Goodfellow, S.T. Williams
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    ABSTRACT: Nocardiae were isolated from 15 out of 47 soils using Diagnostic Sensitivity Test Agar supplemented with antibiotics. Up to 7.3 × 104 g−1 dry wt. soil were counted, indicating that these bacteria might be more widespread and important than previously thought. Study of randomly selected isolates showed that they formed fragmenting mycelium, contained arabinose, galactose, meso-diaminopimelic acid and nocardomycolic acids. They clustered with Nocardia asteroides markers in a numerical taxonomic analysis.
    Soil Biology and Biochemistry 9(4):233–238. · 4.41 Impact Factor