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M Goodfellow

Publications and source records attributed to M Goodfellow.

At least 19 recordsLinked to original sources
PubMed2001

Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter.

The taxonomic position of a group of moderately thermophilic actinomycetes isolated from vegetable matter was determined using a suite of genotypic and phenotypic properties. The organisms were found to share a range of chemical and morphological markers typical of members of the genus Amycolatopsis. A representative of the group, strain K24T, formed a distinct phyletic line within the range of variation occupied by the genus Amycolatopsis in the 16S rDNA tree. The strains have many phenotypic properties in common and some of these distinguish the group from representatives of the validly described species of Amycolatopsis. It is clear from the combined datasets that the strains merit recognition as a new species of Amycolatopsis. The name proposed for the new species is Amycolatopsis sacchari; the type strain is K24T (= DSM 44468T = KCTC 9863T).

Actinomycetales↗
PubMed2001

Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp.nov., novel actinomycetes from soil.

The generic position of two aerobic, Gram-positive, non-acid-alcohol-fast actinomycetes was established following the isolation of their PCR-amplified 16S rRNA genes and alignment of the resultant sequences with the corresponding sequences from representatives of the families Actinosynnemataceae and Pseudonocardiaceae. The assignment of the organisms to the genus Saccharopolyspora was strongly supported by chemotaxonomic and morphological data. The strains were distinguished both from one another and from representatives of validly described Saccharopolyspora species on the basis of a number of phenotypic properties. It is proposed that the organisms, strains 07T (= AS4.1520T = IFO 16345T = JCM 10665T) and 216T (= AS4.1511T = IFO 16346T = JCM 10664T), be classified in the genus Saccharopolyspora as Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., respectively.

Bacterial Typing Techniques↗
PubMed2001

Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil.

The taxonomic position of a soil isolate, strain 13.4T, was established using a polyphasic approach. The organism was found to have chemical and morphological properties consistent with its classification in the genus Amycolatopsis. Phylogenetic analysis of the strain based on its 16S rDNA sequence showed that it forms a distinct phyletic line within members of the genus Amycolatopsis. The organism was also readily distinguished from the type strains of all validly described Amycolatopsis species by its phenotypic features. The name Amycolatopsis rubida sp. nov. is proposed for this new species. The type strain is strain 13.4T (= AS 4.1541T = JCM 10871T).

Actinomycetales↗
PubMed2001

Corynebacterium mooreparkense sp. nov. and Corynebacterium casei sp. nov., isolated from the surface of a smear-ripened cheese.

Ten isolates each of two different bacterial species isolated from the surface of a smear-ripened cheese were found to exhibit many characteristics of the genus Corynebacterium. The isolates were Gram-positive, catalase-positive, non-spore-forming rods that did not undergo a rod/coccus transformation when grown on complex media. Chemotaxonomic investigation revealed that the strains belonged unambiguously to the genus Corynebacterium. Their cell walls contained arabinose, galactose and short-chain mycolic acids (C22 to C36) and their peptidoglycan contained meso-diaminopimelic acid. The G+C content of the DNA was 51-60 mol%. MK-9 (H2) was the principal menaquinone. The 16S rDNA sequences of four isolates of each bacterium were determined and aligned with those of other members of the coryneform group. Phylogenetic analysis showed that the strains represented two new sublines within the genus Corynebacterium; Corynebacterium variabile and Corynebacterium ammoniagenes were their nearest known phylogenetic neighbours. Corynebacterium variabile and Corynebacterium ammoniagenes showed the highest levels of sequence homology with the isolates; however, DNA-DNA hydridization studies indicated that the Corynebacterium strains isolated from the cheese smear did not belong to either Corynebacterium variabile or Corynebacterium ammoniagenes (26 and 46% chromosomal similarity, respectively). On the basis of the phylogenetic and phenotypic distinctiveness of the unknown isolates, it is proposed that the bacteria be classified as two new Corynebacterium species, for which the names Corynebacterium mooreparkense sp. nov. and Corynebacterium casei sp. nov. are proposed. Type strains have been deposited in culture collections as Corynebacterium mooreparkense LMG S-19265T (= NCIMB 30131T) and Corynebacterium casei LMG S-19264T (= NCIMB 30130T).

Biomass↗
PubMed2001

Nocardia africana sp. nov., a new pathogen isolated from patients with pulmonary infections.

Eight actinomycete strains, isolated from 8 out of 400 sputum samples examined, taken from patients with pulmonary diseases at the Chest Unit of Khartoum Teaching Hospital in the Sudan, were provisionally assigned to the genus Nocardia according to morphological criteria. These isolates were studied further in order to establish their taxonomic status. They were found to have morphological and chemical properties typical of nocardiae and formed a monophyletic clade in the 16S ribosomal DNA tree together with Nocardia vaccinii. The strains showed a unique pattern of phenotypic properties that distinguished them from representatives of recognized Nocardia species, including Nocardia vaccinii. The strains were considered to merit species status and were designated Nocardia africana sp. nov. The findings of the present study are consistent with the view that pulmonary nocardiosis may occur in a substantial proportion of patients who exhibit chronic lung diseases in African countries. It is important, therefore, that clinicians in such countries consider this condition, especially when patients with respiratory infections fail to respond to antitubercular therapy.

Africa↗
PubMed2000

Taxonomic position of "Pseudomonas oxalaticus" strain ox14T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov.

"Pseudomonas oxalaticus" strain Ox1T (= DSM 1105T), which was described as an oxalate-decomposing bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this species is phylogenetically related to the species of the genus Ralstonia. and represents a new species. The result of the DNA-DNA hybridization value was supported in this placement. Strain Ox1T is closely related to Ralstonia eutropha with a less than 60% DNA-DNA hybridization value. The new name Ralstonia oxalatica comb. nov. is proposed to strain Ox1T, on the basis of these results and previously published data for the G+C content of the genomic DNA and the phenotypic characters.

Bacterial Typing Techniques↗
PubMed2000

Rapid characterisation of deep-sea actinomycetes for biotechnology screening programmes.

A continual need in natural product discovery is dereplication, that is the ability to exclude previously tested microorganisms from screening programmes. Whole-cell fingerprinting techniques offer an ideal solution to this problem because of their rapidity and reproducibility, dependence on small samples, and automation. One such technique, Curie-point pyrolysis mass spectrometry (PyMS), has been deployed for the characterisation of a unique collection of actinomycetes recovered from Pacific Ocean sediments approximately 2000 to 6500 m below sea level. This paper addresses the question: to what extent are pyrogroups, defined on the basis of PyMS fingerprinting, related to classifications derived from more conventional microbial systematics? A collection of 44 randomly chosen deep-sea rhodococci were coded and subjected to a double-blind PyMS and numerical taxonomic (NT) analysis; the latter sorted the strains into clusters (taxospecies) using large sets of equally weighted phenotypic data. At the end of the experiment the codes were disclosed and the NT classification shown to generate 6 homogeneous clusters corresponding to different deep-sea sites. The matching of these clusters with the resulting pyrogroups was very high with an overall congruence of nearly 98%. Thus, PyMS characterisation is directly ascribable to the phenotypic variation being sought for biotechnology screens. Moreover, the exquisite discriminatory power of PyMS readily revealed infraspecific diversity in these industrially important bacteria.

Actinomycetales↗
PubMed2000

Biosystematic studies on novel streptomycetes from soil.

Members of three putatively novel Streptomyces species, designated Streptomyces groups A, B and C, were repeatedly isolated from environmental samples taken from four hay meadow plots at Cockle Park Experimental Farm, Northumberland (UK). Representative isolates were found to have properties consistent with their classification in the genus Streptomyces and were recovered in three taxa using different phenotypic criteria, namely morphological and pigmentation properties, rapid enzyme tests, and whole-organism fatty acid, protein electrophoretic and pyrolysis mass-spectrometric data. The isolates were rapidly characterised as three taxonomic groups using pyrolysis mass spectrometry. The three taxa were also distinguished from one another and from validly described species of Streptomyces using rapid enzyme tests based on the fluorophores 7-amino-methylcoumarin and 4-methylumbelliferone, and computer-assisted identification procedures. The results indicate that selective isolation and rapid characterisation of streptomycetes using pyrolysis mass spectrometry provide a practical way of determining the phenotypic species diversity of streptomycetes in natural habitats. The experimental data also indicate that representative sampling of cultivable streptomycetes from soil can best be achieved using a multi-step extraction procedure coupled with the use of selective isolation procedures.

Bacterial Proteins↗
PubMed2000

Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria.

Large numbers of putatively novel streptomycetes were isolated from environmental samples collected from in and around the root system of the tropical angiosperm, Paraserianthes falcataria. Representative isolates were assigned to 37 multi-membered and 107 single membered colour groups based on their ability to form pigments on oatmeal and peptone yeast extract iron agars. The largest taxon, colour group 3, encompassed 94 isolates which had morphological properties typical of members of the Streptomyces violaceusniger clade. Twelve representatives of this taxon chosen on the basis of Curie-point pyrolysis mass spectrometric data were compared with representatives of the validly described species which constitute the Streptomyces violaceusniger clade. Six out of the twelve representative strains were readily distinguished from one another and from the marker strains using a combination of genotypic and phenotypic properties. These organisms were consequently considered to merit species status as Streptomyces asiaticus sp. nov., Streptomyces cangkringensis sp. nov., Streptomyces indonesiensis sp. nov., Streptomycesjavensis sp. nov., Streptomyces rhizosphaerius sp. nov. and Streptomyces yogyakartensis sp. nov.

Bacteriological Techniques↗
PubMed2000

The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov.

Large numbers of strains selectively isolated from soil, water and deteriorating vulcanised natural rubber pipe rings were provisionally assigned to the genus Nocardia. Twenty-eight representative isolates were found to have chemical and morphological properties typical of nocardiae. These organisms formed a monophyletic clade in the 16S rDNA tree together with Nocardia salmonicida. Three of the strains, isolates S1, W30 and R89, were distinguished from one another and from representatives of the validly described species of Nocardia using genotypic and phenotypic data. These organisms were considered to merit species status and were named Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. respectively. Additional comparative studies are needed to resolve the finer taxonomic relationships of the remaining isolates assigned to the Nocardia salmonicida clade and to further unravel the extent of nocardial diversity in artificial and natural ecosystems.

DNA, Bacterial↗
PubMed2000

Genomic and phenomic differentiation of Rhodococcus equi and related strains.

16S rDNA sequence and pyrolysis mass spectrometric analyses were carried out on representatives of Rhodococcus equi and marker strains of genera that encompass mycolic acid containing actinomycetes. The R. equi strains formed a monophyletic clade within the evolutionary radiation occupied by members of the genera Nocardia and Rhodococcus. The 16S rDNA sequence data also showed R. equi to be an heterogeneous taxon. This heterogeneity was underscored by the pyrolysis mass spectrometric data. These observations are in line with those of previous studies where similar profiles of relatedness were found between pyrolysis mass spectral data and the results of DNA:DNA pairing and numerical phenetic studies.

Actinomycetales↗
PubMed2000

Streptomyces thermocoprophilus sp. nov., a cellulase-free endo-xylanase-producing streptomycete.

The taxonomic position of a thermophilic actinomycete strain isolated from poultry faeces was examined using a polyphasic approach. The isolate, designated B19T, was assigned to the genus Streptomyces on the basis of chemotaxonomic and morphological criteria. An almost complete 16S rRNA gene (rDNA) sequence obtained for the test strain was compared with those of representative streptomycetes, notably thermophilic streptomycetes. 16S rDNA sequence data not only supported the assignment of the strain to the genus Streptomyces but also showed that the isolate formed a distinct phyletic line within the evolutionary branch composed of Streptomyces thermodiastaticus and related species. The strain was distinguished from related validly described Streptomyces species by a number of phenotypic properties. It is, therefore, proposed that strain B19T be classified in the genus Streptomyces as Streptomyces thermocoprophilus sp. nov.

Animals↗
PubMed2000

Mycobacterium elephantis sp. nov., a rapidly growing non-chromogenic Mycobacterium isolated from an elephant.

A strain isolated from a lung abscess in an elephant that died from chronic respiratory disease was found to have properties consistent with its classification in the genus Mycobacterium. An almost complete sequence of the 165 rDNA of the strain was determined following the cloning and sequencing of the amplified gene. The sequence was aligned with those available on mycobacteria and phylogenetic trees inferred by using three tree-making algorithms. The organism, which formed a distinct phyletic line within the evolutionary radiation occupied by rapidly growing mycobacteria, was readily distinguished from members of validly described species of rapidly growing mycobacteria on the basis of its mycolic acid pattern and by a number of other phenotypic features, notably its ability to grow at higher temperatures. The type strain is Mycobacterium elephantis DSM 44368T.

Animals↗
PubMed2000

Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete.

The taxonomic position of a dibenzothiophene-desulphurizing soil actinomycete was established using a polyphasic taxonomic approach. The organism, strain IEGMT, was shown to have chemical and morphological properties typical of members of the genus Gordonia. The tested strain formed a distinct phyletic line within the evolutionary radiation occupied by the genus Gordonia, with Gordonia alkanivorans DSM 44369T, Gordonia desulfuricans NCIMB 40816T and Gordonia rubropertincta DSM 43197T as the most closely related organisms. Strain IEGMT has a range of phenotypic properties that distinguish it from representatives of all of the validly described species of Gordonia. It was also sharply distinguished from the type strains of Gordonia desulfuricans and Gordonia rubropertincta on the basis of DNA-DNA relatedness data. The combined genotypic and phenotypic data show that strain IEGMT merits recognition as a new species of Gordonia. The name proposed for the new species is Gordonia amicalis; the type strain is IEGMT (= DSM 44461T = KCTC 9899T).

Actinomycetales↗
PubMed2000

Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants.

The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P << 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m(3) completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 x 10(6) cells ml(-1) or 4 x 10(12) cells m(-2). We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge.

Actinomycetales↗
PubMed2000

Search and discovery strategies for biotechnology: the paradigm shift.

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Biotechnology↗
PubMed1999

A phylogenetic analysis of the genus Catellatospora based on 16S ribosomal DNA sequences, including transfer of Catellatospora matsumotoense to the genus Micromonospora as Micromonospora matsumotoense comb. nov.

Phylogenetic studies based on the 16S ribosomal gene sequences showed that members of the genus Catellatospora revealed phylogenetic heterogeneity within the family Micromonosporaceae as well as a heterogeneous menaquinone composition. Among them, Catellatospora matsumotoense was closely related to members of the genus Micromonospora, indicating that this organism should be excluded from the genus Catellatospora. On the basis of classical taxonomic characteristics and phylogenetic evidence, Catellatospora matsumotoense is proposed to be transferred to the genus Micromonospora as M. matsumotoense comb. nov.

DNA, Ribosomal↗